Publications from CoRe members are listed below to illustrate the breadth and depth of our research activities. The current selection reflects research published by our members from January 2021 to November 2025.

To view a CoRe member’s recent publication history, click their name to open the dropdown. For further information about a member’s publication history, please visit the webpage linked on their Member Profile.

Featured Publication

Nikitin Lab

Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39366996; PMCID: PMC11452611.

Dr. Alexander Nikitin‘s (Professor of Pathology, Department of Biomedical Sciences) laboratory published an article in Nature Communications earlier this month, co-first authored by Dr. Andrea Flesken-Nikitin (Assistant Research Professor) and graduate student Coulter Ralston. The article, titled “Pre-ciliated tubal epithelial cells are prone to initiating of high-grade serous ovarian carcinoma,” highlights transitional cells in the fallopian tube, known as a pre-ciliated tubal epithelial cells, as being particularly susceptible to cancer. High-grade serous carcinoma (HGSC) can develop in both the ovary and a section of the fallopian tube, and this publication reflects the lab’s first time identifying susceptible cells in the fallopian tube.

VISIT PUBLICATION

Clark Lab

2025

Chen J, Liu C, Li W, Clark AG, Wang Z, Lu J. Pervasive sex-dependent effects in the genetic architecture of starvation resistance in Drosophila melanogaster. Sci Adv. 2025 Sep 26;11(39):eadt3560. doi: 10.1126/sciadv.adt3560. Epub 2025 Sep 26. PMID: 41004585; PMCID: PMC12466915.
Shah SR, Chen Y, Leung AK, Navarro PVC, Paramo MI, Gupta J, Gurumurthy A, Fite RF, Weimer AK, Du Q, Mohyeldin AM, Egli D, Creusot RJ, Ryan RJH, Snyder MP, Clark AG, Lis JT, Yu H. The regulatory landscape of nascent transcription in human health and disease. bioRxiv [Preprint]. 2025 Sep 26:2025.09.24.676871. doi: 10.1101/2025.09.24.676871. PMID: 41040139; PMCID: PMC12485982.
Chen DS, Marrero K, Sanchez-Lopez JA, Belenky M, Thomalla JM, Buehner NA, Apel I, Levi Y, Hafezi Y, Wang S, Clark AG, Heifetz Y, Siegal ML, Wolfner MF. Asymmetric development and function of paired sperm-storage organs in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2025 Aug 26;122(34):e2512096122. doi: 10.1073/pnas.2512096122. Epub 2025 Aug 19. PMID: 40828028; PMCID: PMC12403100.
Forsberg SKG, Melo D, Wolf SW, Grenier JK, Tang M, Henry LP, Pallares LF, Clark AG, Ayroles JF. Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection. Proc Natl Acad Sci U S A. 2025 Jun 24;122(25):e2410452122. doi: 10.1073/pnas.2410452122. Epub 2025 Jun 18. PMID: 40531879; PMCID: PMC12207516.
Cappello L, Lo WT’, Zhang JZ, Xu P, Barrow D, Chopra I, Clark AG, Wells MT, Kim J. Bayesian phylodynamic inference of population dynamics with dormancy. Proc Natl Acad Sci U S A. 2025 May 6;122(18):e2501394122. doi: 10.1073/pnas.2501394122. Epub 2025 May 2. PMID: 40314983; PMCID: PMC12067208.
Dong C, Xia S, Zhang L, Arsala D, Fang C, Tan S, Clark AG, Long M. Subcellular Enrichment Patterns of New Genes in Drosophila Evolution. Mol Biol Evol. 2025 Feb 3;42(2):msaf038. doi: 10.1093/molbev/msaf038. PMID: 39920336; PMCID: PMC11843443.

2024

Xue H, Delbare SYN, Wells MT, Basu S, Clark AG. Integrative Analysis of Differentially Expressed Genes in Time-Course Multi-Omics Data with MINT-DE. Res Sq [Preprint]. 2024 Dec 23:rs.3.rs-3806701. doi: 10.21203/rs.3.rs-3806701/v2. PMID: 38260696; PMCID: PMC10802680.
Said I, Barbash DA, Clark AG. The Structure of Simple Satellite Variation in the Human Genome and Its Correlation With Centromere Ancestry. Genome Biol Evol. 2024 Aug 5;16(8):evae153. doi: 10.1093/gbe/evae153. PMID: 39018452; PMCID: PMC11305138.
Srivastav SP, Feschotte C, Clark AG. Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary. Genome Res. 2024 Jun 25;34(5):711-724. doi: 10.1101/gr.278062.123. PMID: 38749655; PMCID: PMC11216404.
Barad A, Clark AG, Pressman EK, O’Brien KO. Associations Between Genetically Predicted Iron Status and Cardiovascular Disease Risk: A Mendelian Randomization Study. J Am Heart Assoc. 2024 Jun 4;13(11):e034991. doi: 10.1161/JAHA.124.034991. Epub 2024 May 31. PMID: 38818967; PMCID: PMC11255641.
Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. Commun Biol. 2024 Jan 12;7(1):90. doi: 10.1038/s42003-023-05717-x. PMID: 38216628; PMCID: PMC10786823.
Flynn JM, Ahmed-Braimah YH, Long M, Wing RA, Clark AG. High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup. Genome Biol Evol. 2024 Jan 5;16(1):evad238. doi: 10.1093/gbe/evad238. PMID: 38159044; PMCID: PMC10783647.

2023

Brown NC, Gordon B, McDonough-Goldstein CE, Misra S, Findlay GD, Clark AG, Wolfner MF. The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster. Elife. 2023 Dec 21;12:e86409. doi: 10.7554/eLife.86409. PMID: 38126735; PMCID: PMC10834028.
Jones KA, Clark AG, Greiner MA, Sandoe E, Giri A, Hammill BG, Van Houtven CH, Higgins A, Kaufman B. Linking Medicare-Medicaid Claims for Patient-Centered Outcomes Research Among Dual-Eligible Beneficiaries. Med Care. 2023 Dec 1;61(12 Suppl 2):S131-S138. doi: 10.1097/MLR.0000000000001895. Epub 2023 Nov 9. PMID: 37963032; PMCID: PMC10635344.
Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins DJ, Mogoi D, Pajukanta P, Perry GH, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman DE, Ayroles JF. Applying an evolutionary mismatch framework to understand disease susceptibility. PLoS Biol. 2023 Sep 11;21(9):e3002311. doi: 10.1371/journal.pbio.3002311. PMID: 37695771; PMCID: PMC10513379.
Delbare SYN, Jain AM, Clark AG, Wolfner MF. Transcriptional programs are activated and microRNAs are repressed within minutes after mating in the Drosophila melanogaster female reproductive tract. BMC Genomics. 2023 Jun 27;24(1):356. doi: 10.1186/s12864-023-09397-z. PMID: 37370014; PMCID: PMC10294459.
Flynn JM, Hu KB, Clark AG. Three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain with high satellite DNA content. Genetics. 2023 May 26;224(2):iyad062. doi: 10.1093/genetics/iyad062. PMID: 37052958; PMCID: PMC10213488.
Cao W, Douglas KC, Samollow PB, VandeBerg JL, Wang X, Clark AG. Origin and Evolution of Marsupial-specific Imprinting Clusters Through Lineage-specific Gene Duplications and Acquisition of Promoter Differential Methylation. Mol Biol Evol. 2023 Feb 3;40(2):msad022. doi: 10.1093/molbev/msad022. PMID: 36721950; PMCID: PMC9937046.
Delbare SYN, Venkatraman S, Scuderi K, Wells MT, Wolfner MF, Basu S, Clark AG. Time series transcriptome analysis implicates the circadian clock in the Drosophila melanogaster female’s response to sex peptide. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2214883120. doi: 10.1073/pnas.2214883120. Epub 2023 Jan 27. Erratum in: Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2305270120. doi: 10.1073/pnas.2305270120. PMID: 36706221; PMCID: PMC9945991.

2022

Champer SE, Kim IK, Clark AG, Messer PW, Champer J. Anopheles homing suppression drive candidates exhibit unexpected performance differences in simulations with spatial structure. Elife. 2022 Oct 14;11:e79121. doi: 10.7554/eLife.79121. PMID: 36239372; PMCID: PMC9596161.
Langmüller AM, Champer J, Lapinska S, Xie L, Metzloff M, Champer SE, Liu J, Xu Y, Du J, Clark AG, Messer PW. Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. Elife. 2022 Sep 22;11:e71809. doi: 10.7554/eLife.71809. PMID: 36135925; PMCID: PMC9545523.
Chen DS, Clark AG, Wolfner MF. Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster. Genetics. 2022 Jul 30;221(4):iyac096. doi: 10.1093/genetics/iyac096. PMID: 35809068; PMCID: PMC9339280.
Wang Y, Guo X, Hong X, Wang G, Pearson C, Zuckerman B, Clark AG, O’Brien KO, Wang X, Gu Z. Association of mitochondrial DNA content, heteroplasmies and inter-generational transmission with autism. Nat Commun. 2022 Jul 1;13(1):3790. doi: 10.1038/s41467-022-30805-7. PMID: 35778412; PMCID: PMC9249801.
Nguyen TN, Chen N, Cosgrove EJ, Bowman R, Fitzpatrick JW, Clark AG. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays,Aphelocoma coerulescens. Evol Appl. 2022 Jun 1;15(6):1018-1027. doi: 10.1111/eva.13421. PMID: 35782006; PMCID: PMC9234620.
Yang E, Metzloff M, Langmüller AM, Xu X, Clark AG, Messer PW, Champer J. A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles. G3 (Bethesda). 2022 May 30;12(6):jkac081. doi: 10.1093/g3journal/jkac081. PMID: 35394026; PMCID: PMC9157102.
Metzloff M, Yang E, Dhole S, Clark AG, Messer PW, Champer J. Experimental demonstration of tethered gene drive systems for confined population modification or suppression. BMC Biol. 2022 May 24;20(1):119. doi: 10.1186/s12915-022-01292-5. PMID: 35606745; PMCID: PMC9128227.
Chen Y, Clark AG, Yu H. Advancing discovery of risk-altering variants for complex diseases by functionally informed fine-mapping. Neuron. 2022 Mar 16;110(6):905-907. doi: 10.1016/j.neuron.2022.02.018. PMID: 35298913.
New FN, Baer BR, Clark AG, Wells MT, Brito IL. Collective effects of human genomic variation on microbiome function. Sci Rep. 2022 Mar 9;12(1):3839. doi: 10.1038/s41598-022-07632-3. PMID: 35264618; PMCID: PMC8907173.
Munasinghe M, Haller BC, Clark AG. Migration restores hybrid incompatibility driven by mitochondrial-nuclear sexual conflict. Proc Biol Sci. 2022 Jan 26;289(1967):20212561. doi: 10.1098/rspb.2021.2561. Epub 2022 Jan 26. PMID: 35078356; PMCID: PMC8790342.
Said I, McGurk MP, Clark AG, Barbash DA. Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference. Mol Biol Evol. 2022 Jan 7;39(1):msab336. doi: 10.1093/molbev/msab336. PMID: 34921315; PMCID: PMC8788220.

2021

Shahrestani P, King E, Ramezan R, Phillips M, Riddle M, Thornburg M, Greenspan Z, Estrella Y, Garcia K, Chowdhury P, Malarat G, Zhu M, Rottshaefer SM, Wraight S, Griggs M, Vandenberg J, Long AD, Clark AG, Lazzaro BP. The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping. G3 (Bethesda). 2021 Dec 8;11(12):jkab324. doi: 10.1093/g3journal/jkab324. PMID: 34534291; PMCID: PMC8664422.
Ding Q, Edwards MM, Wang N, Zhu X, Bracci AN, Hulke ML, Hu Y, Tong Y, Hsiao J, Charvet CJ, Ghosh S, Handsaker RE, Eggan K, Merkle FT, Gerhardt J, Egli D, Clark AG, Koren A. The genetic architecture of DNA replication timing in human pluripotent stem cells. Nat Commun. 2021 Nov 19;12(1):6746. doi: 10.1038/s41467-021-27115-9. PMID: 34799581; PMCID: PMC8604924.
Razali RM, Rodriguez-Flores J, Ghorbani M, Naeem H, Aamer W, Aliyev E, Jubran A; Qatar Genome Program Research Consortium; Clark AG, Fakhro KA, Mokrab Y. Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. Nat Commun. 2021 Oct 12;12(1):5929. doi: 10.1038/s41467-021-25287-y. PMID: 34642339; PMCID: PMC8511259.
Kang W, Barad A, Clark AG, Wang Y, Lin X, Gu Z, O’Brien KO. Ethnic Differences in Iron Status. Adv Nutr. 2021 Oct 1;12(5):1838-1853. doi: 10.1093/advances/nmab035. PMID: 34009254; PMCID: PMC8483971.
Marderstein AR, Kulm S, Peng C, Tamimi R, Clark AG, Elemento O. A polygenic-score-based approach for identification of gene-drug interactions stratifying breast cancer risk. Am J Hum Genet. 2021 Sep 2;108(9):1752-1764. doi: 10.1016/j.ajhg.2021.07.008. Epub 2021 Aug 6. PMID: 34363748; PMCID: PMC8456164.
Flynn JM, Brown EJ, Clark AG. Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines. G3 (Bethesda). 2021 Aug 7;11(8):jkab184. doi: 10.1093/g3journal/jkab184. PMID: 34849804; PMCID: PMC8496272.
Patchen BK, Clark AG, Gaddis N, Hancock DB, Cassano PA. Genetically predicted serum vitamin D and COVID-19: a Mendelian randomisation study. BMJ Nutr Prev Health. 2021 May 4;4(1):213-225. doi: 10.1136/bmjnph-2021-000255. PMID: 34308129; PMCID: PMC8098235.
Schlamp F, Delbare SYN, Early AM, Wells MT, Basu S, Clark AG. Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response. BMC Genomics. 2021 Apr 26;22(1):304. doi: 10.1186/s12864-021-07593-3. PMID: 33902461; PMCID: PMC8074482.
Ding Q, Hu Y, Koren A, Clark AG. Mutation Rate Variability across Human Y-Chromosome Haplogroups. Mol Biol Evol. 2021 Mar 9;38(3):1000-1005. doi: 10.1093/molbev/msaa268. PMID: 33049047; PMCID: PMC7947773.
Ahmed-Braimah YH, Wolfner MF, Clark AG. Differences in Postmating Transcriptional Responses between Conspecific and Heterospecific Matings in Drosophila. Mol Biol Evol. 2021 Mar 9;38(3):986-999. doi: 10.1093/molbev/msaa264. PMID: 33035303; PMCID: PMC7947788.
Champer J, Kim IK, Champer SE, Clark AG, Messer PW. Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type alleles. Mol Ecol. 2021 Feb;30(4):1086-1101. doi: 10.1111/mec.15788. Epub 2021 Jan 23. PMID: 33404162; PMCID: PMC7887089.
Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG. Leveraging phenotypic variability to identify genetic interactions in human phenotypes. Am J Hum Genet. 2021 Jan 7;108(1):49-67. doi: 10.1016/j.ajhg.2020.11.016. Epub 2020 Dec 15. PMID: 33326753; PMCID: PMC7820920.

Cohen, Paula Lab

2025

Wood AJ, Ahmed RM, Simon LE, Bradley RA, Gray S, Wolff ID, Cohen PE. CNTD1 is crucial for crossover formation in female meiosis and for establishing the ovarian reserve. J Cell Biol. 2025 Aug 4;224(8):e202401021. doi: 10.1083/jcb.202401021. Epub 2025 Jun 9. PMID: 40488668; PMCID: PMC12147665.
Carro MLM, Dziubek A, Touey A, Popkowski EA, Abdelmassih M, Simon L, Tanis S, Ahmed F, Grenier JK, Grimson A, Cohen PE. Argonaute proteins regulate the timing of the spermatogenic transcriptional program. bioRxiv [Preprint]. 2025 Jan 1:2024.12.31.630913. doi: 10.1101/2024.12.31.630913. PMID: 39803480; PMCID: PMC11722363.

2024

Condezo YB, Sainz-Urruela R, Gomez-H L, Salas-Lloret D, Felipe-Medina N, Bradley R, Wolff ID, Tanis S, Barbero JL, Sánchez-Martín M, de Rooij D, Hendriks IA, Nielsen ML, Gonzalez-Prieto R, Cohen PE, Pendas AM, Llano E. RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse. Proc Natl Acad Sci U S A. 2024 Jun 18;121(25):e2320995121. doi: 10.1073/pnas.2320995121. Epub 2024 Jun 12. Erratum in: Proc Natl Acad Sci U S A. 2024 Oct 8;121(41):e2418611121. doi: 10.1073/pnas.2418611121. PMID: 38865271; PMCID: PMC11194559.
Horan TS, Ascenção CFR, Mellor C, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in double strand break repair processing, but not crossover formation during prophase I of meiosis in male mice. PLoS Genet. 2024 Feb 20;20(2):e1011175. doi: 10.1371/journal.pgen.1011175. PMID: 38377115; PMCID: PMC10906868.

2023

Alexander AK, Rice EJ, Lujic J, Simon LE, Tanis S, Barshad G, Zhu L, Lama J, Cohen PE, Danko CG. A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis. Nat Commun. 2023 Mar 29;14(1):1753. doi: 10.1038/s41467-023-37408-w. PMID: 36990976; PMCID: PMC10060231.
Brieño-Enríquez MA, Faykoo-Martinez M, Goben M, Grenier JK, McGrath A, Prado AM, Sinopoli J, Wagner K, Walsh PT, Lopa SH, Laird DJ, Cohen PE, Wilson MD, Holmes MM, Place NJ. Postnatal oogenesis leads to an exceptionally large ovarian reserve in naked mole-rats. Nat Commun. 2023 Feb 21;14(1):670. doi: 10.1038/s41467-023-36284-8. PMID: 36810851; PMCID: PMC9944903.

2022

Wang S, Lee K, Gray S, Zhang Y, Tang C, Morrish RB, Tosti E, van Oers J, Amin MR, Cohen PE, MacCarthy T, Roa S, Scharff MD, Edelmann W, Chahwan R. Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice. Nucleic Acids Res. 2022 Aug 12;50(14):8093-8106. doi: 10.1093/nar/gkac616. PMID: 35849338; PMCID: PMC9371890.
Carro MLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol. 2023;151:245-279. doi: 10.1016/bs.ctdb.2022.06.001. Epub 2022 Jul 25. PMID: 36681472.
Sims JR, Faça VM, Pereira C, Ascenção C, Comstock W, Badar J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. Phosphoproteomics of ATR signaling in mouse testes. Elife. 2022 Feb 8;11:e68648. doi: 10.7554/eLife.68648. PMID: 35133275; PMCID: PMC8824463.
Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. Elife. 2022 Feb 8;11:e68677. doi: 10.7554/eLife.68677. PMID: 35133274; PMCID: PMC8824475.

2021

Roy JCL, Vitalo A, Andrew MA, Mota-Silva E, Kovalenko M, Burch Z, Nhu AM, Cohen PE, Grabczyk E, Wheeler VC, Mouro Pinto R. Somatic CAG expansion in Huntington’s disease is dependent on the MLH3 endonuclease domain, which can be excluded via splice redirection. Nucleic Acids Res. 2021 Apr 19;49(7):3907-3918. doi: 10.1093/nar/gkab152. PMID: 33751106; PMCID: PMC8053082.

Cohen, Roy Lab

2025

White MA, Cohen R, Travis AJ. Real-Time Imaging of Calcium Dynamics in Human Sperm After Precise Single-Cell Stimulation. Methods Mol Biol. 2025;2861:247-256. doi: 10.1007/978-1-0716-4164-4_18. PMID: 39395110.

2023

Cohen R, Sosnicki DM, White MA, Nelson JL, Mukai C, Travis AJ. Real-Time Imaging of Acrosomal Calcium Dynamics and Exocytosis in Live Mouse Sperm. J Vis Exp. 2023 Oct 13;(200). doi: 10.3791/65962. PMID: 37902325.
Sosnicki DM, Cohen R, Asano A, Nelson JL, Mukai C, Comizzoli P, Travis AJ. Segmental differentiation of the murine epididymis: identification of segment-specific, GM1-enriched vesicles and regulation by luminal fluid factors†. Biol Reprod. 2023 Dec 11;109(6):864-877. doi: 10.1093/biolre/ioad120. PMID: 37694824; PMCID: PMC10724454.

2022

Cohen R, Mukai C, Nelson JL, Zenilman SS, Sosnicki DM, Travis AJ. A genetically targeted sensor reveals spatial and temporal dynamics of acrosomal calcium and sperm acrosome exocytosis. J Biol Chem. 2022 May;298(5):101868. doi: 10.1016/j.jbc.2022.101868. Epub 2022 Mar 27. PMID: 35346690; PMCID: PMC9046242.

Comizzoli

2025

Sandoval EDP, Lee PC, Duarte JMB, Comizzoli P. Slow Freezing vs. Vitrification of Testicular Tissue in Nontraditional Animal Models. Biopreserv Biobank. 2025 Oct 28. doi: 10.1177/19475535251391026. Epub ahead of print. PMID: 41151088.
Cavalcante YCS, Santos CS, Dantas LL, Santos RP, Matos YG, Pereira AG, Beraldo KRF, Juliano MA, Brandão FZ, Feijó FMC, Franco de Oliveira M, Mota RA, Comizzoli P, Silva AR. Relationship between the composition of vaginal bacterial populations and the reproductive stage in captive collared peccaries. Reprod Fertil. 2025 Oct 14;6(4):e250072. doi: 10.1530/RAF-25-0072. PMID: 41026639; PMCID: PMC12524037.
da Silva Cavalcante YC, Comizzoli P, Silva AR. How deciphering the reproductive microbiomes can contribute to the conservation of wild mammalian species – A review. Anim Reprod Sci. 2025 Oct;281:107981. doi: 10.1016/j.anireprosci.2025.107981. Epub 2025 Aug 26. PMID: 40886421.
Amelkina O, Lee PC, Sosnicki DM, Martinez P, Nussbaum J, Willis H, Comizzoli P. Effects of microwave-assisted dehydration on the structure and function of ovarian cortex in the domestic cat model – New insights for future storage of living tissues at ambient temperatures†. Biol Reprod. 2025 Sep 2:ioaf203. doi: 10.1093/biolre/ioaf203. Epub ahead of print. PMID: 40891504.
DeCandia AL, Tennenbaum SR, Santymire R, Livieri T, Bortner R, Garelle D, Crosier A, Marinari P, Pukazhenthi BS, Comizzoli P, Maldonado JE, Koepfli KP, vonHoldt BM. Ex situ reared black-footed ferrets exhibit altered sperm DNA methylation. J Hered. 2025 Aug 23:esaf056. doi: 10.1093/jhered/esaf056. Epub ahead of print. PMID: 40847813.
Pereira AG, da Silva AM, Pereira Bezerra LG, Cottin de Albuquerque JL, Costa Bezerra GS, Pereira AF, Bezerra de Moura CE, Comizzoli P, Silva AR. Use of organotypic or three-dimensional systems with basic fibroblast growth factor for in vitro culture of immature collared peccary testicle. Reprod Fertil. 2025 Aug 8;6(3):e250026. doi: 10.1530/RAF-25-0026. PMID: 40737041; PMCID: PMC12344399.
Yang Y, Kittisirikul N, Langkaphin W, Angkawanish T, Comizzoli P, Chatdarong K. Differentiating the estrous cycle phases using vaginal vestibule pH and cytology in Asian elephants (Elephas maximus) in human care. Vet J. 2025 Jun;311:106324. doi: 10.1016/j.tvjl.2025.106324. Epub 2025 Mar 8. PMID: 40064394.
Silva AM, Pereira AG, Bezerra GSC, Matos YG, Bezerra LGP, Pereira AF, Oliveira MF, Comizzoli P, Silva AR. Solid Surface Vitrification Is Better than Slow Freezing for the Long-Term Preservation of Testicular Fragments from Prepubertal Collared Peccaries (Pecari tajacu Linnaeus, 1758). Animals (Basel). 2025 May 20;15(10):1488. doi: 10.3390/ani15101488. PMID: 40427365; PMCID: PMC12108413.
Comizzoli P, Paulson RJ. Bridging studies in wild animal species and humans to better understand, assist, and control reproduction. F S Rep. 2025 Apr 15;6(Suppl 1):1-2. doi: 10.1016/j.xfre.2025.01.013. PMID: 40487322; PMCID: PMC12139229.
Fujihara M, Comizzoli P. Human and wildlife biobanks of germplasms and reproductive tissues can contribute to a broader concept of One Health. F S Rep. 2025 Apr 15;6(Suppl 1):63-66. doi: 10.1016/j.xfre.2025.01.004. PMID: 40487327; PMCID: PMC12139243.
Silva AM, Lima GL, Comizzoli P, Silva AR. Gonadal tissue preservation technologies and culture offer opportunities to bridge knowledge between wildlife and humans. F S Rep. 2025 Apr 15;6(Suppl 1):50-54. doi: 10.1016/j.xfre.2025.01.009. PMID: 40487320; PMCID: PMC12139249.
Bovell RTM, Comizzoli P, Nagashima JB, Santiestevan J, Crosier AE, Place NJ. Anti-Müllerian hormone concentration measured before gonadotropin stimulation is associated with quality of subsequent ovarian response in the cheetah (Acinonyx jubatus) and domestic cat (Felis catus)†. Biol Reprod. 2025 Apr 13;112(4):754-766. doi: 10.1093/biolre/ioaf025. PMID: 39903683.
Driancourt MA, Comizzoli P, Brito LFC. Celebrating a milestone and looking at the future of Theriogenology. Theriogenology. 2025 Mar 1;234:151-152. doi: 10.1016/j.theriogenology.2024.12.013. Epub 2024 Dec 13. PMID: 39700756.
Sosnicki DM, Travis AJ, Comizzoli P. In vitro exposure to epididymal extracellular vesicles from normospermic domestic cats improves developmental potential of sperm from teratospermic cats. Front Vet Sci. 2025 Jan 17;12:1547175. doi: 10.3389/fvets.2025.1547175. PMID: 39896847; PMCID: PMC11783848.
Lima GL, Brasil AV, Silva AM, Antunes JMAP, Comizzoli P, Silva AR. Characterization of the Population of Ovarian Preantral Follicles in Juvenile Six-Banded Armadillos Infected or Not by Mycobacterium leprae. Vet Sci. 2025 Jan 9;12(1):37. doi: 10.3390/vetsci12010037. PMID: 39852911; PMCID: PMC11768727.

2024

Sosnicki DM, Travis AJ, Comizzoli P. Extracellular vesicles are involved in the paracrine communication between epithelial cells in different regions of the domestic cat epididymis†. Biol Reprod. 2024 Nov 11;111(5):1056-1070. doi: 10.1093/biolre/ioae129. PMID: 39190878.
Hutchinson AM, Appeltant R, Burdon T, Bao Q, Bargaje R, Bodnar A, Chambers S, Comizzoli P, Cook L, Endo Y, Harman B, Hayashi K, Hildebrandt T, Korody ML, Lakshmipathy U, Loring JF, Munger C, Ng AHM, Novak B, Onuma M, Ord S, Paris M, Pask AJ, Pelegri F, Pera M, Phelan R, Rosental B, Ryder OA, Sukparangsi W, Sullivan G, Tay NL, Traylor-Knowles N, Walker S, Weberling A, Whitworth DJ, Williams SA, Wojtusik J, Wu J, Ying QL, Zwaka TP, Kohler TN. Advancing stem cell technologies for conservation of wildlife biodiversity. Development. 2024 Oct 15;151(20):dev203116. doi: 10.1242/dev.203116. Epub 2024 Oct 9. PMID: 39382939; PMCID: PMC11491813.
Silva AMD, Pereira AG, Bezerra LGP, Brasil AV, Pereira AF, de Oliveira MF, Rodrigues APR, Ñaupas LVS, Comizzoli P, Silva AR. Synergistic effects of glial cell line-derived neurotrophic factor and base-medium on in vitro culture of testicular tissue derived from prepubertal collared peccary. Cell Biol Int. 2024 Sep;48(9):1364-1377. doi: 10.1002/cbin.12203. Epub 2024 Jun 21. PMID: 39007507.
Sosnicki DM, Travis AJ, Comizzoli P. Extracellular vesicles are involved in the paracrine communication between epithelial cells in different regions of the domestic cat epididymis. Biol Reprod. 2024 Aug 27:ioae129. doi: 10.1093/biolre/ioae129. Epub ahead of print. PMID: 39190878.
Lee PC, Comizzoli P. Microwave-assisted dehydration, long-term storage at non-freezing temperatures, and rehydration of cat germinal vesicles†. Biol Reprod. 2024 Aug 15;111(2):312-321. doi: 10.1093/biolre/ioae060. PMID: 38637297; PMCID: PMC11327313.
Hagedorn M, Parenti LR, Craddock RA, Comizzoli P, Mabee P, Meinke B, Wolf SM, Bischof JC, Sandlin RD, Tessier SN, Toner M. Safeguarding Earth’s biodiversity by creating a lunar biorepository. Bioscience. 2024 Jul 31;74(8):561-566. doi: 10.1093/biosci/biae058. PMID: 39229623; PMCID: PMC11367668.
DeCandia AL, Adeduro L, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz C, Bornbusch SL. Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets. J Hered. 2024 Jul 10;115(4):385-398. doi: 10.1093/jhered/esad065. PMID: 37886904.
Bezerra LGP, Oliveira REM, Comizzoli P, Silva AR. Collection, Handling, and Preservation of Wild Bird Semen: Current Status, Challenges, and Perspectives. Biopreserv Biobank. 2024 Jun;22(3):191-210. doi: 10.1089/bio.2023.0053. Epub 2023 Sep 12. PMID: 37699234.
Ali N, Amelkina O, Santymire RM, Koepfli KP, Comizzoli P, Vazquez JM. Semen proteome and transcriptome of the endangered black-footed ferret (Mustela nigripes) show association with the environment and fertility outcome. Sci Rep. 2024 Mar 25;14(1):7063. doi: 10.1038/s41598-024-57096-w. PMID: 38528039; PMCID: PMC10963785.
Bornbusch SL, Bamford A, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz CR, DeCandia AL. Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes). Commun Biol. 2024 Feb 23;7(1):224. doi: 10.1038/s42003-024-05908-0. Erratum in: Commun Biol. 2024 Sep 10;7(1):1110. doi: 10.1038/s42003-024-06793-3. PMID: 38396133; PMCID: PMC10891159.
Cowl VB, Comizzoli P, Appeltant R, Bolton RL, Browne RK, Holt WV, Penfold LM, Swegen A, Walker SL, Williams SA. Cloning for the Twenty-First Century and Its Place in Endangered Species Conservation. Annu Rev Anim Biosci. 2024 Feb 15;12:91-112. doi: 10.1146/annurev-animal-071423-093523. Epub 2023 Nov 21. PMID: 37988633.
Tennenbaum SR, Bortner R, Lynch C, Santymire R, Crosier A, Santiestevan J, Marinari P, Pukazhenthi BS, Comizzoli P, Hawkins MTR, Maldonado JE, Koepfli KP, vonHoldt BM, DeCandia AL. Epigenetic changes to gene pathways linked to male fertility in ex situ black-footed ferrets. Evol Appl. 2024 Jan 26;17(1):e13634. doi: 10.1111/eva.13634. PMID: 38283602; PMCID: PMC10818088.
Bezerra LGP, Silva AM, Dantas MRT, Dos Santos RP, Moreira SSJ, Pereira AG, de Oliveira MF, Comizzoli P, Silva AR. Development of assays for the characterization of sperm motility parameters, viability, and membrane integrity in the epididymis and vas deferens of the greater rhea (Rhea americana). Anim Reprod. 2024 Jan 5;20(4):e20230113. doi: 10.1590/1984-3143-AR2023-0113. PMID: 38213765; PMCID: PMC10782801.

2023

Sosnicki DM, Cohen R, Asano A, Nelson JL, Mukai C, Comizzoli P, Travis AJ. Segmental differentiation of the murine epididymis: identification of segment-specific, GM1-enriched vesicles and regulation by luminal fluid factors†. Biol Reprod. 2023 Dec 11;109(6):864-877. doi: 10.1093/biolre/ioad120. PMID: 37694824; PMCID: PMC10724454.
O’Mahony SM, Comizzoli P. Special series on the role of the microbiome in reproduction and fertility. Reprod Fertil. 2023 Nov 30;4(4):e230080. doi: 10.1530/RAF-23-0080. PMID: 37947768; PMCID: PMC10762581.
Orozco Cabral JA, Lee PC, Wang S, Wang Y, Zhang Y, Comizzoli P, Elliott GD. The Effect of Choline Salt Addition to Trehalose Solution for Long-Term Storage of Dried and Viable Nuclei from Fully Grown Oocytes. Bioengineering (Basel). 2023 Aug 24;10(9):1000. doi: 10.3390/bioengineering10091000. PMID: 37760102; PMCID: PMC10525460.
Lee PC, Stewart S, Amelkina O, Sylvester H, He X, Comizzoli P. Trehalose delivered by cold-responsive nanoparticles improves tolerance of cumulus-oocyte complexes to microwave drying. J Assist Reprod Genet. 2023 Aug;40(8):1817-1828. doi: 10.1007/s10815-023-02831-x. Epub 2023 Jun 1. PMID: 37261586; PMCID: PMC10371938.
Rowlison T, Nagashima J, Acker JP, Ben R, Daly J, Hagedorn M, Comizzoli P. First Report of Successful Laser Warming for Frozen Gonadal Tissues and Oocytes in the Domestic Cat Model. Biopreserv Biobank. 2023 Aug;21(4):433-438. doi: 10.1089/bio.2022.0071. Epub 2022 Aug 29. PMID: 36037060.
Bezerra LGP, Silva AM, Jurema AP, Dantas MRT, Pereira AG, Oliveira MF, Comizzoli P, Silva AR. Changes in Sperm Morphology, Morphometry, and Motility from the Epididymis to the Vas Deferens in Rheas (Rhea americana, Linnaeus, 1758). Animals (Basel). 2023 Apr 27;13(9):1483. doi: 10.3390/ani13091483. PMID: 37174520; PMCID: PMC10177575.
Comizzoli P, Luvoni C, Kutzler M. Introduction to the special issue ‘Canine and Feline Reproduction: Reproductive biology and medicine of domestic and exotic carnivores’. Theriogenology. 2023 Apr 1;200:77-78. doi: 10.1016/j.theriogenology.2023.01.017. Epub 2023 Feb 1. PMID: 36764188.
Howell LG, Mawson PR, Comizzoli P, Witt RR, Frankham R, Clulow S, O’Brien JK, Clulow J, Marinari P, Rodger JC. Modeling genetic benefits and financial costs of integrating biobanking into the conservation breeding of managed marsupials. Conserv Biol. 2023 Apr;37(2):e14010. doi: 10.1111/cobi.14010. Epub 2023 Mar 20. PMID: 36178038.
Silva AR, Pereira AF, Comizzoli P. Biobanking and use of gonadal tissues – a promising strategy for conserving wildlife from the Caatinga biome. Anim Reprod. 2023 Feb 13;19(4):e20220135. doi: 10.1590/1984-3143-AR2022-0135. PMID: 36819484; PMCID: PMC9924771.
Rowlison T, Comizzoli P. Transfer of Galectin-3-Binding Protein via Epididymal Extracellular Vesicles Promotes Sperm Fertilizing Ability and Developmental Potential in the Domestic Cat Model. Int J Mol Sci. 2023 Feb 4;24(4):3077. doi: 10.3390/ijms24043077. PMID: 36834494; PMCID: PMC9966717.
Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. R Soc Open Sci. 2023 Feb 1;10(2):220810. doi: 10.1098/rsos.220810. PMID: 36756057; PMCID: PMC9890126.
Comizzoli P, Amelkina O, Chavez DR, Rowlison TR, Lee PC. Current knowledge in the biology of gametes and embryos from Carnivora. Theriogenology. 2023 Jan 15;196:254-263. doi: 10.1016/j.theriogenology.2022.11.024. Epub 2022 Nov 18. PMID: 36434847.

2022

Comizzoli P, Amelkina O, Lee PC. Damages and stress responses in sperm cells and other germplasms during dehydration and storage at nonfreezing temperatures for fertility preservation. Mol Reprod Dev. 2022 Dec;89(12):565-578. doi: 10.1002/mrd.23651. Epub 2022 Nov 12. PMID: 36370428.
Amelkina O, da Silva AM, Silva AR, Comizzoli P. Feline microRNAome in ovary and testis: Exploration of in-silico miRNA-mRNA networks involved in gonadal function and cellular stress response. Front Genet. 2022 Sep 26;13:1009220. doi: 10.3389/fgene.2022.1009220. PMID: 36226169; PMCID: PMC9548565.
Holt WV, Comizzoli P. Conservation Biology and Reproduction in a Time of Developmental Plasticity. Biomolecules. 2022 Sep 14;12(9):1297. doi: 10.3390/biom12091297. PMID: 36139136; PMCID: PMC9496186.
Moreira SSJ, Santos CS, Castelo TS, Bezerra LGP, Praxedes ÉCG, Matos TM, Souza-Junior JBF, Feijó FMC, Comizzoli P, Silva AR. Investigating the need for antibiotic supplementation to the extender used for semen cryopreservation in collared peccaries. Front Vet Sci. 2022 Sep 2;9:954921. doi: 10.3389/fvets.2022.954921. PMID: 36118351; PMCID: PMC9478795.
Macente BI, Fonseca-Alves CE, Magalhães GM, Tavares MR, Mansano CFM, Mouttham L, Apparício M, Toniollo GH, Comizzoli P. Influence of Vitrification Device, Warming Protocol, and Subsequent In Vitro Culture on Structural Integrity of Testicular Fragments from Adult Domestic Cats. Biopreserv Biobank. 2022 Aug;20(4):392-400. doi: 10.1089/bio.2021.0092. Epub 2022 Jan 11. PMID: 35020470.
Crosier AE, Byron MJ, Comizzoli P. Connecting the spots: Understanding cheetah reproduction to improve assisted breeding and population management. Theriogenology. 2022 Jun;185:70-77. doi: 10.1016/j.theriogenology.2022.03.025. Epub 2022 Mar 28. PMID: 35381475.
Comizzoli P, He X, Lee PC. Long-term preservation of germ cells and gonadal tissues at ambient temperatures. Reprod Fertil. 2022 Mar 21;3(2):R42-R50. doi: 10.1530/RAF-22-0008. PMID: 35514540; PMCID: PMC9066944.
Silva AM, Pereira AG, Bezerra LGP, Jerônimo Moreira SS, Pereira AF, Oliveira MF, Comizzoli P, Silva AR. Cryopreservation of Testicular Tissue from Adult Red-Rumped Agoutis (Dasyprocta leporina Linnaeus, 1758). Animals (Basel). 2022 Mar 16;12(6):738. doi: 10.3390/ani12060738. PMID: 35327135; PMCID: PMC8944822.
Pomeroy KO, Comizzoli P, Rushing JS, Lersten IL, Nel-Themaat L. The ART of cryopreservation and its changing landscape. Fertil Steril. 2022 Mar;117(3):469-476. doi: 10.1016/j.fertnstert.2022.01.018. PMID: 35219471.
Comizzoli P, Holt WV. Recent Progress in Spermatology Contributing to the Knowledge and Conservation of Rare and Endangered Species. Annu Rev Anim Biosci. 2022 Feb 15;10:469-490. doi: 10.1146/annurev-animal-020420-040600. Epub 2021 Nov 10. PMID: 34758275.
Holt WV, Comizzoli P. Opportunities and Limitations for Reproductive Science in Species Conservation. Annu Rev Anim Biosci. 2022 Feb 15;10:491-511. doi: 10.1146/annurev-animal-013120-030858. Epub 2021 Oct 26. PMID: 34699258.
Rowlison T, Comizzoli P. The Knowns and Unknowns about Epididymal Extracellular Vesicles in Different Animal Species. Adv Biol (Weinh). 2022 Jan;6(1):e2101066. doi: 10.1002/adbi.202101066. Epub 2021 Nov 23. PMID: 34816626.
Lee PC, Zahmel J, Jewgenow K, Comizzoli P. Desiccated cat spermatozoa retain DNA integrity and developmental potential after prolonged storage and shipping at non-cryogenic temperatures. J Assist Reprod Genet. 2022 Jan;39(1):141-151. doi: 10.1007/s10815-021-02337-4. Epub 2021 Oct 5. PMID: 34609666; PMCID: PMC8866589.

2021

Comizzoli P, Power ML, Bornbusch SL, Muletz-Wolz CR. Interactions between reproductive biology and microbiomes in wild animal species. Anim Microbiome. 2021 Dec 23;3(1):87. doi: 10.1186/s42523-021-00156-7. PMID: 34949226; PMCID: PMC8697499.
Holt WV , Comizzoli P . Genome resource banking for wildlife conservation: promises and caveats. Cryo Letters. 2021 Nov-Dec;42(6):309-320. PMID: 35366296.
Amelkina O, Silva AMD, Silva AR, Comizzoli P. Transcriptome dynamics in developing testes of domestic cats and impact of age on tissue resilience to cryopreservation. BMC Genomics. 2021 Nov 23;22(1):847. doi: 10.1186/s12864-021-08099-8. PMID: 34814833; PMCID: PMC8611880.
Santos CS, Campos LB, Praxedes ÉCG, Moreira SSJ, Souza-Júnior JBF, Comizzoli P, Feijó FMC, Silva AR. Influence of antibiotics on bacterial load and sperm parameters during short-term preservation of collared peccary semen. Anim Reprod. 2021 Sep 13;18(3):e20210021. doi: 10.1590/1984-3143-AR2021-0021. PMID: 34539871; PMCID: PMC8444550.
Rowlison T, Ottinger MA, Comizzoli P. Exposure to epididymal extracellular vesicles enhances immature sperm function and sustains vitality of cryopreserved spermatozoa in the domestic cat model. J Assist Reprod Genet. 2021 Aug;38(8):2061-2071. doi: 10.1007/s10815-021-02214-0. Epub 2021 May 5. PMID: 33950331; PMCID: PMC8417210.
Maria da Silva A, Pereira AG, Brasil AV, Macedo LB, Souza-Junior J, Bezerra de Moura CE, Pereira AF, Franco de Oliveira M, Comizzoli P, Silva AR. Influence of freezing techniques and glycerol-based cryoprotectant combinations on the survival of testicular tissues from adult collared peccaries. Theriogenology. 2021 Jun;167:111-119. doi: 10.1016/j.theriogenology.2021.03.013. Epub 2021 Mar 26. PMID: 33813051.
Thuwanut P, Comizzoli P, Pimpin A, Srituravanich W, Sereepapong W, Pruksananonda K, Taweepolcharoen C, Tuntiviriyapun P, Suebthawinkul C, Sirayapiwat P. Influence of hydrogel encapsulation during cryopreservation of ovarian tissues and impact of post-thawing in vitro culture systems in a research animal model. Clin Exp Reprod Med. 2021 Jun;48(2):111-123. doi: 10.5653/cerm.2020.04056. Epub 2021 May 24. PMID: 34024082; PMCID: PMC8176157.
Comizzoli P, Ottinger MA. Understanding Reproductive Aging in Wildlife to Improve Animal Conservation and Human Reproductive Health. Front Cell Dev Biol. 2021 May 19;9:680471. doi: 10.3389/fcell.2021.680471. PMID: 34095152; PMCID: PMC8170016.
Chavez DR, Lee PC, Comizzoli P. Oocyte Meiotic Competence in the Domestic Cat Model: Novel Roles for Nuclear Proteins BRD2 and NPM1. Front Cell Dev Biol. 2021 May 3;9:670021. doi: 10.3389/fcell.2021.670021. PMID: 34012967; PMCID: PMC8126674.
Comizzoli P. Adding new ingredients to the recipe for successful embryo transfers. J Assist Reprod Genet. 2021 May;38(5):1019-1020. doi: 10.1007/s10815-021-02148-7. Epub 2021 Mar 15. PMID: 33723750; PMCID: PMC8190410.
Jiang B, Li W, Stewart S, Ou W, Liu B, Comizzoli P, He X. Sand-mediated ice seeding enables serum-free low-cryoprotectant cryopreservation of human induced pluripotent stem cells. Bioact Mater. 2021 Apr 30;6(12):4377-4388. doi: 10.1016/j.bioactmat.2021.04.025. PMID: 33997514; PMCID: PMC8111032.
Paulson EE, Comizzoli P. Endometrial receptivity and embryo implantation in carnivores-commonalities and differences with other mammalian species. Biol Reprod. 2021 Apr 1;104(4):771-783. doi: 10.1093/biolre/ioab001.
Comizzoli P, Pagenkopp Lohan KM, Muletz-Wolz C, Hassell J, Coyle B. The Interconnected Health Initiative: A Smithsonian Framework to Extend One Health Research and Education. Front Vet Sci. 2021 Mar 23;8:629410. doi: 10.3389/fvets.2021.629410. PMID: 33834047; PMCID: PMC8021902.
Zainuddin ZZ, Sipangkui S, Farqhan Kelana M, Chee YK, Tarmizi MRM, Comizzoli P. Repeated Evaluations of Testes and Semen Characteristics in Two Binturongs (Arctictis binturong). Front Vet Sci. 2021 Mar 12;8:658573. doi: 10.3389/fvets.2021.658573. PMID: 33778042; PMCID: PMC7994327.

Cosgrove Lab

2025

Flesken-Nikitin A, Pirtz MG, Ashe CS, Ellenson LH, Yemelyanova A, Cosgrove BD, Nikitin AY. Cell state dynamics during early stages of serous endometrial carcinoma. J Pathol. 2025 Nov;267(3):289-303. doi: 10.1002/path.6470. Epub 2025 Sep 9. PMID: 40923619.
Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, Elisseeff J, Farzad N, Fertig EJ, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur NK, Li D, Ma A, Ma Q, Menon V, Mitchell JT, Mora AL, Nagaraj S, Nelson AC, Niedernhofer LJ, Rojas M, Taha HB, Wang J, Wang S, Wu PH, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams PD, Aguayo-Mazzucato C, Baker DJ, Benz C, Bernlohr DA, Bueno M, Chen J, Childs BG, Chuang JH, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn WF, Franco AC, Furman D, Garovic V, Halene S, Herman AB, Hertzel AV, Iwasaki K, Jeon H, Kang JW, Karmakar S, Kirkland JL, Korstanje R, Kummerfeld E, Lee JH, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos JF, Peters ST, Rahman I, Ramasamy R, Rindone AN, Robbins PD, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer MJ, Schilling B, Schmidt EL, Schneider K, Sengupta K, Shu J, So PTC, Sun L, Tchkonia T, Teneche MG, Vanegas N, Wang J, Xie J, Yin S, Zhang K, Zhu Q, Fan R; SenNet Consortium. Advancing biological understanding of cellular senescence with computational multiomics. Nat Genet. 2025 Oct;57(10):2381-2394. doi: 10.1038/s41588-025-02314-y. Epub 2025 Sep 15. PMID: 40954249.
Hoang P, McKellar DW, Kowalczewski A, Mai NY, Chai M, Lian XL, Zheng Y, Amack J, Tucker N, De Vlaminck I, Yang H, Cosgrove BD, Ma Z. Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids. bioRxiv [Preprint]. 2025 Sep 19:2025.09.17.676874. doi: 10.1101/2025.09.17.676874. PMID: 41000917; PMCID: PMC12458260.
Phuong DJ, Pirtz MG, Ralston CQ, Cosgrove BD, Schimenti JC, Flesken-Nikitin A, Nikitin AY. Aggressive Serous Carcinomas of the Female Reproductive Tract: Cancer-Prone Cell States and Genetic Drivers. Cancers (Basel). 2025 Feb 11;17(4):604. doi: 10.3390/cancers17040604. PMID: 40002199; PMCID: PMC11852459.

2024

Walter LD, Orton JL, Ntekas I, Fong EHH, Maymi VI, Rudd BD, De Vlaminck I, Elisseeff JH, Cosgrove BD. Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states. Nat Aging. 2024 Dec;4(12):1862-1881. doi: 10.1038/s43587-024-00756-3. Epub 2024 Nov 22. PMID: 39578558; PMCID: PMC11645289.
Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Author Correction: Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Nov 20;15(1):10053. doi: 10.1038/s41467-024-54465-x. Erratum for: Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39567528; PMCID: PMC11579345.
Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39366996; PMCID: PMC11452611.

2023

Norris AM, Appu AB, Johnson CD, Zhou LY, McKellar DW, Renault MA, Hammers D, Cosgrove BD, Kopinke D. Hedgehog signaling via its ligand DHH acts as cell fate determinant during skeletal muscle regeneration. Nat Commun. 2023 Jun 24;14(1):3766. doi: 10.1038/s41467-023-39506-1. PMID: 37355632; PMCID: PMC10290686.
Shah SB, Carlson CR, Lai K, Zhong Z, Marsico G, Lee KM, Félix Vélez NE, Abeles EB, Allam M, Hu T, Walter LD, Martin KE, Gandhi K, Butler SD, Puri R, McCleary-Wheeler AL, Tam W, Elemento O, Takata K, Steidl C, Scott DW, Fontan L, Ueno H, Cosgrove BD, Inghirami G, García AJ, Coskun AF, Koff JL, Melnick A, Singh A. Combinatorial treatment rescues tumour-microenvironment-mediated attenuation of MALT1 inhibitors in B-cell lymphomas. Nat Mater. 2023 Apr;22(4):511-523. doi: 10.1038/s41563-023-01495-3. Epub 2023 Mar 16. PMID: 36928381; PMCID: PMC10069918.
McKellar DW, Mantri M, Hinchman MM, Parker JSL, Sethupathy P, Cosgrove BD, De Vlaminck I. Spatial mapping of the total transcriptome by in situ polyadenylation. Nat Biotechnol. 2023 Apr;41(4):513-520. doi: 10.1038/s41587-022-01517-6. Epub 2022 Nov 3. PMID: 36329320; PMCID: PMC10110464.

2022

Lee U, Stuelsatz P, Karaz S, McKellar DW, Russeil J, Deak M, De Vlaminck I, Lepper C, Deplancke B, Cosgrove BD, Feige JN. A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. iScience. 2022 Jun 14;25(7):104589. doi: 10.1016/j.isci.2022.104589. PMID: 35789856; PMCID: PMC9250016.

2021

McKellar DW, Walter LD, Song LT, Mantri M, Wang MFZ, De Vlaminck I, Cosgrove BD. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol. 2021 Nov 12;4(1):1280. doi: 10.1038/s42003-021-02810-x. PMID: 34773081; PMCID: PMC8589952.
Chovatiya G, Ghuwalewala S, Walter LD, Cosgrove BD, Tumbar T. High-resolution single-cell transcriptomics reveals heterogeneity of self-renewing hair follicle stem cells. Exp Dermatol. 2021 Apr;30(4):457-471. doi: 10.1111/exd.14262. Epub 2021 Jan 6. PMID: 33319418; PMCID: PMC8016723.
Gheller BJ, Blum JE, Lim EW, Handzlik MK, Hannah Fong EH, Ko AC, Khanna S, Gheller ME, Bender EL, Alexander MS, Stover PJ, Field MS, Cosgrove BD, Metallo CM, Thalacker-Mercer AE. Extracellular serine and glycine are required for mouse and human skeletal muscle stem and progenitor cell function. Mol Metab. 2021 Jan;43:101106. doi: 10.1016/j.molmet.2020.101106. Epub 2020 Oct 23. PMID: 33122122; PMCID: PMC7691553.

Danko Lab

2025

Barshad G, Danko CG. Revisiting models of enhancer-promoter communication in gene regulation. Genome Res. 2025 Jun 2;35(6):1277-1286. doi: 10.1101/gr.278389.123. PMID: 40456606; PMCID: PMC12129020.
Chang HY, McMurry SE, Ma S, Mansour CA, Schwab SMT, Danko CG, Lee SS. Transcriptomic and chromatin accessibility profiling unveils new regulators of heat hormesis in Caenorhabditis elegans. bioRxiv [Preprint]. 2025 Mar 14:2025.03.11.642714. doi: 10.1101/2025.03.11.642714. PMID: 40161833; PMCID: PMC11952391.
Munn PR, Chia J, Danko CG. Accurate de novo transcription unit annotation from run-on and sequencing data. bioRxiv [Preprint]. 2025 Feb 17:2025.02.12.637853. doi: 10.1101/2025.02.12.637853. PMID: 40027686; PMCID: PMC11870431.
He AY, Palamuttam NP, Danko CG. Training deep learning models on personalized genomic sequences improves variant effect prediction. bioRxiv [Preprint]. 2025 Feb 15:2024.10.15.618510. doi: 10.1101/2024.10.15.618510. PMID: 39463940; PMCID: PMC11507713.

2024

Wang Z, Song A, Tao B, Miao M, Luo YQ, Wang J, Yin Z, Xiao R, Zhou X, Shang XY, Hu S, Liang K, Danko CG, Chen FX. The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release. Mol Cell. 2024 Dec 19;84(24):4824-4842.e7. doi: 10.1016/j.molcel.2024.10.046. Epub 2024 Nov 26. PMID: 39603240.
Wen W, Zhong J, Zhang Z, Jia L, Chu T, Wang N, Danko CG, Wang Z. dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility. Brief Bioinform. 2024 Sep 23;25(6):bbae459. doi: 10.1093/bib/bbae459. PMID: 39316943; PMCID: PMC11421843.
Vill AC, Rice EJ, De Vlaminck I, Danko CG, Brito IL. Precision run-on sequencing (PRO-seq) for microbiome transcriptomics. Nat Microbiol. 2024 Jan;9(1):241-250. doi: 10.1038/s41564-023-01558-w. Epub 2024 Jan 3. PMID: 38172625; PMCID: PMC11059318.

2023

Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ, Ma Y, Wang Z, Rando OJ, Hadjantonakis AK, Danko CG. RNA polymerase II dynamics shape enhancer-promoter interactions. Nat Genet. 2023 Aug;55(8):1370-1380. doi: 10.1038/s41588-023-01442-7. Epub 2023 Jul 10. PMID: 37430091; PMCID: PMC10714922.
Alexander AK, Rice EJ, Lujic J, Simon LE, Tanis S, Barshad G, Zhu L, Lama J, Cohen PE, Danko CG. A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis. Nat Commun. 2023 Mar 29;14(1):1753. doi: 10.1038/s41467-023-37408-w. PMID: 36990976; PMCID: PMC10060231.
Marks BA, Pipia IM, Mukai C, Horibata S, Rice EJ, Danko CG, Coonrod SA. GDNF-RET signaling and EGR1 form a positive feedback loop that promotes tamoxifen resistance via cyclin D1. BMC Cancer. 2023 Feb 10;23(1):138. doi: 10.1186/s12885-023-10559-1. PMID: 36765275; PMCID: PMC9912664.
Wang N, Wang Z, Danko CG, Chu T. Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway. Methods Mol Biol. 2023;2599:215-226. doi: 10.1007/978-1-0716-2847-8_15. PMID: 36427152.

2022

Villanueva JW, Kwong L, Han T, Martinez SA, Shanahan MT, Kanke M, Dow LE, Danko CG, Sethupathy P. Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival. BMC Genomics. 2022 Dec 1;23(1):792. doi: 10.1186/s12864-022-09018-1. PMID: 36457077; PMCID: PMC9716731.
Abuhashem A, Chivu AG, Zhao Y, Rice EJ, Siepel A, Danko CG, Hadjantonakis AK. RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes Dev. 2022 Aug 18;36(13-14):770–89. doi: 10.1101/gad.349565.122. Epub ahead of print. PMID: 35981753; PMCID: PMC9480856.
Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov. 2022 Jul 6;12(7):1782-1803. doi: 10.1158/2159-8290.CD-21-1514. PMID: 35443279; PMCID: PMC9262862.
Chou SP, Alexander AK, Rice EJ, Choate LA, Danko CG. Genetic dissection of the RNA polymerase II transcription cycle. Elife. 2022 Jul 1;11:e78458. doi: 10.7554/eLife.78458. PMID: 35775732; PMCID: PMC9286732.
Chu T, Wang Z, Pe’er D, Danko CG. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nat Cancer. 2022 Apr;3(4):505-517. doi: 10.1038/s43018-022-00356-3. Epub 2022 Apr 25. PMID: 35469013; PMCID: PMC9046084.
Barshad G, Webb LM, Ting HA, Oyesola OO, Onyekwere OG, Lewis JJ, Rice EJ, Matheson MK, Sun XH, von Moltke J, Danko CG, Tait Wojno ED. E-Protein Inhibition in ILC2 Development Shapes the Function of Mature ILC2s during Allergic Airway Inflammation. J Immunol. 2022 Mar 1;208(5):1007-1020. doi: 10.4049/jimmunol.2100414. Epub 2022 Feb 18. PMID: 35181641; PMCID: PMC8881320.
Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou SP, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, Danko CG. Prediction of histone post-translational modification patterns based on nascent transcription data. Nat Genet. 2022 Mar;54(3):295-305. doi: 10.1038/s41588-022-01026-x. Epub 2022 Mar 10. PMID: 35273399; PMCID: PMC9444190.
Stephan T, Burgess SM, Cheng H, Danko CG, Gill CA, Jarvis ED, Koepfli KP, Koltes JE, Lyons E, Ronald P, Ryder OA, Schriml LM, Soltis P, VandeWoude S, Zhou H, Ostrander EA, Karlsson EK. Darwinian genomics and diversity in the tree of life. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115644119. doi: 10.1073/pnas.2115644119. PMID: 35042807; PMCID: PMC8795533.

2021

Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. 2021 Dec 11;37(24):4727-4736. doi: 10.1093/bioinformatics/btab582. PMID: 34382072; PMCID: PMC8665767.
Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun. 2021 Nov 15;12(1):6590. doi: 10.1038/s41467-021-26854-z. PMID: 34782625; PMCID: PMC8592990.
Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Wang Z, Ercan S, Danko CG. Identification and prediction of developmental enhancers in sea urchin embryos. BMC Genomics. 2021 Oct 19;22(1):751. doi: 10.1186/s12864-021-07936-0. PMID: 34666684; PMCID: PMC8527612.
Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH. Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. Mol Biol Evol. 2021 Sep 27;38(10):4449-4462. doi: 10.1093/molbev/msab185. PMID: 34146107; PMCID: PMC8476138.
Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol. 2021 Jul 6;13(7):evab128. doi: 10.1093/gbe/evab128. PMID: 34117762; PMCID: PMC8290107.
Wang MFZ, Mantri M, Chou SP, Scuderi GJ, McKellar DW, Butcher JT, Danko CG, De Vlaminck I. Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. Nat Commun. 2021 Apr 12;12(1):2158. doi: 10.1038/s41467-021-22496-3. PMID: 33846360; PMCID: PMC8042062.
Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol. 2021 Feb 15;19(1):30. doi: 10.1186/s12915-021-00949-x. PMID: 33588838; PMCID: PMC7885420.
Saikia M, Holter MM, Donahue LR, Lee IS, Zheng QC, Wise JL, Todero JE, Phuong DJ, Garibay D, Coch R, Sloop KW, Garcia-Ocana A, Danko CG, Cummings BP. GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells. JCI Insight. 2021 Feb 8;6(3):e141851. doi: 10.1172/jci.insight.141851. PMID: 33554958; PMCID: PMC7934853.

Das Lab

2025

Tower CA, Manske G, Ferrell EL, Anbarci DN, Jorgensen K, Ma B, Aboelenain M, Ranjan R, Chakraborty S, Moritz L, Das A, Boiani M, Black BE, Chavez S, Marsh EE, Shikanov A, Schindler K, Chen X, Hammoud SS. Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation. Dev Cell. 2025 Sep 24:S1534-5807(25)00537-4. doi: 10.1016/j.devcel.2025.08.017. Epub ahead of print. PMID: 40997799; PMCID: PMC12479092.

2024

Joshi JN, Changela N, Mahal L, Jang J, Defosse T, Wang LI, Das A, Shapiro JG, McKim K. Meiosis-specific functions of kinetochore protein SPC105R required for chromosome segregation in Drosophila oocytes. Mol Biol Cell. 2024 Aug 1;35(8):ar105. doi: 10.1091/mbc.E24-02-0067. Epub 2024 Jun 12. PMID: 38865189; PMCID: PMC11321039.

2023

Das A, Boese KG, Tachibana K, Baek SH, Lampson MA, Black BE. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. Curr Biol. 2023 Sep 11;33(17):3759-3765.e3. doi: 10.1016/j.cub.2023.07.032. Epub 2023 Aug 14. PMID: 37582374; PMCID: PMC10528140.
Das A, Destouni A. Novel insights into reproductive ageing and menopause from genomics. Hum Reprod. 2023 Feb 1;38(2):195-203. doi: 10.1093/humrep/deac256. PMID: 36478237.

2022

Das A, Iwata-Otsubo A, Destouni A, Dawicki-McKenna JM, Boese KG, Black BE, Lampson MA. Epigenetic, genetic and maternal effects enable stable centromere inheritance. Nat Cell Biol. 2022 May;24(5):748-756. doi: 10.1038/s41556-022-00897-w. Epub 2022 May 9. PMID: 35534577; PMCID: PMC9107508.

Daugherity

2023

Lavin ES, Getchell RG, Daugherity EK, Kent ML, Frosolone AD, Ivanek R. Assessment of Oral Albendazole and Fumagillin in the Treatment of Pseudoloma neurophilia in Adult Zebrafish. Comp Med. 2023 Oct 29;73(5):335-345. doi: 10.30802/AALAS-CM-23-000035. PMID: 38087410; PMCID: PMC10702170.

2022

Draper JM, Savson DJ, Lavin ES, Feldman ER, Singh B, Martin-Flores M, Daugherity EK. Comparison of Effects of Capromorelin and Mirtazapine on Appetite in New Zealand White Rabbits (Oryctolagus cuniculus). J Am Assoc Lab Anim Sci. 2022 Sep 1;61(5):495-505. doi: 10.30802/AALAS-JAALAS-22-000003. Epub 2022 Aug 18. PMID: 35981857; PMCID: PMC9536823.
Savson DJ, Zenilman SS, Smith CR, Daugherity EK, Singh B, Getchell RG. Comparison of Alfaxalone and Tricaine Methanesulfonate Immersion Anesthesia And Alfaxalone Residue Clearance In Rainbow Trout (Oncorhynchus Mykiss). Comp Med. 2022 Jun 1;72(3):181-194. doi: 10.30802/AALAS-CM-22-000052. Epub 2022 Jun 3. PMID: 35659382; PMCID: PMC9334004.

de Mestre Lab

2025

Mouncey R, de Mestre AM, Verheyen KL. Born to run? Racing and training outcomes, population dynamics and traceability of a Thoroughbred birth cohort. Vet Rec. 2025 Oct 4;197(7):e5777. doi: 10.1002/vetr.5777. Epub 2025 Sep 26. PMID: 41000051; PMCID: PMC12494123.
Fehin B, Scott CJ, Arango-Sabogal JC, de Mestre AM, Mouncey R. Associations between endometrial swab bacteriology and cytology findings and live foal rates in Thoroughbred broodmares in the United Kingdom. Equine Vet J. 2025 Sep 1. doi: 10.1111/evj.70086. Epub ahead of print. PMID: 40888035.
Mouncey R, de Mestre AM, Arango-Sabogal JC, Verheyen KL. Born to run? Associations between gestational and early-life exposures and later-life performance outcomes in Thoroughbreds. Equine Vet J. 2025 Aug 25. doi: 10.1111/evj.70084. Epub ahead of print. PMID: 40851510.

2024

Mouncey R, Arango-Sabogal JC, de Mestre A, Verheyen KL. Associations between turn out practices and rates of musculoskeletal disease and injury in Thoroughbred foals and yearlings on stud farms in the United Kingdom. Equine Vet J. 2024 Sep;56(5):892-901. doi: 10.1111/evj.14038. Epub 2023 Dec 26. PMID: 38146768.
Lawson JM, Salem SE, Miller D, Kahler A, van den Boer WJ, Shilton CA, Sever T, Mouncey RR, Ward J, Hampshire DJ, Foote AK, Bryan JS, Juras R, Pynn OD, Davis BW, Bellone RR, Raudsepp T, de Mestre AM. Naturally occurring horse model of miscarriage reveals temporal relationship between chromosomal aberration type and point of lethality. Proc Natl Acad Sci U S A. 2024 Aug 13;121(33):e2405636121. doi: 10.1073/pnas.2405636121. Epub 2024 Aug 5. PMID: 39102548; PMCID: PMC11331123.
Lawson JM, Verheyen K, Smith KC, Bryan JS, Foote AK, de Mestre AM. The equine umbilical cord in clinically healthy pregnancies. Equine Vet J. 2024 Jul;56(4):742-750. doi: 10.1111/evj.14055. Epub 2024 Jan 14. PMID: 38219774.
Lawson JM, Shilton CA, Lindsay-McGee V, Psifidi A, Wathes DC, Raudsepp T, de Mestre AM. Does inbreeding contribute to pregnancy loss in Thoroughbred horses? Equine Vet J. 2024 Jul;56(4):711-718. doi: 10.1111/evj.14057. Epub 2024 Jan 14. PMID: 38221707.
Wagner B, Babasyan S, Wilford S, Robbin MG, de Mestre AM. Monoclonal antibodies for equine CD25 improve detection of regulatory T cells in horses. Vet Immunol Immunopathol. 2024 Aug;274:110790. doi: 10.1016/j.vetimm.2024.110790. Epub 2024 Jun 6. PMID: 38901326.
Sielhorst J, Koether K, Volkmann N, Blanco M, Vicioso R, Baade S, Kemper N, de Mestre AM, Sieme H. Occurrence of ultrasonographic assessed placental abnormalities, treatments, pregnancy outcome, and subsequent fertility on a large warmblood stud farm: A retrospective field study. J Equine Vet Sci. 2024 May 1;137:105076. doi: 10.1016/j.jevs.2024.105076. Epub ahead of print. PMID: 38697370.
Mouncey R, Arango-Sabogal JC, Rathbone P, Scott CJ, de Mestre AM. Prevalence of Microbial Isolates Cultured from Endometrial Swab Samples Collected from United Kingdom Thoroughbred Mares from 2014 to 2020. Vet Sci. 2024 Feb 9;11(2):82. doi: 10.3390/vetsci11020082. PMID: 38393100; PMCID: PMC10891641.

2023

Mouncey R, Arango-Sabogal JC, de Mestre AM, Verheyen K. Gestation Length is Associated With Early-Life Limb Deformities in Thoroughbred Foals. J Equine Vet Sci. 2023 Oct;129:104896. doi: 10.1016/j.jevs.2023.104896. Epub 2023 Aug 2. PMID: 37541603.
Mouncey R, Arango-Sabogal JC, de Mestre AM, Verheyen KL. Incidence of disease, injury and death in Thoroughbred foals and yearlings on stud farms in the UK and Ireland. Vet Rec. 2023 Jun-Jan 17;192(12):e2994. doi: 10.1002/vetr.2994. Epub 2023 May 14. PMID: 37183185.
Mouncey R, Arango-Sabogal JC, de Mestre AM, Verheyen KL. Incidence of disease, injury and death in Thoroughbred foals and yearlings on stud farms in the UK and Ireland. Vet Rec. 2023 Jun-Jan 17;192(12):e2994. doi: 10.1002/vetr.2994. Epub 2023 May 14. PMID: 37183185.
Thompson RE, Meyers MA, Palmer J, Veeramachaneni DNR, Magee C, de Mestre AM, Antczak DF, Hollinshead FK. Production of Mare Chorionic Girdle Organoids That Secrete Equine Chorionic Gonadotropin. Int J Mol Sci. 2023 May 31;24(11):9538. doi: 10.3390/ijms24119538. PMID: 37298490; PMCID: PMC10253530.

2022

Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction? Reprod Fertil Dev. 2022 Dec;35(2):51-69. doi: 10.1071/RD22239. PMID: 36592981.
Scott CJ, de Mestre AM, Verheyen KL, Arango-Sabogal JC. Bayesian accuracy estimates and fit for purpose thresholds of cytology and culture of endometrial swab samples for detecting endometritis in mares. Prev Vet Med. 2022 Dec;209:105783. doi: 10.1016/j.prevetmed.2022.105783. Epub 2022 Oct 20. PMID: 36306641.
Jaworska J, de Mestre AM, Wiśniewska J, Wagner B, Nowicki A, Kowalczyk-Zięba I, Wocławek-Potocka I. Populations of NK Cells and Regulatory T Cells in the Endometrium of Cycling Mares-A Preliminary Study. Animals (Basel). 2022 Nov 30;12(23):3373. doi: 10.3390/ani12233373. PMID: 36496894; PMCID: PMC9740928.
Roach J, Arango Sabogal JC, Smith K, Foote A, Verheyen K, de Mestre AM. Multivariable analysis to determine risk factors associated with abortion in mares. Reprod Fertil. 2022 Nov 1;3(4):301–12. doi: 10.1530/RAF-22-0087. Epub ahead of print. PMID: 36374277; PMCID: PMC9782406.
Mouncey R, Arango-Sabogal JC, de Mestre A, Verheyen K. Descriptive Study of Medication Usage and Occurrence of Disease and Injury During Gestation in Thoroughbred Broodmares. J Equine Vet Sci. 2022 Nov;118:104104. doi: 10.1016/j.jevs.2022.104104. Epub 2022 Aug 11. PMID: 35964852.
Grillos AS, Roach JM, de Mestre AM, Foote AK, Kinglsey NB, Mienaltowski MJ, Bellone RR. First reported case of fragile foal syndrome type 1 in the Thoroughbred caused by PLOD1 c.2032G>A. Equine Vet J. 2022 Nov;54(6):1086-1093. doi: 10.1111/evj.13547. Epub 2022 Feb 1. PMID: 34939209; PMCID: PMC9213567.
Arango-Sabogal JC, Mouncey R, de Mestre AM, Verheyen K. Date of birth and purchase price as foals or yearlings are associated with Thoroughbred flat race performance in the United Kingdom and Ireland. Vet Rec Open. 2022 Sep 23;9(1):e43. doi: 10.1002/vro2.43. PMID: 36185419; PMCID: PMC9508327.
Salem SE, Sinnott A, Roach JM, Verheyen KLP, de Mestre AM. Mixed-Effects Modelling of the Risk Factors Associated with Multiple Pregnancies in Thoroughbred Mares. Animals (Basel). 2022 Jul 20;12(14):1841. doi: 10.3390/ani12141841. PMID: 35883388; PMCID: PMC9312083.
Kinnison T, Lumbis R, de Mestre AM, Cardwell JM. Preliminary testing of psychometric properties of the ‘student perceptions of veterinary interprofessional education and work scale’ (SP-VIEWS). J Interprof Care. 2022 May-Jun;36(3):449-457. doi: 10.1080/13561820.2021.1902961. Epub 2021 May 18. PMID: 34000950.
Mouncey R, Arango-Sabogal JC, de Mestre AM, Foote AK, Verheyen KL. Retrospective analysis of post-mortem findings in Thoroughbreds aged from birth to 18 months presented to a UK pathology laboratory. Vet J. 2022 Mar;281:105813. doi: 10.1016/j.tvjl.2022.105813. Epub 2022 Mar 5. PMID: 35259541.
Robles M, Loux S, de Mestre AM, Chavatte-Palmer P. Environmental constraints and pathologies that modulate equine placental genes and development. Reproduction. 2022 Feb 14;163(3):R25-R38. doi: 10.1530/REP-21-0116. PMID: 35019860.
Loux S, Robles M, Chavatte-Palmer P, de Mestre A. Markers of equine placental differentiation: insights from gene expression studies. Reproduction. 2022 Feb 14;163(3):R39-R54. doi: 10.1530/REP-21-0115. PMID: 35038309.

2021

Arango-Sabogal JC, Mouncey R, de Mestre AM, Verheyen K. Retrospective analysis of the population dynamics and racing outcomes of the 2014 and 2015 UK and Ireland Thoroughbred foal crops. Vet Rec. 2021 Sep;189(5):e298. doi: 10.1002/vetr.298. Epub 2021 Apr 18. PMID: 33870524.
Roach JM, Foote AK, Smith KC, Verheyen KL, de Mestre AM. Incidence and causes of pregnancy loss after Day 70 of gestation in Thoroughbreds. Equine Vet J. 2021 Sep;53(5):996-1003. doi: 10.1111/evj.13386. Epub 2020 Dec 14. PMID: 33205445.
Kahler A, McGonnell IM, Smart H, Kowalski AA, Smith KC, Wathes DC, de Mestre AM. Fetal morphological features and abnormalities associated with equine early pregnancy loss. Equine Vet J. 2021 May;53(3):530-541. doi: 10.1111/evj.13340. Epub 2020 Sep 19. PMID: 32869365.

de Vlaminck Lab

2025

Shimizu C, Pérez Pomares JM, Loy CJ, De Vlaminck I, Tremoulet AH, Ruiz-Villalba A, Burns JC. Pathology of the Coronary Arteries and Myocardium in Kawasaki Disease. Annu Rev Pathol. 2025 Oct 28. doi: 10.1146/annurev-pathmechdis-111523-023453. Epub ahead of print. PMID: 41150874.
Hemberg M, Marini F, Ghazanfar S, Al Ajami A, Abassi N, Anchang B, Benayoun BA, Cao Y, Chen K, Cuesta-Astroz Y, DeBruine Z, Dendrou CA, De Vlaminck I, Imkeller K, Korsunsky I, Lederer AR, Li JJ, Meysman P, Miller CL, Mullan KA, Ohler U, Panwar P, Patikas N, Schuck J, Siu JHY, Triche TJ Jr, Tsankov A, van der Laan SW, Yajima M, Yang J, Zanini F, Jelic I. Insights, opportunities, and challenges provided by large cell atlases. Genome Biol. 2025 Oct 20;26(1):358. doi: 10.1186/s13059-025-03771-8. PMID: 41116172; PMCID: PMC12536537.
Mzava O, Agun GF, Loy CJ, Gonzalez-Bocco IH, Djomnang Kounatse LA, Bliss A, Wells SL, Lenz J, Belcher E, Chen K, Koo S, Baden LR, Chu T, Cheng MP, Ritz J, Gupta S, De Vlaminck I. Urine Cell-Free RNA vs Plasma Cell-Free RNA for Monitoring of Kidney Injury and Immune Complications. Clin Chem. 2025 Oct 3;71(10):1058-1066. doi: 10.1093/clinchem/hvaf082. PMID: 40796157; PMCID: PMC12490885.
Hoang P, McKellar DW, Kowalczewski A, Mai NY, Chai M, Lian XL, Zheng Y, Amack J, Tucker N, De Vlaminck I, Yang H, Cosgrove BD, Ma Z. Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids. bioRxiv [Preprint]. 2025 Sep 19:2025.09.17.676874. doi: 10.1101/2025.09.17.676874. PMID: 41000917; PMCID: PMC12458260.
Zuela-Sopilniak N, Morival JLP, Ntekas I, Elpers MA, Agarwal R, Henretta SJ, Odell JD, De Vlaminck I, Lammerding J. Nuclear envelope rupture in cardiomyocytes orchestrates early transcriptomic changes and immune activation in LMNA -DCM that are reversed by LINC complex disruption. bioRxiv [Preprint]. 2025 Sep 15:2024.06.11.598511. doi: 10.1101/2024.06.11.598511. PMID: 38915720; PMCID: PMC11195185.
Holdener C, Jiang S, Sutherland DM, Griswold KA, Dermody TS, Parker JSL, De Vlaminck I. Spatial Transcriptomics to Study Virus-Host Interactions. Annu Rev Virol. 2025 Sep;12(1):379-399. doi: 10.1146/annurev-virology-092623-104926. Epub 2025 Jun 16. PMID: 40523107.
Jones J, García-Martínez KY, Lee YY, Rhee M, Nath RR, Takahashi S, Grodner B, De Vlaminck I, Leifer CA, Brito IL. Gut commensal microbiota drive tailored macrophage responses. Cell Rep. 2025 Aug 26;44(8):116157. doi: 10.1016/j.celrep.2025.116157. Epub 2025 Aug 18. PMID: 40828655.
Gardella AE, Eweis-LaBolle D, Loy CJ, Belcher ED, Lenz JS, Franconi CJ, Scofield SY, Grimson A, Hanson MR, De Vlaminck I. Circulating cell-free RNA signatures for the characterization and diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome. Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2507345122. doi: 10.1073/pnas.2507345122. Epub 2025 Aug 11. PMID: 40789036; PMCID: PMC12377778.
Loy CJ, Wang H, Kim J, Shimizu C, Lenz J, Belcher E, Tremoulet AH, Burns JC, De Vlaminck I. Molecular characterization of Kawasaki disease subgroups using cell-free RNA profiling. Sci Rep. 2025 Aug 14;15(1):29799. doi: 10.1038/s41598-025-15843-7. PMID: 40813796; PMCID: PMC12354920.
Tabula Microcebus Consortium; Ezran C, Liu S, Chang S, Ming J, Botvinnik O, Penland L, Tarashansky A, de Morree A, Travaglini KJ, Zhao J, Wang G, Hasegawa K, Sin H, Sit R, Okamoto J, Sinha R, Zhang Y, Karanewsky CJ, Pendleton JL, Morri M, Perret M, Aujard F, Stryer L, Artandi S, Fuller MT, Weissman IL, Rando TA, Ferrell JE Jr, Wang B, De Vlaminck I, Yang C, Casey KM, Albertelli MA, Pisco AO, Karkanias J, Neff N, Wu AR, Quake SR, Krasnow MA. A molecular cell atlas of mouse lemur, an emerging model primate. Nature. 2025 Aug;644(8075):173-184. doi: 10.1038/s41586-025-09113-9. Epub 2025 Jul 30. PMID: 40739356; PMCID: PMC12328211.
Ezran C, Liu S, Chang S, Ming J, Guethlein LA, Wang MFZ, Dehghannasiri R, Olivieri J, Frank HK, Tarashansky A, Koh W, Jing Q, Botvinnik O, Antony J; Tabula Microcebus Consortium; Pisco AO, Karkanias J, Yang C, Ferrell JE Jr, Boyd SD, Parham P, Long JZ, Wang B, Salzman J, De Vlaminck I, Wu AR, Quake SR, Krasnow MA. Mouse lemur cell atlas informs primate genes, physiology and disease. Nature. 2025 Aug;644(8075):185-196. doi: 10.1038/s41586-025-09114-8. Epub 2025 Jul 30. PMID: 40739355; PMCID: PMC12328237.
Stephanou A, Mantri M, Shankaranarayanan D, Li C, Lagman M, Xiang J, Pan C, Sun Y, Muthukumar T, Machaca K, De Vlaminck I, Suthanthiran M. Single-cell transcriptomics reveals targeted modulation of inflammatory repertoire by SOCE blockers. bioRxiv [Preprint]. 2025 May 1:2025.04.28.651042. doi: 10.1101/2025.04.28.651042. PMID: 40654653; PMCID: PMC12247835.
Loy C, Agun G, Cheng MP, Gonzalez-Bocco IH, Lenz J, Belcher E, Bliss A, Eweis-LaBolle D, Chu T, Pidala J, Ritz J, De Vlaminck I. Plasma Cell-Free RNA Captures Immune Dynamics and Predicts GVHD after Hematopoietic Stem Cell Transplantation. medRxiv [Preprint]. 2025 Apr 17:2024.05.15.24307448. doi: 10.1101/2024.05.15.24307448. PMID: 38798589; PMCID: PMC11118637
Whitman MA, Mantri M, Spanos E, Estroff LA, De Vlaminck I, Fischbach C. Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity. Biomaterials. 2025 Apr;315:122916. doi: 10.1016/j.biomaterials.2024.122916. Epub 2024 Oct 24. PMID: 39490060; PMCID: PMC11658005
Pang Y, Prieto T, Gonzalez-Pena V, Aragon A, Xia Y, Kao S, Rajagopalan S, Zinno J, Quentin J, Laval J, Yuan D, Omans N, Klein D, MacKay M, De Vlaminck I, Easton J, Evans W, Landau DA, Gawad C. Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution. bioRxiv [Preprint]. 2025 Mar 19:2025.03.19.644196. doi: 10.1101/2025.03.19.644196. PMID: 40166290; PMCID: PMC11957134.
Holdener C, De Vlaminck I. Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data. bioRxiv [Preprint]. 2025 Mar 2:2025.02.26.640406. doi: 10.1101/2025.02.26.640406. PMID: 40060619; PMCID: PMC11888426.
Jiang S, Mantri M, Maymi V, Leddon SA, Schweitzer P, Bhandari S, Holdener C, Ntekas I, Vollmers C, Flyak AI, Fowell DJ, Rudd BD, De Vlaminck I. A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection. bioRxiv [Preprint]. 2025 Feb 6:2025.01.31.635509. doi: 10.1101/2025.01.31.635509. PMID: 39975238; PMCID: PMC11838507.

2024

Walter LD, Orton JL, Ntekas I, Fong EHH, Maymi VI, Rudd BD, De Vlaminck I, Elisseeff JH, Cosgrove BD. Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states. Nat Aging. 2024 Dec;4(12):1862-1881. doi: 10.1038/s43587-024-00756-3. Epub 2024 Nov 22. PMID: 39578558; PMCID: PMC11645289.
Whitman MA, Mantri M, Spanos E, Estroff LA, De Vlaminck I, Fischbach C. Bone mineral density affects tumor growth by shaping microenvironmental heterogeneity. Biomaterials. 2024 Oct 24;315:122916. doi: 10.1016/j.biomaterials.2024.122916. Epub ahead of print. PMID: 39490060.
Shankaranarayanan D, Mantri M, Lagman M, Li C, Sharma VK, Muthukumar T, Xiang JZ, De Vlaminck I, Machaca K, Suthanthiran M. Blockade of store-operated calcium entry by BTP2 preserves anti-inflammatory gene expression in human peripheral blood mononuclear cells. Hum Immunol. 2024 Sep 26;85(6):111144. doi: 10.1016/j.humimm.2024.111144. Epub ahead of print. PMID: 39332042.
Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz JS, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA; P.E.M.K.D.R.G.; C.H.A.R.M.S. the Study Group; Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet AH, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, De Vlaminck I. Plasma cell-free RNA signatures of inflammatory syndromes in children. Proc Natl Acad Sci U S A. 2024 Sep 10;121(37):e2403897121. doi: 10.1073/pnas.2403897121. Epub 2024 Sep 6. PMID: 39240972; PMCID: PMC11406294.
Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, Diebold PJ, Wu DT, Chen CY, Kim DM, Zipfel WR, Brito IL, De Vlaminck I. Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Nat Microbiol. 2024 Sep;9(9):2262-2277. doi: 10.1038/s41564-024-01735-5. Epub 2024 Jun 25. PMID: 38918467; PMCID: PMC11371653.
Ntekas I, De Vlaminck I. Spatial methods for microbiome-host interactions. Nat Biotechnol. 2024 Sep;42(9):1359-1360. doi: 10.1038/s41587-023-01996-1. PMID: 37985877.
Overbey EG, Kim J, Tierney BT, Park J, Houerbi N, Lucaci AG, Garcia Medina S, Damle N, Najjar D, Grigorev K, Afshin EE, Ryon KA, Sienkiewicz K, Patras L, Klotz R, Ortiz V, MacKay M, Schweickart A, Chin CR, Sierra MA, Valenzuela MF, Dantas E, Nelson TM, Cekanaviciute E, Deards G, Foox J, Narayanan SA, Schmidt CM, Schmidt MA, Schmidt JC, Mullane S, Tigchelaar SS, Levitte S, Westover C, Bhattacharya C, Lucotti S, Wain Hirschberg J, Proszynski J, Burke M, Kleinman AS, Butler DJ, Loy C, Mzava O, Lenz J, Paul D, Mozsary C, Sanders LM, Taylor LE, Patel CO, Khan SA, Suhail Mohamad M, Byhaqui SGA, Aslam B, Gajadhar AS, Williamson L, Tandel P, Yang Q, Chu J, Benz RW, Siddiqui A, Hornburg D, Blease K, Moreno J, Boddicker A, Zhao J, Lajoie B, Scott RT, Gilbert RR, Lai Polo SH, Altomare A, Kruglyak S, Levy S, Ariyapala I, Beer J, Zhang B, Hudson BM, Rininger A, Church SE, Beheshti A, Church GM, Smith SM, Crucian BE, Zwart SR, Matei I, Lyden DC, Garrett-Bakelman F, Krumsiek J, Chen Q, Miller D, Shuga J, Williams S, Nemec C, Trudel G, Pelchat M, Laneuville O, De Vlaminck I, Gross S, Bolton KL, Bailey SM, Granstein R, Furman D, Melnick AM, Costes SV, Shirah B, Yu M, Menon AS, Mateus J, Meydan C, Mason CE. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank. Nature. 2024 Aug;632(8027):1145-1154. doi: 10.1038/s41586-024-07639-y. Epub 2024 Jun 11. PMID: 38862028; PMCID: PMC11357981.
Mason CE, Green J, Adamopoulos KI, Afshin EE, Baechle JJ, Basner M, Bailey SM, Bielski L, Borg J, Borg J, Broddrick JT, Burke M, Caicedo A, Castañeda V, Chatterjee S, Chin CR, Church G, Costes SV, De Vlaminck I, Desai RI, Dhir R, Diaz JE, Etlin SM, Feinstein Z, Furman D, Garcia-Medina JS, Garrett-Bakelman F, Giacomello S, Gupta A, Hassanin A, Houerbi N, Irby I, Javorsky E, Jirak P, Jones CW, Kamal KY, Kangas BD, Karouia F, Kim J, Kim JH, Kleinman AS, Lam T, Lawler JM, Lee JA, Limoli CL, Lucaci A, MacKay M, McDonald JT, Melnick AM, Meydan C, Mieczkowski J, Muratani M, Najjar D, Othman MA, Overbey EG, Paar V, Park J, Paul AM, Perdyan A, Proszynski J, Reynolds RJ, Ronca AE, Rubins K, Ryon KA, Sanders LM, Glowe PS, Shevde Y, Schmidt MA, Scott RT, Shirah B, Sienkiewicz K, Sierra MA, Siew K, Theriot CA, Tierney BT, Venkateswaran K, Hirschberg JW, Walsh SB, Walter C, Winer DA, Yu M, Zea L, Mateus J, Beheshti A. A second space age spanning omics, platforms and medicine across orbits. Nature. 2024 Aug;632(8027):995-1008. doi: 10.1038/s41586-024-07586-8. Epub 2024 Jun 11. PMID: 38862027.
Loy C, Ahmann L, De Vlaminck I, Gu W. Liquid Biopsy Based on Cell-Free DNA and RNA. Annu Rev Biomed Eng. 2024 Jul;26(1):169-195. doi: 10.1146/annurev-bioeng-110222-111259. Epub 2024 Jun 20. PMID: 38346275.
Kim J, Tierney BT, Overbey EG, Dantas E, Fuentealba M, Park J, Narayanan SA, Wu F, Najjar D, Chin CR, Meydan C, Loy C, Mathyk B, Klotz R, Ortiz V, Nguyen K, Ryon KA, Damle N, Houerbi N, Patras LI, Schanzer N, Hutchinson GA, Foox J, Bhattacharya C, Mackay M, Afshin EE, Hirschberg JW, Kleinman AS, Schmidt JC, Schmidt CM, Schmidt MA, Beheshti A, Matei I, Lyden D, Mullane S, Asadi A, Lenz JS, Mzava O, Yu M, Ganesan S, De Vlaminck I, Melnick AM, Barisic D, Winer DA, Zwart SR, Crucian BE, Smith SM, Mateus J, Furman D, Mason CE. Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight. Nat Commun. 2024 Jun 11;15(1):4954. doi: 10.1038/s41467-024-49211-2. PMID: 38862516; PMCID: PMC11166952.
Borg J, Loy C, Kim J, Buhagiar A, Chin C, Damle N, De Vlaminck I, Felice A, Liu T, Matei I, Meydan C, Muratani M, Mzava O, Overbey E, Ryon KA, Smith SM, Tierney BT, Trudel G, Zwart SR, Beheshti A, Mason CE, Borg J. Spatiotemporal expression and control of haemoglobin in space. Nat Commun. 2024 Jun 11;15(1):4927. doi: 10.1038/s41467-024-49289-8. PMID: 38862545; PMCID: PMC11166948.
Chang A, Loy CJ, Eweis-LaBolle D, Lenz JS, Steadman A, Andgrama A, Nhung NV, Yu C, Worodria W, Denkinger CM, Nahid P, Cattamanchi A, De Vlaminck I. Circulating cell-free RNA in blood as a host response biomarker for detection of tuberculosis. Nat Commun. 2024 Jun 10;15(1):4949. doi: 10.1038/s41467-024-49245-6. PMID: 38858368; PMCID: PMC11164910.
Djomnang LK, Li C, Mzava O, Cheng AP, Chang A, Lenz JS, Suthanthiran M, Lee JR, Dadhania DM, De Vlaminck I. A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers. Sci Rep. 2024 May 13;14(1):10872. doi: 10.1038/s41598-024-54239-x. PMID: 38740837; PMCID: PMC11091160.
Sanketi BD, Mantri M, Huang L, Tavallaei MA, Hu S, Wang MFZ, De Vlaminck I, Kurpios NA. Villus myofibroblasts are developmental and adult progenitors of mammalian gut lymphatic musculature. Dev Cell. 2024 May 6;59(9):1159-1174.e5. doi: 10.1016/j.devcel.2024.03.005. Epub 2024 Mar 26. PMID: 38537630; PMCID: PMC11078612.
Garcia-Medina JS, Sienkiewicz K, Narayanan SA, Overbey EG, Grigorev K, Ryon KA, Burke M, Proszynski J, Tierney B, Schmidt CM, Mencia-Trinchant N, Klotz R, Ortiz V, Foox J, Chin C, Najjar D, Matei I, Chan I, Cruchaga C, Kleinman A, Kim J, Lucaci A, Loy C, Mzava O, De Vlaminck I, Singaraju A, Taylor LE, Schmidt JC, Schmidt MA, Blease K, Moreno J, Boddicker A, Zhao J, Lajoie B, Altomare A, Kruglyak S, Levy S, Yu M, Hassane DC, Bailey SM, Bolton K, Mateus J, Mason CE. Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight. Precis Clin Med. 2024 Apr 8;7(1):pbae007. doi: 10.1093/pcmedi/pbae007. PMID: 38634106; PMCID: PMC11022651.
Liu S, Ezran C, Wang MFZ, Li Z, Awayan K; Tabula Microcebus Consortium; Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE Jr. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nat Commun. 2024 Mar 11;15(1):2188. doi: 10.1038/s41467-024-46070-9. PMID: 38467625; PMCID: PMC10928088.
Mantri M, Zhang HH, Spanos E, Ren YA, De Vlaminck I. A spatiotemporal molecular atlas of the ovulating mouse ovary. Proc Natl Acad Sci U S A. 2024 Jan 30;121(5):e2317418121. doi: 10.1073/pnas.2317418121. Epub 2024 Jan 22. PMID: 38252830; PMCID: PMC10835069.
Vill AC, Rice EJ, De Vlaminck I, Danko CG, Brito IL. Precision run-on sequencing (PRO-seq) for microbiome transcriptomics. Nat Microbiol. 2024 Jan;9(1):241-250. doi: 10.1038/s41564-023-01558-w. Epub 2024 Jan 3. PMID: 38172625; PMCID: PMC11059318.

2023

Khan I, Wu S, Hudson A, Hughes C, Stryjniak G, Westblade LF, Satlin MJ, Tedrow N, Uhlemann AC, Kraft C, Dadhania DM, Silberzweig J, De Vlaminck I, Li C, Srivatana V, Lee JR. A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients. Kidney360. 2023 Oct 1;4(10):1419-1429. doi: 10.34067/KID.0000000000000249. Epub 2023 Aug 29. PMID: 37642987; PMCID: PMC10615377.
Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep Med. 2023 Jun 20;4(6):101034. doi: 10.1016/j.xcrm.2023.101034. Epub 2023 Apr 21. PMID: 37279751; PMCID: PMC10121104.
Sarathy JP, Xie M, Jones RM, Chang A, Osiecki P, Weiner D, Tsao WS, Dougher M, Blanc L, Fotouhi N, Via LE, Barry CE 3rd, De Vlaminck I, Sherman DR, Dartois VA. A Novel Tool to Identify Bactericidal Compounds against Vulnerable Targets in Drug-Tolerant M. tuberculosis found in Caseum. mBio. 2023 Apr 25;14(2):e0059823. doi: 10.1128/mbio.00598-23. Epub 2023 Apr 5. PMID: 37017524; PMCID: PMC10127596.
McKellar DW, Mantri M, Hinchman MM, Parker JSL, Sethupathy P, Cosgrove BD, De Vlaminck I. Spatial mapping of the total transcriptome by in situ polyadenylation. Nat Biotechnol. 2023 Apr;41(4):513-520. doi: 10.1038/s41587-022-01517-6. Epub 2022 Nov 3. PMID: 36329320; PMCID: PMC10110464.

2022

Chang A, Mzava O, Djomnang LK, Lenz JS, Burnham P, Kaplinsky P, Andama A, Connelly J, Bachman CM, Cattamanchi A, Steadman A, De Vlaminck I. Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis. Sci Rep. 2022 Oct 10;12(1):16972. doi: 10.1038/s41598-022-21244-x. PMID: 36216964; PMCID: PMC9551046.
Mantri M, Hinchman MM, McKellar DW, Wang MFZ, Cross ST, Parker JSL, De Vlaminck I. Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis. Nat Cardiovasc Res. 2022 Oct;1(10):946-960. doi: 10.1038/s44161-022-00138-1. Epub 2022 Oct 10. PMID: 36970396; PMCID: PMC10035375.
Mzava O, Cheng AP, Chang A, Smalling S, Djomnang LK, Lenz JS, Longman R, Steadman A, Gómez-Escobar LG, Schenck EJ, Salvatore M, Satlin MJ, Suthanthiran M, Lee JR, Mason CE, Dadhania D, De Vlaminck I. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Nat Commun. 2022 Jul 21;13(1):4197. doi: 10.1038/s41467-022-31654-0. PMID: 35864089; PMCID: PMC9304412.
Lee U, Stuelsatz P, Karaz S, McKellar DW, Russeil J, Deak M, De Vlaminck I, Lepper C, Deplancke B, Cosgrove BD, Feige JN. A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. iScience. 2022 Jun 14;25(7):104589. doi: 10.1016/j.isci.2022.104589. PMID: 35789856; PMCID: PMC9250016.
Cheng AP, Cheng MP, Loy CJ, Lenz JS, Chen K, Smalling S, Burnham P, Timblin KM, Orejas JL, Silverman E, Polak P, Marty FM, Ritz J, De Vlaminck I. Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2113476118. doi: 10.1073/pnas.2113476118. PMID: 35058359; PMCID: PMC8795552.

2021

Chang A, Mzava O, Lenz JS, Cheng AP, Burnham P, Motley ST, Bennett C, Connelly JT, Dadhania DM, Suthanthiran M, Lee JR, Steadman A, De Vlaminck I. Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays. Clin Chem. 2021 Dec 30;68(1):163-171. doi: 10.1093/clinchem/hvab142. PMID: 34718476; PMCID: PMC8718127.
McKellar DW, Walter LD, Song LT, Mantri M, Wang MFZ, De Vlaminck I, Cosgrove BD. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol. 2021 Nov 12;4(1):1280. doi: 10.1038/s42003-021-02810-x. PMID: 34773081; PMCID: PMC8589952.
Agbor-Enoh S, Oellerich M, Wu A, Halloran PF, De Vlaminck I, Keller M. Molecular Approaches to Transplant Monitoring; Is the Horizon Here? Clin Chem. 2021 Nov 1;67(11):1443-1449. doi: 10.1093/clinchem/hvab183. PMID: 34632495.
Burnham P, Chen F, Cheng AP, Srivatana V, Zhang LT, Edusei E, Albakry S, Botticelli B, Guo X, Renaghan A, Silberzweig J, Dadhania DM, Lenz JS, Heyang M, Iliev ID, Hayden JA, Westblade LF, De Vlaminck I, Lee JR. Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis. Kidney Med. 2021 Oct 28;4(1):100383. doi: 10.1016/j.xkme.2021.08.017. PMID: 35072047; PMCID: PMC8767090.
Shi H, Grodner B, De Vlaminck I. Recent advances in tools to map the microbiome. Curr Opin Biomed Eng. 2021 Sep;19:100289. doi: 10.1016/j.cobme.2021.100289. Epub 2021 Apr 23. PMID: 34151052; PMCID: PMC8208594.
Wang MFZ, Mantri M, Chou SP, Scuderi GJ, McKellar DW, Butcher JT, Danko CG, De Vlaminck I. Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. Nat Commun. 2021 Apr 12;12(1):2158. doi: 10.1038/s41467-021-22496-3. PMID: 33846360; PMCID: PMC8042062.
Cheng AP, Cheng MP, Gu W, Sesing Lenz J, Hsu E, Schurr E, Bourque G, Bourgey M, Ritz J, Marty FM, Chiu CY, Vinh DC, De Vlaminck I. Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity. Med. 2021 Apr 9;2(4):411-422.e5. doi: 10.1016/j.medj.2021.01.001. Epub 2021 Jan 16. PMID: 33521749; PMCID: PMC7836424.
Mantri M, Scuderi GJ, Abedini-Nassab R, Wang MFZ, McKellar D, Shi H, Grodner B, Butcher JT, De Vlaminck I. Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. Nat Commun. 2021 Mar 19;12(1):1771. doi: 10.1038/s41467-021-21892-z. PMID: 33741943; PMCID: PMC7979764.
Khush KK, De Vlaminck I, Luikart H, Ross DJ, Nicolls MR. Donor-derived, cell-free DNA levels by next-generation targeted sequencing are elevated in allograft rejection after lung transplantation. ERJ Open Res. 2021 Jan 25;7(1):00462-2020. doi: 10.1183/23120541.00462-2020. PMID: 33532456; PMCID: PMC7836440.

Diel de Amorim Lab

2024

Cheong SH, Franklin-Guild R, Goodman LB, Lago-Alvarez Y, Lee YL, de Aguiar LH, de Amorim MD, Altier C. Detection of fungal and bacterial organisms from clinical uterine samples of horses using Next-Generation Sequencing in comparison with culture. J Equine Vet Sci. 2024 Nov 9:105214. doi: 10.1016/j.jevs.2024.105214. Epub ahead of print. PMID: 39527989.
Byron M, Lection J, Foster RA, Chenier T, Wagner B, Diel de Amorim M. Prostaglandin-related genes are differentially expressed in equine endometrium with different biopsy grade, degrees of inflammation, and fibrosis. Theriogenology. 2024 Oct 1;227:151-156. doi: 10.1016/j.theriogenology.2024.07.014. Epub 2024 Jul 19. PMID: 39089078.
Lection J, Wagner B, Byron M, Miller A, Rollins A, Chenier T, Cheong SH, Diel de Amorim M. Inflammatory markers for differentiation of endometritis in the mare. Equine Vet J. 2024 Jul;56(4):678-687. doi: 10.1111/evj.14058. Epub 2024 Jan 14. PMID: 38219734.
Bernard M, Donnelly CG, Miller A, Diel de Amorim M. Diagnosis and management of placentitis with severe funisitis in a multiparous Warmblood mare. J Equine Vet Sci. 2024 Jun;137:105075. doi: 10.1016/j.jevs.2024.105075. Epub 2024 May 1. PMID: 38697371.

2023

Castillo J, Hilburger L, Rosenberg L, Cheong SH, Duhamel GE, de Amorim MD. Unilateral right mammary gland enlargement in a multiparous, pregnant 14-year-old American Quarter Horse mare. J Am Vet Med Assoc. 2023 Sep 4;261(12):1901-1902. doi: 10.2460/javma.23.08.0459. PMID: 37669747.
Abdelhady AWA, Aguiar LH, Lee YL, Guo Z, Bovell RT, Crane PL, Diel de Amorim M, Cheong SH. Rho-associated coiled-coil containing kinase inhibitor improves outcomes of direct-transfer slow-cooled bovine blastocysts. Theriogenology. 2023 Nov;211:19-27. doi: 10.1016/j.theriogenology.2023.07.030. Epub 2023 Jul 24. PMID: 37556931.
Diel de Amorim M, Dong L, Byron M, Foster RA, Klein C, Saleh M, Saleh T, Card C. Characterization of serum and tissue oxytocinase and tissue oxytocin in the pregnant and non-pregnant mare. Sci Rep. 2023 Mar 21;13(1):4616. doi: 10.1038/s41598-023-31540-9. PMID: 36944665; PMCID: PMC10030782.
Diel de Amorim M, Bramer SA, Rajamanickam GD, Klein C, Card C. Serum progesterone and oxytocinase, and endometrial and luteal gene expression in pregnant, nonpregnant, oxytocin, carbetocin and meclofenamic acid treated mares. Theriogenology. 2023 Mar 1;198:47-60. doi: 10.1016/j.theriogenology.2022.10.019. Epub 2022 Oct 18. PMID: 36549183.
Back B, Mejia S, Hackett E, Byron M, Westermann T, de Amorim MD. Right-sided ovarian enlargement in an 8-year-old maiden warmblood mare. J Am Vet Med Assoc. 2023 Jan 25;261(4):569-571. doi: 10.2460/javma.22.12.0561. PMID: 36701223.

2022

Diel de Amorim M, Bramer SA, Rajamanickam GD, Klein C, Card C. Endometrial and luteal gene expression of putative gene regulators of the equine maternal recognition of pregnancy. Anim Reprod Sci. 2022 Oct;245:107064. doi: 10.1016/j.anireprosci.2022.107064. Epub 2022 Sep 1. PMID: 36087407.
Diel de Amorim M, Klein C, Foster R, Dong L, Lopez-Rodriguez MF, Card C. Expression of Oxytocin/Neurophysin I and Oxytocinase in the Equine Conceptus from Day 8 to Day 21 Post-Ovulation. Animals (Basel). 2022 Mar 22;12(7):799. doi: 10.3390/ani12070799. PMID: 35405789; PMCID: PMC8996865.

2021

Lection J, Cornelius AJ, Moxon R, Russenberger J, Diel de Amorim M, Cheong SH. Incidence and risk factors for canine mastitis and metritis in two guide dog populations. Anim Reprod Sci. 2021 Aug;231:106802. doi: 10.1016/j.anireprosci.2021.106802. Epub 2021 Jul 7. PMID: 34280749.
Lection J, Delvescovo B, Percival A, Wu T, Southard T, Diel de Amorim M, Cheong SH. Malunion of an In Utero Metacarpal Fracture in a Standardbred Mare Presenting for Dystocia. J Equine Vet Sci. 2021 Jan;96:103321. doi: 10.1016/j.jevs.2020.103321. Epub 2020 Nov 10. PMID: 33349407.

Duan Lab

2025

Su Y, Zhao R, Fang Y, Renxiu M, Li G, Jin L, Liu J, Yang Z, Li N, Zhu J, Mishra N, Kaback D, Yee SP, Luo Y, Wan W, Zhao Y, Wang X, Han S, Xiao P, Lei C, Duan JE, Tang Y, Tian XC. Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation. Stem Cells. 2025 Oct 23:sxaf068. doi: 10.1093/stmcls/sxaf068. Epub ahead of print. PMID: 41129285.
Shi M, Li G, Araujo HM, Lee AS, Zhang J, Lee YL; IISAGE Consortium; Cheong SH, Duan JE. Sex-biased transcriptome in in vitro produced bovine early embryos. Cell Biosci. 2025 Aug 27;15(1):123. doi: 10.1186/s13578-025-01459-x. PMID: 40866999; PMCID: PMC12392601.
Yu X, Harman RM, Danev N, Li G, Fang Y, Van de Walle GR, Duan JE. Heat stress and recovery induce transcriptomic changes in lactogenic-like bovine mammary epithelial (MAC-T) cells. Physiol Genomics. 2025 Sep 1;57(9):551-565. doi: 10.1152/physiolgenomics.00127.2024. Epub 2025 Jul 18. PMID: 40679625.
Biga PR, Duan JE, Young TE, Marks JR, Bronikowski A, Decena LP, Randolph EC, Pavuluri AG, Li G, Fang Y, Wilkinson GS, Singh G, Nigrin NT, Larschan EN, Lonski AJ, Riddle NC; IISAGE Consortium. Hallmarks of aging: A user’s guide for comparative biologists. Ageing Res Rev. 2025 Feb;104:102616. doi: 10.1016/j.arr.2024.102616. Epub 2024 Dec 4. PMID: 39643212.

2024

Danev N, Li G, Duan JE, Van de Walle GR. Comparative transcriptomic analysis of bovine mesenchymal stromal cells reveals tissue-source and species-specific differences. iScience. 2024 Jan 12;27(2):108886. doi: 10.1016/j.isci.2024.108886. PMID: 38318381; PMCID: PMC10838956.

2023

Li G, Yu X, Portela Fontoura AB, Javaid A, de la Maza-Escolà VS, Salandy NS, Fubini SL, Grilli E, McFadden JW, Duan JE. Transcriptomic regulations of heat stress response in the liver of lactating dairy cows. BMC Genomics. 2023 Jul 20;24(1):410. doi: 10.1186/s12864-023-09484-1. PMID: 37474909; PMCID: PMC10360291.

2022

Li G, Duan JE. Dosage compensation: A new player in X chromosome upregulation. Curr Biol. 2022 Oct 24;32(20):R1030-R1032. doi: 10.1016/j.cub.2022.09.027. PMID: 36283351.
Duan JE, Jiang J, He Y. Editorial: Bridging (Epi-) Genomics and Environmental Changes: The Livestock Research. Front Genet. 2022 Jul 5;13:961232. doi: 10.3389/fgene.2022.961232. PMID: 35865017; PMCID: PMC9294534.
Ranjitkar S, Duan JE, Srirattana K, Alqahtani F, Tulman ER, Mandoiu I, Venkitanarayanan K, Tian X. Transcriptomic Responses of Mycoplasma bovis Upon Treatments of trans-Cinnamaldehyde, Carvacrol, and Eugenol. Front Microbiol. 2022 Jun 6;13:888433. doi: 10.3389/fmicb.2022.888433. PMID: 35733968; PMCID: PMC9207385.
Johnson EJ, Duan JE, Srirattana K, Venkitanarayanan K, Tulman ER, Tian XC. Effects of intramuscularly injected plant-derived antimicrobials in the mouse model. Sci Rep. 2022 Apr 8;12(1):5937. doi: 10.1038/s41598-022-09705-9. PMID: 35396364; PMCID: PMC8993793.
Bronikowski AM, Meisel RP, Biga PR, Walters JR, Mank JE, Larschan E, Wilkinson GS, Valenzuela N, Conard AM, de Magalhães JP, Duan JE, Elias AE, Gamble T, Graze RM, Gribble KE, Kreiling JA, Riddle NC. Sex-specific aging in animals: Perspective and future directions. Aging Cell. 2022 Feb;21(2):e13542. doi: 10.1111/acel.13542. Epub 2022 Jan 23. PMID: 35072344; PMCID: PMC8844111.

2021

Duan J, Rieder L, Colonnetta MM, Huang A, Mckenney M, Watters S, Deshpande G, Jordan W, Fawzi N, Larschan E. CLAMP and Zelda function together to promote Drosophila zygotic genome activation. Elife. 2021 Aug 3;10:e69937. doi: 10.7554/eLife.69937. PMID: 34342574; PMCID: PMC8367384.

Gariepy

2024

Schwarz EB, Chiang AY, Lewis CA, Gariepy AM, Reeves MF. Pregnancy after Tubal Sterilization in the United States, 2002 to 2015. NEJM Evid. 2024 Sep;3(9):EVIDoa2400023. doi: 10.1056/EVIDoa2400023. Epub 2024 Aug 27. PMID: 39189861.
Starosta A, Harris J, Gariepy A, Pathy S, Cron J. Medication abortion for adolescents in the United States: Strengthening the role of pediatric primary care providers. Perspect Sex Reprod Health. 2024 Jun;56(2):76-84. doi: 10.1111/psrh.12264. Epub 2024 Apr 25. PMID: 38661101.
Markowitz MA, Lundsberg LS, Gariepy AM. A Multidimensional and Longitudinal Exploratory Study of the Stability of Pregnancy Contexts in the United States. Womens Health Rep (New Rochelle). 2024 Mar 12;5(1):211-222. doi: 10.1089/whr.2024.0008. PMID: 38516649; PMCID: PMC10956533.

2023

Aguilar GA, Lundsberg LS, Stanwood NL, Gariepy AM. Exploratory study of race- or ethnicity-based discrimination among patients receiving procedural abortion care. Contraception. 2023 Apr;120:109949. doi: 10.1016/j.contraception.2023.109949. Epub 2023 Jan 11. PMID: 36641096.
Schwarz EB, Gariepy A, Sonalkar S. Comparing IUC and Tubal Ligation. J Gen Intern Med. 2023 Jan;38(1):240. doi: 10.1007/s11606-022-07845-2. Epub 2022 Oct 21. PMID: 36271169; PMCID: PMC9849622.

2022

Schwarz EB, Lewis CA, Dove MS, Murphy E, Zuckerman D, Nunez-Eddy C, Tancredi DJ, McDonald-Mosley R, Sonalkar S, Hathaway M, Gariepy AM. Comparative Effectiveness and Safety of Intrauterine Contraception and Tubal Ligation. J Gen Intern Med. 2022 Dec;37(16):4168-4175. doi: 10.1007/s11606-022-07433-4. Epub 2022 Feb 23. PMID: 35194746; PMCID: PMC8863411.
Cutler AS, Lundsberg LS, White MA, Stanwood NL, Gariepy AM. The Impact of First-Person Abortion Stories on Community-Level Abortion Stigma: A Randomized Trial. Womens Health Issues. 2022 Nov-Dec;32(6):578-585. doi: 10.1016/j.whi.2022.06.006. Epub 2022 Jun 15. PMID: 35778255.
Stark EL, Gariepy AM, Son M. What Is Long-Acting Reversible Contraception? JAMA. 2022 Oct 4;328(13):1362. doi: 10.1001/jama.2022.14239. PMID: 35960529.
Robledo-Gil T, Kemet S, Pensak M, Cutler A, McNamara B, Kennedy HP, Lundsberg L, Gariepy A. “Un abrazo a la distancia“: An Exploration of Spanish-Speaking Women’s Experiences with Pregnancy and Social Isolation in an Urban U.S. Setting. Hisp Health Care Int. 2022 Jun;20(2):107-114. doi: 10.1177/15404153211041013. Epub 2021 Sep 14. PMID: 34520260.
Gariepy AM, Lewis C, Zuckerman D, Tancredi DJ, Murphy E, McDonald-Mosley R, Sonalkar S, Hathaway M, Nunez-Eddy C, Schwarz EB. Comparative effectiveness of hysteroscopic and laparoscopic sterilization for women: a retrospective cohort study. Fertil Steril. 2022 Jun;117(6):1322-1331. doi: 10.1016/j.fertnstert.2022.03.001. Epub 2022 Apr 12. PMID: 35428480.
Gariepy AM, Lewis C, Zuckerman D, Tancredi DJ, Murphy E, McDonald-Mosley R, Sonalkar S, Hathaway M, Nunez-Eddy C, Schwarz EB. Patient-Centered Safety Outcomes After Hysteroscopic Compared With Laparoscopic Sterilization. Obstet Gynecol. 2022 Mar 1;139(3):423-432. doi: 10.1097/AOG.0000000000004690. PMID: 35115444.

2021

Benfield N, Dempsey A, Gariepy A, Haider S, Madden T. Featured research at the 2021 Society of Family Planning Annual Meeting. Contraception. 2021 Oct;104(4):448-449. doi: 10.1016/j.contraception.2021.07.007. Epub 2021 Jul 18. PMID: 34283950.
Gariepy AM, Tancredi DJ, Lewis C, Zuckerman D, Schwarz EB. Comparing Essure® and Tubal Ligation to Prevent Pregnancy [Internet]. Washington (DC): Patient-Centered Outcomes Research Institute (PCORI); 2021 Oct. PMID: 39236206.
Cutler AS, Lundsberg LS, White MA, Stanwood NL, Gariepy AM. Characterizing community-level abortion stigma in the United States. Contraception. 2021 Sep;104(3):305-313. doi: 10.1016/j.contraception.2021.03.021. Epub 2021 Mar 28. PMID: 33789081.

Gerhardt Lab

2025

McCarter K, Deshpande M, Romanski P, Stratopoulou CA, Zaninovic N, Tareen M, Al-Mousawi R, James D, Madireddy A, Rosenwaks Z, Gerhardt J. Dysregulation of the actin cytoskeleton and FMRP causes polar body protrusion defects in human fragile X premutation and aged oocytes. bioRxiv [Preprint]. 2025 Feb 26:2025.02.23.639319. doi: 10.1101/2025.02.23.639319. PMID: 40060650; PMCID: PMC11888274.
Ummarino S, Poluben L, Ebralidze AK, Autiero I, Zhang Y, Paniza T, Deshpande M, Rinaldi L, Lee JD, Bassal MA, Trinh BQ, Balk SP, Flaumenhaft R, Gerhardt J, Mirkin SM, Tenen DG, Di Ruscio A. RNAs anchoring replication complex control initiation and firing of DNA replication. Res Sq [Preprint]. 2025 Jan 28:rs.3.rs-5723221. doi: 10.21203/rs.3.rs-5723221/v1. PMID: 39975922; PMCID: PMC11838740.
Niljikar M, Barreto-Galvez A, Patel S, Gagliardi JE, Kumar V, Pradeep A, Juwarwala A, Gerhardt J, Chang Y, Montagna C, Madireddy A. Polymerase Eta Recruits FANCD2 to Common Fragile Sites to Maintain Genome Stability. bioRxiv [Preprint]. 2025 Jan 8:2025.01.06.631600. doi: 10.1101/2025.01.06.631600. PMID: 39829787; PMCID: PMC11741286.

2024

Edwards MM, Wang N, Sagi I, Kinreich S, Benvenisty N, Gerhardt J, Egli D, Koren A. Parent-of-origin-specific DNA replication timing is confined to large imprinted regions. Cell Rep. 2024 Sep 24;43(9):114700. doi: 10.1016/j.celrep.2024.114700. Epub 2024 Sep 4. PMID: 39235941.
Xu S, Wang N, Zuccaro MV, Gerhardt J, Iyyappan R, Scatolin GN, Jiang Z, Baslan T, Koren A, Egli D. DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility. Nat Commun. 2024 Jun 19;15(1):5247. doi: 10.1038/s41467-024-49565-7. PMID: 38898078; PMCID: PMC11187207.
Gerhardt J. The discovery of simple repeats that cause complex disorders. Nat Rev Mol Cell Biol. 2024 Mar;25(3):161. doi: 10.1038/s41580-023-00666-z. PMID: 37697011.

2023

Madireddy A, Gerhardt J. Visualizing DNA replication by single-molecule analysis of replicated DNA. STAR Protoc. 2023 Dec 15;4(4):102721. doi: 10.1016/j.xpro.2023.102721. Epub 2023 Dec 3. PMID: 38048218; PMCID: PMC10730367.

2022

Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. Mol Cell. 2022 Oct 20;82(20):3781-3793.e7. doi: 10.1016/j.molcel.2022.08.017. Epub 2022 Sep 12. PMID: 36099913.
Jasra S, Giricz O, Zeig-Owens R, Pradhan K, Goldfarb DG, Barreto-Galvez A, Silver AJ, Chen J, Sahu S, Gordon-Mitchell S, Choudhary GS, Aluri S, Bhagat TD, Shastri A, Bejan CA, Stockton SS, Spaulding TP, Thiruthuvanathan V, Goto H, Gerhardt J, Haider SH, Veerappan A, Bartenstein M, Nwankwo G, Landgren O, Weiden MD, Lekostaj J, Bender R, Fletcher F, Greenberger L, Ebert BL, Steidl U, Will B, Nolan A, Madireddy A, Savona MR, Prezant DJ, Verma A. High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster. Nat Med. 2022 Mar;28(3):468-471. doi: 10.1038/s41591-022-01708-3. Epub 2022 Mar 7. PMID: 35256801; PMCID: PMC9394171.

2021

Ding Q, Edwards MM, Wang N, Zhu X, Bracci AN, Hulke ML, Hu Y, Tong Y, Hsiao J, Charvet CJ, Ghosh S, Handsaker RE, Eggan K, Merkle FT, Gerhardt J, Egli D, Clark AG, Koren A. The genetic architecture of DNA replication timing in human pluripotent stem cells. Nat Commun. 2021 Nov 19;12(1):6746. doi: 10.1038/s41467-021-27115-9. PMID: 34799581; PMCID: PMC8604924.
Fan Y, Köberlin MS, Ratnayeke N, Liu C, Deshpande M, Gerhardt J, Meyer T. LRR1-mediated replisome disassembly promotes DNA replication by recycling replisome components. J Cell Biol. 2021 Aug 2;220(8):e202009147. doi: 10.1083/jcb.202009147. Epub 2021 May 26. PMID: 34037657; PMCID: PMC8160578.

Grimson Lab

2025

Zhu H, Ganapathi Sankaran D, Smith NL, Daly CWP, Yee Mon K, Tabilas C, Wissink EM, Rudd BD, Grimson A. An efficient framework to decipher microRNA regulatory programs applied to T cells. Genes Immun. 2025 Oct;26(5):486-496. doi: 10.1038/s41435-025-00351-5. Epub 2025 Aug 18. PMID: 40825847; PMCID: PMC12527941.
Gardella AE, Eweis-LaBolle D, Loy CJ, Belcher ED, Lenz JS, Franconi CJ, Scofield SY, Grimson A, Hanson MR, De Vlaminck I. Circulating cell-free RNA signatures for the characterization and diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome. Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2507345122. doi: 10.1073/pnas.2507345122. Epub 2025 Aug 11. PMID: 40789036; PMCID: PMC12377778.
Ganapathi Sankaran D, Zhu H, Maymi VI, Forlastro IM, Jiang Y, Laniewski N, Scheible KM, Rudd BD, Grimson A. Gene-regulatory programs that specify age-related differences during thymocyte development. Cell Rep. 2025 Jul 22;44(7):115903. doi: 10.1016/j.celrep.2025.115903. Epub 2025 Jun 25. PMID: 40570375.
West JD, Smith HJ, Vu LT, Fogarty EA, Matreyek KA, Fowler DM, Grimson A. The quantitative impact of 3’UTRs on gene expression. Nucleic Acids Res. 2025 Jun 20;53(12):gkaf568. doi: 10.1093/nar/gkaf568. PMID: 40586305; PMCID: PMC12207410.
Zhang S, Jahanbani F, Chander V, Kjellberg M, Liu M, Glass KA, Iu DS, Ahmed F, Li H, Maynard RD, Chou T, Cooper-Knock J, Zhang MJ, Thota D, Zeineh M, Grenier JK, Grimson A, Hanson MR, Snyder MP. Dissecting the genetic complexity of myalgic encephalomyelitis/chronic fatigue syndrome via deep learning-powered genome analysis. medRxiv [Preprint]. 2025 May 11:2025.04.15.25325899. doi: 10.1101/2025.04.15.25325899. PMID: 40321247; PMCID: PMC12047926.
Carro MLM, Dziubek A, Touey A, Popkowski EA, Abdelmassih M, Simon L, Tanis S, Ahmed F, Grenier JK, Grimson A, Cohen PE. Argonaute proteins regulate the timing of the spermatogenic transcriptional program. bioRxiv [Preprint]. 2025 Jan 1:2024.12.31.630913. doi: 10.1101/2024.12.31.630913. PMID: 39803480; PMCID: PMC11722363.

2024

Iu DS, Maya J, Vu LT, Fogarty EA, McNairn AJ, Ahmed F, Franconi CJ, Munn PR, Grenier JK, Hanson MR, Grimson A. Transcriptional reprogramming primes CD8+ T cells toward exhaustion in Myalgic encephalomyelitis/chronic fatigue syndrome. Proc Natl Acad Sci U S A. 2024 Dec 10;121(50):e2415119121. doi: 10.1073/pnas.2415119121. Epub 2024 Dec 2. PMID: 39621903; PMCID: PMC11648872.
Yee Mon KJ, Kim S, Dai Z, West JD, Zhu H, Jain R, Grimson A, Rudd BD, Singh A. Functionalized nanowires for miRNA-mediated therapeutic programming of naïve T cells. Nat Nanotechnol. 2024 Aug;19(8):1190-1202. doi: 10.1038/s41565-024-01649-7. Epub 2024 Apr 29. PMID: 38684809; PMCID: PMC11330359.
Maymí VI, Zhu H, Jager M, Johnson S, Getchell R, Casey JW, Grenier JK, Wherry EJ, Smith NL, Grimson A, Rudd BD. Neonatal CD8+ T Cells Resist Exhaustion during Chronic Infection. J Immunol. 2024 Mar 1;212(5):834-843. doi: 10.4049/jimmunol.2300396. PMID: 38231127; PMCID: PMC11298781.
Ascenção C, Sims JR, Dziubek A, Comstock W, Fogarty EA, Badar J, Freire R, Grimson A, Weiss RS, Cohen PE, Smolka MB. A TOPBP1 allele causing male infertility uncouples XY silencing dynamics from sex body formation. Elife. 2024 Feb 23;12:RP90887. doi: 10.7554/eLife.90887. PMID: 38391183; PMCID: PMC10942628.
Watson NB, Patel RK, Kean C, Veazey J, Oyesola OO, Laniewski N, Grenier JK, Wang J, Tabilas C, Yee Mon KJ, McNairn AJ, Peng SA, Wesnak SP, Nzingha K, Davenport MP, Tait Wojno ED, Scheible KM, Smith NL, Grimson A, Rudd BD. The gene regulatory basis of bystander activation in CD8+ T cells. Sci Immunol. 2024 Feb 23;9(92):eadf8776. doi: 10.1126/sciimmunol.adf8776. Epub 2024 Feb 23. PMID: 38394230.
Vu LT, Ahmed F, Zhu H, Iu DSH, Fogarty EA, Kwak Y, Chen W, Franconi CJ, Munn PR, Tate AE, Levine SM, Stevens J, Mao X, Shungu DC, Moore GE, Keller BA, Hanson MR, Grenier JK, Grimson A. Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation. Cell Rep Med. 2024 Jan 16;5(1):101373. doi: 10.1016/j.xcrm.2023.101373. PMID: 38232699; PMCID: PMC10829790.

2022

Tabilas C, Iu DS, Daly CWP, Yee Mon KJ, Reynaldi A, Wesnak SP, Grenier JK, Davenport MP, Smith NL, Grimson A, Rudd BD. Early microbial exposure shapes adult immunity by altering CD8+ T cell development. Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2212548119. doi: 10.1073/pnas.2212548119. Epub 2022 Nov 28. PMID: 36442114; PMCID: PMC9894172.
Zhang DX, Dang XTT, Vu LT, Lim CMH, Yeo EYM, Lam BWS, Leong SM, Omar N, Putti TC, Yeh YC, Ma V, Luo JY, Cho WC, Chen G, Lee VKM, Grimson A, Le MTN. αvβ1 integrin is enriched in extracellular vesicles of metastatic breast cancer cells: A mechanism mediated by galectin-3. J Extracell Vesicles. 2022 Aug;11(8):e12234. doi: 10.1002/jev2.12234. PMID: 35923105; PMCID: PMC9451529.
Carro MLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol. 2023;151:245-279. doi: 10.1016/bs.ctdb.2022.06.001. Epub 2022 Jul 25. PMID: 36681472.
Germain A, Giloteaux L, Moore GE, Levine SM, Chia JK, Keller BA, Stevens J, Franconi CJ, Mao X, Shungu DC, Grimson A, Hanson MR. Plasma metabolomics reveals disrupted response and recovery following maximal exercise in myalgic encephalomyelitis/chronic fatigue syndrome. JCI Insight. 2022 May 9;7(9):e157621. doi: 10.1172/jci.insight.157621. PMID: 35358096; PMCID: PMC9090259.
Kwak Y, Daly CWP, Fogarty EA, Grimson A, Kwak H. Dynamic and widespread control of poly(A) tail length during macrophage activation. RNA. 2022 Jul;28(7):947-971. doi: 10.1261/rna.078918.121. Epub 2022 May 5. PMID: 35512831; PMCID: PMC9202586.

2021

Yee Mon KJ, Zhu H, Daly CWP, Vu LT, Smith NL, Patel R, Topham DJ, Scheible K, Jambo K, Le MTN, Rudd BD, Grimson A. MicroRNA-29 specifies age-related differences in the CD8+ T cell immune response. Cell Rep. 2021 Nov 9;37(6):109969. doi: 10.1016/j.celrep.2021.109969. PMID: 34758312.
Zhang DX, Vu LT, Ismail NN, Le MTN, Grimson A. Landscape of extracellular vesicles in the tumour microenvironment: Interactions with stromal cells and with non-cell components, and impacts on metabolic reprogramming, horizontal transfer of neoplastic traits, and the emergence of therapeutic resistance. Semin Cancer Biol. 2021 Sep;74:24-44. doi: 10.1016/j.semcancer.2021.01.007. Epub 2021 Feb 2. PMID: 33545339.
Mo Z, Cheong JYA, Xiang L, Le MTN, Grimson A, Zhang DX. Extracellular vesicle-associated organotropic metastasis. Cell Prolif. 2021 Jan;54(1):e12948. doi: 10.1111/cpr.12948. Epub 2020 Nov 3. PMID: 33145869; PMCID: PMC7791170.

Jaffrey Lab

2025

Hou Q, Oleynikov M, Mei X, Dong L, Hagen T, Jaffrey SR. A portable poison exon for small-molecule control of mammalian gene expression. Nat Methods. 2025 Nov;22(11):2337-2348. doi: 10.1038/s41592-025-02860-7. Epub 2025 Nov 3. PMID: 41184552.
Pandey K, Poh HX, Jaffrey SR. Why does the m6A writer complex require so many proteins? PLoS Biol. 2025 Sep 15;23(9):e3003386. doi: 10.1371/journal.pbio.3003386. PMID: 40953081; PMCID: PMC12453181.
Chen Z, Jiang H, Yuan L, Yao T, Rong X, Gao W, Zeng C, He L, Yin Y, Jaffrey SR, Zhao F, Zhang J, Xu P, Li X. Photoactivatable RNA Tags for Subcellular Photolabeling of RNA. J Am Chem Soc. 2025 Sep 3;147(35):31650-31661. doi: 10.1021/jacs.5c07380. Epub 2025 Aug 25. PMID: 40852906.
Hughes RO, Davis HJ, Nease LA, Zumbo P, Danielli M, Tran W, Maidhof K, Kosmas K, Kanshin E, Murakami S, Cascio MG, Church KP, Aguirre KN, Delclaux I, Slack FJ, Vlachos IS, Ueberheide B, Jaffrey SR, Erhard F, Banh R, Betel D, Piskounova E. tRNA modifications are required for stress granule formation and melanoma metastasis. bioRxiv [Preprint]. 2025 Aug 25:2025.08.20.671337. doi: 10.1101/2025.08.20.671337. PMID: 40909646; PMCID: PMC12407792.
Murakami S, Olarerin-George AO, Liu JF, Zaccara S, Hawley B, Jaffrey SR. m6A alters ribosome dynamics to initiate mRNA degradation. Cell. 2025 Jul 10;188(14):3728-3743.e20. doi: 10.1016/j.cell.2025.04.020. Epub 2025 May 6. PMID: 40328256; PMCID: PMC12255529.
Linder B, Sharma P, Wu J, Birbaumer T, Eggers C, Murakami S, Ott RE, Fenzl K, Vorgerd H, Erhard F, Jaffrey SR, Leidel SA, Steinmetz LM. tRNA modifications tune m6A-dependent mRNA decay. Cell. 2025 Jul 10;188(14):3715-3727.e13. doi: 10.1016/j.cell.2025.04.013. Epub 2025 Apr 30. PMID: 40311619; PMCID: PMC12255531.
Liu JF, Hawley BR, Nicholson LS, Jaffrey SR. Decoding m6Am by simultaneous transcription-start mapping and methylation quantification. Elife. 2025 Mar 31;13:RP104139. doi: 10.7554/eLife.104139. PMID: 40162895; PMCID: PMC11957539.
Kam CW, Dumelie JG, Ciceri G, Yang WY, Disney MD, Studer L, Jaffrey SR. Sustained Epigenetic Reactivation in Fragile X Neurons with an RNA-Binding Small Molecule. Genes (Basel). 2025 Feb 25;16(3):278. doi: 10.3390/genes16030278. PMID: 40149430; PMCID: PMC11942054.
Verhamme R, Jansens RJJ, Liu J, Van Raemdonck F, Van Waesberghe C, Nicholson L, Jaffrey SR, Favoreel HW. The pseudorabies virus UL13 protein kinase triggers phosphorylation of the RNA demethylase FTO, which is associated with FTO-dependent suppression of interferon-stimulated gene expression. J Virol. 2025 Feb 25;99(2):e0201924. doi: 10.1128/jvi.02019-24. Epub 2025 Jan 10. PMID: 39791911; PMCID: PMC11852732.
Liu JF, Hawley BR, Nicholson LS, Jaffrey SR. Decoding m6Am by simultaneous transcription-start mapping and methylation quantification. bioRxiv [Preprint]. 2025 Feb 21:2024.10.16.618717. doi: 10.1101/2024.10.16.618717. Update in: Elife. 2025 Mar 31;13:RP104139. doi: 10.7554/eLife.104139. PMID: 39677659; PMCID: PMC11642800.
Wu J, Jaffrey SR. Live-Cell Imaging of mRNA Using a Pepper RNA Tag. Methods Mol Biol. 2025;2875:1-7. doi: 10.1007/978-1-0716-4248-1_1. PMID: 39535635.

2024

Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. Elife. 2024 Dec 3;13:RP98540. doi: 10.7554/eLife.98540. PMID: 39625751; PMCID: PMC11614387.
Liu JF, Jaffrey SR. Dinoflagellate mRNA is pervasively modified with m1A. EMBO Rep. 2024 Nov;25(11):4634-4635. doi: 10.1038/s44319-024-00263-x. Epub 2024 Sep 20. PMID: 39304776; PMCID: PMC11549392.
Hagen T, Litke JL, Nasir N, Hou Q, Jaffrey SR. Engineering acyclovir-induced RNA nanodevices for reversible and tunable control of aptamer function. Cell Chem Biol. 2024 Oct 17;31(10):1827-1838.e7. doi: 10.1016/j.chembiol.2024.07.017. Epub 2024 Aug 26. PMID: 39191249; PMCID: PMC11680490.
Unti MJ, Doetsch L, Jaffrey SR. A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements. RNA. 2024 Oct 16;30(11):1529-1540. doi: 10.1261/rna.080008.124. PMID: 39103230; PMCID: PMC11482608.
Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. bioRxiv [Preprint]. 2024 Aug 19:2024.04.11.589009. doi: 10.1101/2024.04.11.589009. Update in: Elife. 2024 Dec 03;13:RP98540. doi: 10.7554/eLife.98540. PMID: 38645201; PMCID: PMC11030352.
Zaccara S, Jaffrey SR. Understanding the redundant functions of the m6A-binding YTHDF proteins. RNA. 2024 Apr 16;30(5):468-481. doi: 10.1261/rna.079988.124. PMID: 38531646; PMCID: PMC11019742.
Dumelie JG, Chen Q, Miller D, Attarwala N, Gross SS, Jaffrey SR. Biomolecular condensates create phospholipid-enriched microenvironments. Nat Chem Biol. 2024 Mar;20(3):302-313. doi: 10.1038/s41589-023-01474-4. Epub 2023 Nov 16. PMID: 37973889; PMCID: PMC10922641.
Mirza AH, Bram Y, Schwartz RE, Jaffrey SR. SCARPET: site-specific quantification of methylated and nonmethylated adenosines reveals m6A stoichiometry. RNA. 2024 Feb 16;30(3):308-324. doi: 10.1261/rna.079776.123. PMID: 38190635; PMCID: PMC10870371.
Zhang Z, Rong X, Xie T, Li Z, Song H, Zhen S, Wang H, Wu J, Jaffrey SR, Li X. Fluorogenic CRISPR for genomic DNA imaging. Nat Commun. 2024 Jan 31;15(1):934. doi: 10.1038/s41467-024-45163-9. PMID: 38296979; PMCID: PMC10831063.
Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. Cell Chem Biol. 2024 Jan 18;31(1):163-176.e5. doi: 10.1016/j.chembiol.2023.09.015. Epub 2023 Oct 25. PMID: 37883972; PMCID: PMC10841545.

2023

Lundquist MR, Jaffrey SR. Gas6-Axl Signaling Induces SRF/MRTF-A Gene Transcription via MICAL2. Genes (Basel). 2023 Dec 18;14(12):2231. doi: 10.3390/genes14122231. PMID: 38137053; PMCID: PMC10742852.
Ries RJ, Pickering BF, Poh HX, Namkoong S, Jaffrey SR. m6A governs length-dependent enrichment of mRNAs in stress granules. Nat Struct Mol Biol. 2023 Oct;30(10):1525-1535. doi: 10.1038/s41594-023-01089-2. Epub 2023 Sep 14. PMID: 37710015; PMCID: PMC10715973.
Zaccara S, Ries RJ, Jaffrey SR. Publisher Correction: Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol. 2023 Oct;24(10):770. doi: 10.1038/s41580-023-00654-3. Erratum for: Nat Rev Mol Cell Biol. 2019 Oct;20(10):608-624. doi: 10.1038/s41580-019-0168-5. PMID: 37604996.
Wang J, Chew BLA, Lai Y, Dong H, Xu L, Liu Y, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nat Protoc. 2023 Sep;18(9):2671-2698. doi: 10.1038/s41596-023-00857-0. Epub 2023 Aug 11. PMID: 37567932.
Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferré-D’Amaré AR. Intricate 3D architecture of a DNA mimic of GFP. Nature. 2023 Jun;618(7967):1078-1084. doi: 10.1038/s41586-023-06229-8. Epub 2023 Jun 21. PMID: 37344591; PMCID: PMC10754392.
Passalacqua LFM, Starich MR, Link KA, Wu J, Knutson JR, Tjandra N, Jaffrey SR, Ferré-D’Amaré AR. Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun. 2023 May 23;14(1):2969. doi: 10.1038/s41467-023-38683-3. PMID: 37221204; PMCID: PMC10205801.
Salisbury DA, Casero D, Zhang Z, Wang D, Kim J, Wu X, Vergnes L, Mirza AH, Leon-Mimila P, Williams KJ, Huertas-Vazquez A, Jaffrey SR, Reue K, Chen J, Sallam T. Author Correction: Transcriptional regulation of N6-methyladenosine orchestrates sex-dimorphic metabolic traits. Nat Metab. 2023 Mar;5(3):530. doi: 10.1038/s42255-023-00748-4. Erratum for: Nat Metab. 2021 Jul;3(7):940-953. doi: 10.1038/s42255-021-00427-2. PMID: 36814000.
Despic V, Jaffrey SR. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature. 2023 Feb;614(7947):358-366. doi: 10.1038/s41586-022-05668-z. Epub 2023 Feb 1. PMID: 36725932; PMCID: PMC9891201.
Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science. 2023 Jan 20;379(6629):eabj7412. doi: 10.1126/science.abj7412. Epub 2023 Jan 20. PMID: 36656933; PMCID: PMC10515739.
Hou Q, Jaffrey SR. Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells. RNA Biol. 2023 Jan;20(1):198-206. doi: 10.1080/15476286.2023.2206248. PMID: 37129556; PMCID: PMC10155629.
Litke JL, Jaffrey SR. Designing and Expressing Circular RNA Aptamers to Regulate Mammalian Cell Biology. Methods Mol Biol. 2023;2570:223-234. doi: 10.1007/978-1-0716-2695-5_17. PMID: 36156786; PMCID: PMC9797029.

2022

Han P, She Y, Yang Z, Zhuang M, Wang Q, Luo X, Yin C, Zhu J, Jaffrey SR, Ji SJ. Cbln1 regulates axon growth and guidance in multiple neural regions. PLoS Biol. 2022 Nov 17;20(11):e3001853. doi: 10.1371/journal.pbio.3001853. PMID: 36395107; PMCID: PMC9671368.
Micaelli M, Dalle Vedove A, Cerofolini L, Vigna J, Sighel D, Zaccara S, Bonomo I, Poulentzas G, Rosatti EF, Cazzanelli G, Alunno L, Belli R, Peroni D, Dassi E, Murakami S, Jaffrey SR, Fragai M, Mancini I, Lolli G, Quattrone A, Provenzani A. Small-Molecule Ebselen Binds to YTHDF Proteins Interfering with the Recognition of N6-Methyladenosine-Modified RNAs. ACS Pharmacol Transl Sci. 2022 Sep 14;5(10):872-891. doi: 10.1021/acsptsci.2c00008. PMID: 36268123; PMCID: PMC9578143.
Dixit S, Jaffrey SR. Expanding the epitranscriptome: Dihydrouridine in mRNA. PLoS Biol. 2022 Jul 20;20(7):e3001720. doi: 10.1371/journal.pbio.3001720. PMID: 35857789; PMCID: PMC9299342.
Jansens RJJ, Verhamme R, Mirza AH, Olarerin-George A, Van Waesberghe C, Jaffrey SR, Favoreel HW. Alphaherpesvirus US3 protein-mediated inhibition of the m6A mRNA methyltransferase complex. Cell Rep. 2022 Jul 19;40(3):111107. doi: 10.1016/j.celrep.2022.111107. PMID: 35858564; PMCID: PMC9347262.
Poh HX, Mirza AH, Pickering BF, Jaffrey SR. Alternative splicing of METTL3 explains apparently METTL3-independent m6A modifications in mRNA. PLoS Biol. 2022 Jul 19;20(7):e3001683. doi: 10.1371/journal.pbio.3001683. PMID: 35853000; PMCID: PMC9295969.
Salisbury DA, Casero D, Zhang Z, Wang D, Kim J, Wu X, Vergnes L, Mirza AH, Leon-Mimila P, Williams KJ, Huertas-Vazquez A, Jaffrey SR, Reue K, Chen J, Sallam T. Author Correction: Transcriptional regulation of N6-methyladenosine orchestrates sex-dimorphic metabolic traits. Nat Metab. 2022 Jul;4(7):960. doi: 10.1038/s42255-022-00614-9. Erratum for: Nat Metab. 2021 Jul;3(7):940-953. doi: 10.1038/s42255-021-00427-2. PMID: 35851380.
Murakami S, Jaffrey SR. Hidden codes in mRNA: Control of gene expression by m6A. Mol Cell. 2022 Jun 16;82(12):2236-2251. doi: 10.1016/j.molcel.2022.05.029. PMID: 35714585; PMCID: PMC9216239.
Moretti J, Jia B, Hutchins Z, Roy S, Yip H, Wu J, Shan M, Jaffrey SR, Coers J, Blander JM. Caspase-11 interaction with NLRP3 potentiates the noncanonical activation of the NLRP3 inflammasome. Nat Immunol. 2022 May;23(5):705-717. doi: 10.1038/s41590-022-01192-4. Epub 2022 Apr 29. PMID: 35487985; PMCID: PMC9106893.
VarnBuhler BS, Moon J, Dey SK, Wu J, Jaffrey SR. Detection of SARS-CoV-2 RNA Using a DNA Aptamer Mimic of Green Fluorescent Protein. ACS Chem Biol. 2022 Apr 15;17(4):840-853. doi: 10.1021/acschembio.1c00893. Epub 2022 Mar 26. PMID: 35341244; PMCID: PMC9780036.
Viegas IJ, de Macedo JP, Serra L, De Niz M, Temporão A, Silva Pereira S, Mirza AH, Bergstrom E, Rodrigues JA, Aresta-Branco F, Jaffrey SR, Figueiredo LM. N6-methyladenosine in poly(A) tails stabilize VSG transcripts. Nature. 2022 Apr;604(7905):362-370. doi: 10.1038/s41586-022-04544-0. Epub 2022 Mar 30. PMID: 35355019; PMCID: PMC9150445.
Wu J, Svensen N, Song W, Kim H, Zhang S, Li X, Jaffrey SR. Self-Assembly of Intracellular Multivalent RNA Complexes Using Dimeric Corn and Beetroot Aptamers. J Am Chem Soc. 2022 Mar 30;144(12):5471-5477. doi: 10.1021/jacs.1c13583. Epub 2022 Mar 16. PMID: 35294188; PMCID: PMC9747565.
Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m6A binding. Genes Dev. 2022 Feb 1;36(3-4):180-194. doi: 10.1101/gad.349190.121. Epub 2022 Jan 20. PMID: 35058317; PMCID: PMC8887132.
Dey SK, Filonov GS, Olarerin-George AO, Jackson BT, Finley LWS, Jaffrey SR. Publisher Correction: Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat Chem Biol. 2022 Feb;18(2):236. doi: 10.1038/s41589-022-00969-w. Erratum for: Nat Chem Biol. 2022 Feb;18(2):180-190. doi: 10.1038/s41589-021-00925-0. PMID: 35064247; PMCID: PMC9116938.
Truong L, Kooshapur H, Dey SK, Li X, Tjandra N, Jaffrey SR, Ferré-D’Amaré AR. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol. 2022 Feb;18(2):191-198. doi: 10.1038/s41589-021-00931-2. Epub 2021 Dec 22. PMID: 34937911; PMCID: PMC9812287.
Dey SK, Filonov GS, Olarerin-George AO, Jackson BT, Finley LWS, Jaffrey SR. Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag. Nat Chem Biol. 2022 Feb;18(2):180-190. doi: 10.1038/s41589-021-00925-0. Epub 2021 Dec 22. Erratum in: Nat Chem Biol. 2022 Feb;18(2):236. doi: 10.1038/s41589-022-00969-w. PMID: 34937909; PMCID: PMC8967656.

2021

Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 2021 Dec;1506(1):118-141. doi: 10.1111/nyas.14713. Epub 2021 Nov 17. Erratum in: Ann N Y Acad Sci. 2022 Jan;1507(1):171. doi: 10.1111/nyas.14751. PMID: 34791665; PMCID: PMC9808899.
Litke JL, Jaffrey SR. Trans ligation of RNAs to generate hybrid circular RNAs using highly efficient autocatalytic transcripts. Methods. 2021 Dec;196:104-112. doi: 10.1016/j.ymeth.2021.05.009. Epub 2021 May 13. PMID: 33992775; PMCID: PMC8589881.
Moon JD, Wu J, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chem Biol. 2021 Nov 18;28(11):1569-1580.e4. doi: 10.1016/j.chembiol.2021.04.022. Epub 2021 May 18. PMID: 34010626; PMCID: PMC8573057.
Li X, Wu J, Jaffrey SR. Engineering Fluorophore Recycling in a Fluorogenic RNA Aptamer. Angew Chem Int Ed Engl. 2021 Nov 2;60(45):24153-24161. doi: 10.1002/anie.202108338. Epub 2021 Oct 4. PMID: 34490956; PMCID: PMC8661118.
Cotter KA, Gallon J, Uebersax N, Rubin P, Meyer KD, Piscuoglio S, Jaffrey SR, Rubin MA. Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance. Mol Cancer Res. 2021 Aug;19(8):1398-1411. doi: 10.1158/1541-7786.MCR-21-0014. Epub 2021 Jun 4. PMID: 34088870; PMCID: PMC8349875.
Cheng Y, Xie W, Pickering BF, Chu KL, Savino AM, Yang X, Luo H, Nguyen DT, Mo S, Barin E, Velleca A, Rohwetter TM, Patel DJ, Jaffrey SR, Kharas MG. N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer Cell. 2021 Jul 12;39(7):958-972.e8. doi: 10.1016/j.ccell.2021.04.017. Epub 2021 May 27. PMID: 34048709; PMCID: PMC8282764.
Salisbury DA, Casero D, Zhang Z, Wang D, Kim J, Wu X, Vergnes L, Mirza AH, Leon-Mimila P, Williams KJ, Huertas-Vazquez A, Jaffrey SR, Reue K, Chen J, Sallam T. Transcriptional regulation of N6-methyladenosine orchestrates sex-dimorphic metabolic traits. Nat Metab. 2021 Jul;3(7):940-953. doi: 10.1038/s42255-021-00427-2. Epub 2021 Jul 19. Erratum in: Nat Metab. 2022 Jul;4(7):960. doi: 10.1038/s42255-022-00614-9. Erratum in: Nat Metab. 2023 Mar;5(3):530. doi: 10.1038/s42255-023-00748-4. PMID: 34282353; PMCID: PMC8422857.
Cho S, Lee G, Pickering BF, Jang C, Park JH, He L, Mathur L, Kim SS, Jung S, Tang HW, Monette S, Rabinowitz JD, Perrimon N, Jaffrey SR, Blenis J. mTORC1 promotes cell growth via m6A-dependent mRNA degradation. Mol Cell. 2021 May 20;81(10):2064-2075.e8. doi: 10.1016/j.molcel.2021.03.010. Epub 2021 Mar 22. PMID: 33756105; PMCID: PMC8356906.
Dixit D, Prager BC, Gimple RC, Poh HX, Wang Y, Wu Q, Qiu Z, Kidwell RL, Kim LJY, Xie Q, Vitting-Seerup K, Bhargava S, Dong Z, Jiang L, Zhu Z, Hamerlik P, Jaffrey SR, Zhao JC, Wang X, Rich JN. The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells. Cancer Discov. 2021 Feb;11(2):480-499. doi: 10.1158/2159-8290.CD-20-0331. Epub 2020 Oct 6. PMID: 33023892; PMCID: PMC8110214.

Johnson, Elizabeth Lab

2024

Lee MT, Tan X, Le HH, Besler K, Thompson S, Harris-Tryon T, Johnson EL. Gut bacterial sphingolipid production modulates dysregulated skin lipid homeostasis. bioRxiv [Preprint]. 2024 Dec 30:2024.12.29.629238. doi: 10.1101/2024.12.29.629238. PMID: 39803564; PMCID: PMC11722302.
Bosch TCG, Wigley M, Colomina B, Bohannan B, Meggers F, Amato KR, Azad MB, Blaser MJ, Brown K, Dominguez-Bello MG, Ehrlich SD, Elinav E, Finlay BB, Geddie K, Geva-Zatorsky N, Giles-Vernick T, Gros P, Guillemin K, Haraoui LP, Johnson E, Keck F, Lorimer J, McFall-Ngai MJ, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Undurraga EA, Zhao L, Melby MK. The potential importance of the built-environment microbiome and its impact on human health. Proc Natl Acad Sci U S A. 2024 May 14;121(20):e2313971121. doi: 10.1073/pnas.2313971121. Epub 2024 Apr 25. PMID: 38662573; PMCID: PMC11098107.
Xiao X, Le HH, Lee M-T, Lamm D, Johnson EL, Brito IL. Prevotella copri variants among a single host diverge in sphingolipid production. mBio. 2024 Feb 14;15(2):e0240923. doi: 10.1128/mbio.02409-23. Epub 2024 Jan 18. PMID: 38236049; PMCID: PMC10865984.

2023

Mitchell SB, Thorn TL, Lee MT, Kim Y, Comrie JMC, Bai ZS, Johnson EL, Aydemir TB. Metal transporter SLC39A14/ZIP14 modulates regulation between the gut microbiome and host metabolism. Am J Physiol Gastrointest Liver Physiol. 2023 Dec 1;325(6):G593-G607. doi: 10.1152/ajpgi.00091.2023. Epub 2023 Oct 24. PMID: 37873588; PMCID: PMC10887856.
Tate BN, Van Guilder GP, Aly M, Spence LA, Diaz-Rubio ME, Le HH, Johnson EL, McFadden JW, Perry CA. Changes in Choline Metabolites and Ceramides in Response to a DASH-Style Diet in Older Adults. Nutrients. 2023 Aug 23;15(17):3687. doi: 10.3390/nu15173687. PMID: 37686719; PMCID: PMC10489641.
Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E, Koren O. Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. Gut. 2023 May;72(5):918-928. doi: 10.1136/gutjnl-2022-328406. Epub 2023 Jan 10. PMID: 36627187; PMCID: PMC10086485.

2022

Heaver SL, Le HH, Tang P, Baslé A, Mirretta Barone C, Vu DL, Waters JL, Marles-Wright J, Johnson EL, Campopiano DJ, Ley RE. Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nat Microbiol. 2022 Jul;7(7):986-1000. doi: 10.1038/s41564-022-01152-6. Epub 2022 Jun 20. PMID: 35725777; PMCID: PMC9246714.
Lee MT, Le HH, Besler KR, Johnson EL. Identification and characterization of 3-ketosphinganine reductase activity encoded at the BT_0972 locus in Bacteroides thetaiotaomicron. J Lipid Res. 2022 Jul;63(7):100236. doi: 10.1016/j.jlr.2022.100236. Epub 2022 Jun 3. PMID: 35667415; PMCID: PMC9278070.
Le HH, Lee MT, Besler KR, Johnson EL. Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids. Cell Host Microbe. 2022 Jun 8;30(6):798-808.e7. doi: 10.1016/j.chom.2022.05.002. Epub 2022 May 26. PMID: 35623356; PMCID: PMC9187616.

2021

Lee MT, Le HH, Johnson EL. A BOSSS method for managing insights into diet-microbiome interactions. Trends Biochem Sci. 2021 Nov;46(11):944-945. doi: 10.1016/j.tibs.2021.08.004. Epub 2021 Sep 8. PMID: 34507873; PMCID: PMC10166533.
Di Rienzi SC, Johnson EL, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT, Ley RE. The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. J Nutr Biochem. 2021 Nov;97:108808. doi: 10.1016/j.jnutbio.2021.108808. Epub 2021 Jun 26. PMID: 34186211; PMCID: PMC8585862.
Lee MT, Le HH, Johnson EL. Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome. J Lipid Res. 2021;62:100034. doi: 10.1194/jlr.RA120000950. Epub 2021 Feb 6. PMID: 32646940; PMCID: PMC7910519.

Johnson, Patricia

2025

Francoeur L, Scoville DM, Ahern JG, Johnson PA. Characterization of Persistency of Lay in Laying Hens. Biol Reprod. 2025 Oct 8:ioaf227. doi: 10.1093/biolre/ioaf227. Epub ahead of print. PMID: 41060289.

2024

Francoeur L, Scoville DM, Johnson PA. Investigations of the function of AMH in granulosa cells in hens. Gen Comp Endocrinol. 2024 Apr 1;349:114454. doi: 10.1016/j.ygcen.2024.114454. Epub 2024 Jan 22. PMID: 38266936.

2023

Francoeur L, Scoville DM, Johnson PA. Effect of IGF1 and FSH on the function of granulosa cells from prehierarchal follicles in chickens†. Biol Reprod. 2023 Oct 13;109(4):498-506. doi: 10.1093/biolre/ioad082. PMID: 37504508.

2022

Stephens CS, Hill-Ricciuti A, Francoeur L, Johnson PA. Feeding level is associated with altered liver transcriptome and follicle selection in hen†. Biol Reprod. 2022 May 17;106(5):943-952. doi: 10.1093/biolre/ioac013. PMID: 35084018.

2021

Francoeur L, Stephens CS, Johnson PA. Ad Libitum Feeding in Broiler Breeder Hens Alters the Transcriptome of Granulosa Cells of Pre-Hierarchal Follicles. Animals (Basel). 2021 Sep 16;11(9):2706. doi: 10.3390/ani11092706. PMID: 34573672; PMCID: PMC8472788.

Keeney Lab

2025

Kim S, Alnaser HF, Keeney S, Murakami H. Insight into meiotic DNA end resection: Mechanisms and regulation. DNA Repair (Amst). 2025 Sep;153:103886. doi: 10.1016/j.dnarep.2025.103886. Epub 2025 Aug 15. PMID: 40850049; PMCID: PMC12453631.
Kim S, Yamada S, Li T, Canasto-Chibuque C, Kim JH, Marcet-Ortega M, Xu J, Eng DY, Feeney L, Petrini JHJ, Keeney S. Mouse MRE11-RAD50-NBS1 is needed to start and extend meiotic DNA end resection. Nat Commun. 2025 Apr 16;16(1):3613. doi: 10.1038/s41467-025-57928-x. PMID: 40240347; PMCID: PMC12003770.
Zheng Z, Zheng L, Arter M, Liu K, Yamada S, Ontoso D, Kim S, Keeney S. Reconstitution of SPO11-dependent double-strand break formation. Nature. 2025 Mar;639(8055):784-791. doi: 10.1038/s41586-025-08601-2. Epub 2025 Feb 19. PMID: 39972129; PMCID: PMC11922745.
Huang PC, Hong S, Alnaser HF, Mimitou EP, Kim KP, Murakami H, Keeney S. Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30. EMBO J. 2025 Jan;44(1):200-224. doi: 10.1038/s44318-024-00318-8. Epub 2024 Nov 29. PMID: 39613969; PMCID: PMC11695836.
Yu Y, Wang J, Liu K, Zheng Z, Arter M, Claeys Bouuaert C, Pu S, Patel DJ, Keeney S. Cryo-EM structures of the Spo11 core complex bound to DNA. Nat Struct Mol Biol. 2025 Jan;32(1):113-124. doi: 10.1038/s41594-024-01382-8. Epub 2024 Sep 20. PMID: 39304764; PMCID: PMC11746154.

2024

Zheng Z, Zheng L, Arter M, Liu K, Yamada S, Ontoso D, Kim S, Keeney S. Reconstitution of SPO11-dependent double-strand break formation. bioRxiv [Preprint]. 2024 Nov 21:2024.11.20.624382. doi: 10.1101/2024.11.20.624382. Update in: Nature. 2025 Mar;639(8055):784-791. doi: 10.1038/s41586-025-08601-2. PMID: 39605552; PMCID: PMC11601517.
Yu Y, Wang J, Liu K, Zheng Z, Arter M, Claeys Bouuaert C, Pu S, Patel DJ, Keeney S. Cryo-EM structures of the Spo11 core complex bound to DNA. Nat Struct Mol Biol. 2024 Sep 20. doi: 10.1038/s41594-024-01382-8. Epub ahead of print. PMID: 39304764.
Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet. 2024 May;25(5):309-325. doi: 10.1038/s41576-023-00669-8. Epub 2023 Nov 30. PMID: 38036793.
Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Tuncay H, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. Nat Commun. 2024 Apr 5;15(1):2941. doi: 10.1038/s41467-024-47020-1. PMID: 38580643; PMCID: PMC10997794.

2023

Xu J, Li T, Kim S, Boekhout M, Keeney S. Essential roles of the ANKRD31-REC114 interaction in meiotic recombination and mouse spermatogenesis. Proc Natl Acad Sci U S A. 2023 Nov 21;120(47):e2310951120. doi: 10.1073/pnas.2310951120. Epub 2023 Nov 17. PMID: 37976262; PMCID: PMC10666023.
Liu K, Grasso EM, Pu S, Zou M, Liu S, Eliezer D, Keeney S. Structure and DNA-bridging activity of the essential Rec114-Mei4 trimer interface. Genes Dev. 2023 Jun 1;37(11-12):518-534. doi: 10.1101/gad.350461.123. Epub 2023 Jul 13. PMID: 37442580; PMCID: PMC10393192.
Najnin RA, Al Mahmud MR, Rahman MM, Takeda S, Sasanuma H, Tanaka H, Murakawa Y, Shimizu N, Akter S, Takagi M, Sunada T, Akamatsu S, He G, Itou J, Toi M, Miyaji M, Tsutsui KM, Keeney S, Yamada S. ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Rep. 2023 Jan 31;42(1):111909. doi: 10.1016/j.celrep.2022.111909. Epub 2022 Dec 30. PMID: 36640339; PMCID: PMC10023214.

2022

Maekawa K, Yamada S, Sharma R, Chaudhuri J, Keeney S. Triple-helix potential of the mouse genome. Proc Natl Acad Sci U S A. 2022 May 10;119(19):e2203967119. doi: 10.1073/pnas.2203967119. Epub 2022 May 3. PMID: 35503911; PMCID: PMC9171763.
Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m6A binding. Genes Dev. 2022 Feb 1;36(3-4):180-194. doi: 10.1101/gad.349190.121. Epub 2022 Jan 20. PMID: 35058317; PMCID: PMC8887132.

2021

Liu R, Kasowitz SD, Homolka D, Leu NA, Shaked JT, Ruthel G, Jain D, Lin H, Keeney S, Luo M, Pillai RS, Wang PJ. YTHDC2 is essential for pachytene progression and prevents aberrant microtubule-driven telomere clustering in male meiosis. Cell Rep. 2021 Dec 14;37(11):110110. doi: 10.1016/j.celrep.2021.110110. PMID: 34910909; PMCID: PMC8720241.
Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, Roy U, Kuper J, Fernández IS, Szakal B, Branzei D, Rizo J, Kisker C, Greene EC, Biggins S, Keeney S, Miller EA, Fromme JC, Hendrickson TL, Cong Q, Baker D. Computed structures of core eukaryotic protein complexes. Science. 2021 Dec 10;374(6573):eabm4805. doi: 10.1126/science.abm4805. Epub 2021 Dec 10. PMID: 34762488; PMCID: PMC7612107.
Li W, Zhang L, Shinohara A, Keeney S. Editorial: Meiosis: From Molecular Basis to Medicine. Front Cell Dev Biol. 2021 Dec 1;9:812292. doi: 10.3389/fcell.2021.812292. PMID: 34926477; PMCID: PMC8671932.
Lukaszewicz A, Lange J, Keeney S, Jasin M. De novo deletions and duplications at recombination hotspots in mouse germlines. Cell. 2021 Nov 24;184(24):5970-5984.e18. doi: 10.1016/j.cell.2021.10.025. Epub 2021 Nov 17. PMID: 34793701; PMCID: PMC8616837.
Arter M, Keeney S. Meiosis: Disentangling polyploid chromosomes with supercharged crossover interference. Curr Biol. 2021 Nov 8;31(21):R1442-R1444. doi: 10.1016/j.cub.2021.09.045. PMID: 34752773.
Johnson D, Crawford M, Cooper T, Claeys Bouuaert C, Keeney S, Llorente B, Garcia V, Neale MJ. Concerted cutting by Spo11 illuminates meiotic DNA break mechanics. Nature. 2021 Jun;594(7864):572-576. doi: 10.1038/s41586-021-03389-3. Epub 2021 Jun 9. PMID: 34108687; PMCID: PMC7611867.
Murakami H, Mu X, Keeney S. How do small chromosomes know they are small? Maximizing meiotic break formation on the shortest yeast chromosomes. Curr Genet. 2021 Jun;67(3):431-437. doi: 10.1007/s00294-021-01160-9. Epub 2021 Feb 18. PMID: 33604699; PMCID: PMC8141002.
Claeys Bouuaert C, Pu S, Wang J, Oger C, Daccache D, Xie W, Patel DJ, Keeney S. DNA-driven condensation assembles the meiotic DNA break machinery. Nature. 2021 Apr;592(7852):144-149. doi: 10.1038/s41586-021-03374-w. Epub 2021 Mar 17. PMID: 33731927; PMCID: PMC8016751.
Guan Y, Keeney S, Jain D, Wang PJ. yama, a mutant allele of Mov10l1, disrupts retrotransposon silencing and piRNA biogenesis. PLoS Genet. 2021 Feb 26;17(2):e1009265. doi: 10.1371/journal.pgen.1009265. PMID: 33635934; PMCID: PMC7946307.
Claeys Bouuaert C, Tischfield SE, Pu S, Mimitou EP, Arias-Palomo E, Berger JM, Keeney S. Structural and functional characterization of the Spo11 core complex. Nat Struct Mol Biol. 2021 Jan;28(1):92-102. doi: 10.1038/s41594-020-00534-w. Epub 2021 Jan 4. PMID: 33398171; PMCID: PMC7855791.

Kim Lab

2025

Matias NR, Gallicchio L, Lu D, Kim JJ, Perez J, Detweiler AM, Lu C, Bolival B, Fuller MT. A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage. Genes Dev. 2025 Aug 6;. doi: 10.1101/gad.352747.125. [Epub ahead of print] PubMed PMID: 40769719; PubMed Central PMCID: PMC12333557.
Kim JJ. Not all CBXs are created equal: A role for the disordered central region of CBX4 in pediatric glioma. Mol Cell. 2025 Jun 5;85(11):2061-2063. doi: 10.1016/j.molcel.2025.05.016. PubMed PMID: 40480193.
Harris DE, Kim JJ, Stern SR, Vicars HM, Matias NR, Gallicchio L, Baker CC, Fuller MT. An RNA-binding regulatory cascade controls the switch from proliferation to differentiation in the Drosophila male germ cell lineage. Proc Natl Acad Sci U S A. 2025 May 20;122(20):e2418279122. doi: 10.1073/pnas.2418279122. Epub 2025 May 16. PubMed PMID: 40377994; PubMed Central PMCID: PMC12107169.

2024

Harris DE, Kim JJ, Stern SR, Vicars HM, Matias NR, Gallicchio L, Baker CC, Fuller MT. An RNA binding regulatory cascade controls the switch from proliferation to differentiation in the Drosophila male germ line stem cell lineage. bioRxiv. 2024 Sep 6;. doi: 10.1101/2024.09.06.611673. PubMed PMID: 39282418; PubMed Central PMCID: PMC11398533.

2023

Kim JJ, Steinson ER, Lau MS, de Rooij DG, Page DC, Kingston RE. Cell type-specific role of CBX2 and its disordered region in spermatogenesis. Genes Dev. 2023 Jul 1;37(13-14):640-660. doi: 10.1101/gad.350393.122. Epub 2023 Aug 8. PubMed PMID: 37553262; PubMed Central PMCID: PMC10499018.

2022

Kim JJ, Kingston RE. Context-specific Polycomb mechanisms in development. Nat Rev Genet. 2022 Nov;23(11):680-695. doi: 10.1038/s41576-022-00499-0. Epub 2022 Jun 9. Review. PubMed PMID: 35681061; PubMed Central PMCID: PMC9933872.

2021

Miller SA, Damle M, Kim J, Kingston RE. Full methylation of H3K27 by PRC2 is dispensable for initial embryoid body formation but required to maintain differentiated cell identity. Development. 2021 Apr 1;148(7). doi: 10.1242/dev.196329. Epub 2021 Apr 15. PubMed PMID: 33688077; PubMed Central PMCID: PMC8077505.

Lee Lab

2025

Chaturbedi A, Lee SS. Different gametogenesis states uniquely impact longevity in Caenorhabditis elegans. Nat Commun. 2025 Oct 21;16(1):9300. doi: 10.1038/s41467-025-64341-x. PMID: 41120259; PMCID: PMC12541034.
Lee SS, Gopal S, Chaturbedi A, Ramachandrula T, OuYang J, Rodell R. A somatic checkpoint through NHR-49/HNF4α governs reproductive investment and longevity in C. elegans. Res Sq [Preprint]. 2025 Sep 3:rs.3.rs-7217416. doi: 10.21203/rs.3.rs-7217416/v1. PMID: 40951264; PMCID: PMC12425103.
Gopal S, Chaturbedi A, Ramachandrula T, OuYang J, Rodell R, Lee SS. Nuclear Hormone Receptor NHR-49/HNF4α Couples Fertility Regulation to Resource Allocation and Longevity in C. elegans. bioRxiv [Preprint]. 2025 Jul 18:2025.07.14.664468. doi: 10.1101/2025.07.14.664468. PMID: 40791495; PMCID: PMC12338712.
Greer EL, Lee SS, Prahlad V. Chromatin and epigenetics in aging biology. Genetics. 2025 May 8;230(1):iyaf055. doi: 10.1093/genetics/iyaf055. PMID: 40202900.
Chang HY, McMurry SE, Ma S, Mansour CA, Schwab SMT, Danko CG, Lee SS. Transcriptomic and chromatin accessibility profiling unveils new regulators of heat hormesis in Caenorhabditis elegans. bioRxiv [Preprint]. 2025 Mar 14:2025.03.11.642714. doi: 10.1101/2025.03.11.642714. PMID: 40161833; PMCID: PMC11952391.

2024

Emerson FJ, Chiu C, Lin LY, Riedel CG, Zhu M, Lee SS. The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans. Nat Commun. 2024 Mar 14;15(1):2320. doi: 10.1038/s41467-024-46510-6. PMID: 38485937; PMCID: PMC10940595.
Fox BW, Helf MJ, Burkhardt RN, Artyukhin AB, Curtis BJ, Palomino DF, Schroeder AF, Chaturbedi A, Tauffenberger A, Wrobel CJJ, Zhang YK, Lee SS, Schroeder FC. Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans. Nat Commun. 2024 Feb 19;15(1):1520. doi: 10.1038/s41467-024-45782-2. Erratum in: Nat Commun. 2024 Jul 19;15(1):6090. doi: 10.1038/s41467-024-50246-8. PMID: 38374083; PMCID: PMC10876521.

2023

Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci. 2023 Oct 9;10:1270285. doi: 10.3389/fmolb.2023.1270285. PMID: 37877123; PMCID: PMC10591336.
Burkhardt RN, Artyukhin AB, Aprison EZ, Curtis BJ, Fox BW, Ludewig AH, Palomino DF, Luo J, Chaturbedi A, Panda O, Wrobel CJJ, Baumann V, Portman DS, Lee SS, Ruvinsky I, Schroeder FC. Sex-specificity of the C. elegans metabolome. Nat Commun. 2023 Jan 19;14(1):320. doi: 10.1038/s41467-023-36040-y. PMID: 36658169; PMCID: PMC9852247.

2022

Emerson FJ, Lee SS. CUT&RUN for Chromatin Profiling in Caenorhabditis elegans. Curr Protoc. 2022 Jun;2(6):e445. doi: 10.1002/cpz1.445. PMID: 35714350; PMCID: PMC9219583.

2021

Li CL, Pu M, Wang W, Chaturbedi A, Emerson FJ, Lee SS. Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PLoS Genet. 2021 Sep 10;17(9):e1009432. doi: 10.1371/journal.pgen.1009432. PMID: 34506495; PMCID: PMC8457455.

LevBuck Lab

2025

Violante S, Kyaw A, Kouatli L, Paladugu K, Apostolakis L, Jenks M, Johnson A, Sheldon RD, Whitten D, Schilmiller AL, Visconti PE, Cross JR, Levin LR, Buck J, Balbach M. Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase. Proc Natl Acad Sci U S A. 2025 Sep 30;122(39):e2506417122. doi: 10.1073/pnas.2506417122. Epub 2025 Sep 24. PMID: 40991431; PMCID: PMC12501146.
Ferreira J, Belliveau H, Steegborn C, Buck J, Levin LR. Updating the Mechanism of Bicarbonate (HCO3-) Activation of Soluble Adenylyl Cyclase (sAC). Int J Mol Sci. 2025 Jul 3;26(13):6401. doi: 10.3390/ijms26136401. PMID: 40650178; PMCID: PMC12250328.
Luque GM, Jabloñski M, Schiavi-Ehrenhaus LJ, Del Prado RC, Balbach M, Romarowski A, Martin-Hidalgo D, Visconti PE, Krapf D, Darszon A, Krapf D, Buck J, Levin LR, Buffone MG. Bovine serum albumin-induced calcium influx triggers soluble adenylyl cyclase activation and cyclic AMP signalling pathways in mouse sperm capacitation. J Physiol. 2025 May;603(9):2633-2653. doi: 10.1113/JP288389. Epub 2025 May 5. PMID: 40320899.
Violante S, Kyaw A, Kouatli L, Paladugu K, Apostolakis L, Jenks M, Johnson A, Sheldon RD, Schilmiller AL, Visconti PE, Cross JR, Levin LR, Buck J, Balbach M. Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase. bioRxiv [Preprint]. 2025 Apr 10:2025.04.09.647926. doi: 10.1101/2025.04.09.647926. Update in: Proc Natl Acad Sci U S A. 2025 Sep 30;122(39):e2506417122. doi: 10.1073/pnas.2506417122. PMID: 40291655; PMCID: PMC12027340.
Ayoub S, Rivera Sanchez NDR, Fischoeder J, Balbach M, Levin LR, Buck J, Ritagliati C. Cyclic AMP Rescue of Motility in Sperm Devoid of Soluble Adenylyl Cyclase. Int J Mol Sci. 2025 Feb 11;26(4):1489. doi: 10.3390/ijms26041489. PMID: 40003956; PMCID: PMC11855772.

2024

Visconti PE, Levin LR, Buck J. David Garbers and the Birth of cAMP Biology in Mammalian Sperm. Mol Reprod Dev. 2024 Oct;91(10):e23773. doi: 10.1002/mrd.23773. PMID: 39385557.
Sanchez NDRR, Ritagliati C, Kopf GS, Kretschmer S, Buck J, Levin LR. The uniqueness of on-demand male contraception. Mol Aspects Med. 2024 Jun;97:101281. doi: 10.1016/j.mam.2024.101281. Epub 2024 May 27. PMID: 38805792; PMCID: PMC11167369.
Sun S, Fushimi M, Rossetti T, Kaur N, Ferreira J, Miller M, Quast J, van den Heuvel J, Steegborn C, Levin LR, Buck J, Myers RW, Kargman S, Liverton N, Meinke PT, Huggins DJ. Addition to “Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation”. J Chem Inf Model. 2024 Feb 12;64(3):1106. doi: 10.1021/acs.jcim.4c00068. Epub 2024 Jan 23. Erratum for: J Chem Inf Model. 2023 May 8;63(9):2828-2841. doi: 10.1021/acs.jcim.2c01577. PMID: 38258980.

2023

Romarowski A, Fejzo J, Nayyab S, Martin-Hidalgo D, Gervasi MG, Balbach M, Violante S, Salicioni AM, Cross J, Levin LR, Buck J, Visconti PE. Mouse sperm energy restriction and recovery (SER) revealed novel metabolic pathways. Front Cell Dev Biol. 2023 Aug 15;11:1234221. doi: 10.3389/fcell.2023.1234221. PMID: 37655160; PMCID: PMC10466171.
Balbach M, Ghanem L, Violante S, Kyaw A, Romarowski A, Cross JR, Visconti PE, Levin LR, Buck J. Capacitation induces changes in metabolic pathways supporting motility of epididymal and ejaculated sperm. Front Cell Dev Biol. 2023 Jun 27;11:1160154. doi: 10.3389/fcell.2023.1160154. PMID: 37440924; PMCID: PMC10335746.
Wiggins SV, Schreiner R, Ferreira J, Marmorstein AD, Levin LR, Buck J. Carbonic Anhydrase Inhibitor Modulation of Intraocular Pressure Is Independent of Soluble Adenylyl Cyclase. J Ocul Pharmacol Ther. 2023 Jun;39(5):317-323. doi: 10.1089/jop.2022.0180. Epub 2023 Apr 25. PMID: 37097314; PMCID: PMC10398745.
Xu W, Qadir MMF, Nasteska D, Mota de Sa P, Gorvin CM, Blandino-Rosano M, Evans CR, Ho T, Potapenko E, Veluthakal R, Ashford FB, Bitsi S, Fan J, Bhondeley M, Song K, Sure VN, Sakamuri SSVP, Schiffer L, Beatty W, Wyatt R, Frigo DE, Liu X, Katakam PV, Arlt W, Buck J, Levin LR, Hu T, Kolls J, Burant CF, Tomas A, Merrins MJ, Thurmond DC, Bernal-Mizrachi E, Hodson DJ, Mauvais-Jarvis F. Architecture of androgen receptor pathways amplifying glucagon-like peptide-1 insulinotropic action in male pancreatic β cells. Cell Rep. 2023 May 30;42(5):112529. doi: 10.1016/j.celrep.2023.112529. Epub 2023 May 17. PMID: 37200193; PMCID: PMC10312392.
Sun S, Fushimi M, Rossetti T, Kaur N, Ferreira J, Miller M, Quast J, van den Heuvel J, Steegborn C, Levin LR, Buck J, Myers RW, Kargman S, Liverton N, Meinke PT, Huggins DJ. Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. J Chem Inf Model. 2023 May 8;63(9):2828-2841. doi: 10.1021/acs.jcim.2c01577. Epub 2023 Apr 15. Erratum in: J Chem Inf Model. 2024 Feb 12;64(3):1106. doi: 10.1021/acs.jcim.4c00068. PMID: 37060320.
Ritagliati C, Ayoub S, Balbach M, Buck J, Levin LR. In vivo characterization of sAC null sperm. Front Cell Dev Biol. 2023 Apr 21;11:1134051. doi: 10.3389/fcell.2023.1134051. PMID: 37152282; PMCID: PMC10160483.
Rossetti T, Ferreira J, Ghanem L, Buck H, Steegborn C, Myers RW, Meinke PT, Levin LR, Buck J. Corrigendum: Assessing potency and binding kinetics of soluble adenylyl cyclase (sAC) inhibitors to maximize therapeutic potential. Front Physiol. 2023 Mar 6;14:1163389. doi: 10.3389/fphys.2023.1163389. Erratum for: Front Physiol. 2022 Sep 28;13:1013845. doi: 10.3389/fphys.2022.1013845. PMID: 36950298; PMCID: PMC10027417.
Balbach M, Rossetti T, Ferreira J, Ghanem L, Ritagliati C, Myers RW, Huggins DJ, Steegborn C, Miranda IC, Meinke PT, Buck J, Levin LR. On-demand male contraception via acute inhibition of soluble adenylyl cyclase. Nat Commun. 2023 Feb 14;14(1):637. doi: 10.1038/s41467-023-36119-6. PMID: 36788210; PMCID: PMC9929232.

2022

Miller M, Rossetti T, Ferreira J, Ghanem L, Balbach M, Kaur N, Levin LR, Buck J, Kehr M, Coquille S, van den Heuvel J, Steegborn C, Fushimi M, Finkin-Groner E, Myers RW, Kargman S, Liverton NJ, Huggins DJ, Meinke PT. Design, Synthesis, and Pharmacological Evaluation of Second-Generation Soluble Adenylyl Cyclase (sAC, ADCY10) Inhibitors with Slow Dissociation Rates. J Med Chem. 2022 Nov 24;65(22):15208-15226. doi: 10.1021/acs.jmedchem.2c01133. Epub 2022 Nov 8. PMID: 36346696; PMCID: PMC9866367.
Rossetti T, Ferreira J, Ghanem L, Buck H, Steegborn C, Myers RW, Meinke PT, Levin LR, Buck J. Assessing potency and binding kinetics of soluble adenylyl cyclase (sAC) inhibitors to maximize therapeutic potential. Front Physiol. 2022 Sep 28;13:1013845. doi: 10.3389/fphys.2022.1013845. Erratum in: Front Physiol. 2022 Nov 21;13:1092217. doi: 10.3389/fphys.2022.1092217. Erratum in: Front Physiol. 2023 Mar 06;14:1163389. doi: 10.3389/fphys.2023.1163389. PMID: 36246105; PMCID: PMC9554468.
Ferreira J, Levin LR, Buck J. Strategies to safely target widely expressed soluble adenylyl cyclase for contraception. Front Pharmacol. 2022 Aug 25;13:953903. doi: 10.3389/fphar.2022.953903. PMID: 36091839; PMCID: PMC9452739.

2021

Balbach M, Ghanem L, Rossetti T, Kaur N, Ritagliati C, Ferreira J, Krapf D, Puga Molina LC, Santi CM, Hansen JN, Wachten D, Fushimi M, Meinke PT, Buck J, Levin LR. Soluble adenylyl cyclase inhibition prevents human sperm functions essential for fertilization. Mol Hum Reprod. 2021 Sep 1;27(9):gaab054. doi: 10.1093/molehr/gaab054. PMID: 34463764; PMCID: PMC8473925.
Fushimi M, Buck H, Balbach M, Gorovyy A, Ferreira J, Rossetti T, Kaur N, Levin LR, Buck J, Quast J, van den Heuvel J, Steegborn C, Finkin-Groner E, Kargman S, Michino M, Foley MA, Miller M, Liverton NJ, Huggins DJ, Meinke PT. Discovery of TDI-10229: A Potent and Orally Bioavailable Inhibitor of Soluble Adenylyl Cyclase (sAC, ADCY10). ACS Med Chem Lett. 2021 Jul 14;12(8):1283-1287. doi: 10.1021/acsmedchemlett.1c00273. PMID: 34413957; PMCID: PMC8366019.
Rossetti T, Jackvony S, Buck J, Levin LR. Bicarbonate, carbon dioxide and pH sensing via mammalian bicarbonate-regulated soluble adenylyl cyclase. Interface Focus. 2021 Apr 6;11(2):20200034. doi: 10.1098/rsfs.2020.0034. Epub 2021 Feb 12. PMID: 33633833; PMCID: PMC7898154.
Chang JC, Go S, Gilglioni EH, Duijst S, Panneman DM, Rodenburg RJ, Li HL, Huang HL, Levin LR, Buck J, Verhoeven AJ, Oude Elferink RPJ. Soluble adenylyl cyclase regulates the cytosolic NADH/NAD+ redox state and the bioenergetic switch between glycolysis and oxidative phosphorylation. Biochim Biophys Acta Bioenerg. 2021 Apr 1;1862(4):148367. doi: 10.1016/j.bbabio.2020.148367. Epub 2021 Jan 5. PMID: 33412125.

Lipkind

2025

Ireland E, Palmsten K, Lipkind HS, Ackerman-Banks CM, Ahrens KA. Characteristics and Incidence of Lactational Mastitis Using State-Wide Data from 2016 to 2022. J Womens Health (Larchmt). 2025 Sep 23. doi: 10.1177/15409996251380127. Epub ahead of print. PMID: 40985104.
Sheth SS, Vazquez-Benitez G, DeSilva MB, Zhu J, Seburg EM, Denoble AE, Daley MF, Getahun D, Klein NP, Vesco KK, Irving SA, Nelson JC, Williams JTB, Hambidge SJ, Donahue JG, Lipkind HS, Kharbanda EO. Coronavirus Disease 2019 (COVID-19) Vaccination and Spontaneous Abortion. Obstet Gynecol. 2025 May 2;146(1):129-137. doi: 10.1097/AOG.0000000000005904. PMID: 40311142; PMCID: PMC12169859.
Ackerman-Banks CM, Spatz ES, Lipkind HS. One Step Closer to Unlocking Preeclampsia Prevention. J Am Coll Cardiol. 2025 Apr 15;85(14):1501-1503. doi: 10.1016/j.jacc.2025.03.455. PMID: 40204379.
Ahrens KA, Palmsten K, Lipkind HS, Ackerman-Banks CM. Prevalence of GLP-1 medication exposure prior to, during, and after pregnancy using state-wide data from 2017 to 2023. Am J Obstet Gynecol MFM. 2025 Feb;7(2):101596. doi: 10.1016/j.ajogmf.2024.101596. Epub 2025 Jan 2. PMID: 39755252; PMCID: PMC12230788.
Shanab BM, Gaffey AE, Schwamm L, Zawalich M, Sarpong DF, Pérez-Escamilla R, Dorney J, Cooperman C, Schafer R, Lipkind HS, Lu Y, Onuma OK, Spatz ES. Closing the Gap: Digital Innovations to Address Hypertension Disparities. Curr Cardiol Rep. 2025 Jan 15;27(1):23. doi: 10.1007/s11886-024-02171-x. PMID: 39812880.
Bebus SM, Palmsten K, Lipkind HS, Ackerman-Banks CM, Ahrens KA. Ambulatory care utilization in the first 24 months’ postpartum by rurality and pregnancy-related conditions: A prospective cohort study from Maine. J Rural Health. 2025 Jan;41(1):e12912. doi: 10.1111/jrh.12912. PMID: 39722432; PMCID: PMC12270079.

2024

Kaufman JS, Yonkers KA, Maltz C, Friedhoff CM, Londoño Tobon A, Mele A, Tessier-Kay M, Grechukhina O, Lipkind H, Byatt N, Forray A. Reporting Perinatal Substance Use to Child Protective Services: Obstetric Provider Perspectives on the Impact on Care. J Womens Health (Larchmt). 2024 Nov;33(11):1501-1508. doi: 10.1089/jwh.2023.0822. Epub 2024 May 21. PMID: 38770764.
Denoble AE, Vazquez-Benitez G, Sheth SS, Ackerman-Banks CM, DeSilva MB, Zhu J, Daley MF, Getahun D, Klein NP, Vesco KK, Irving SA, Nelson J, Williams JTB, Hambidge SJ, Donahue JG, Weintraub ES, Kharbanda EO, Lipkind HS. Coronavirus Disease 2019 (COVID-19) Vaccination and Stillbirth in the Vaccine Safety Datalink. Obstet Gynecol. 2024 Aug 1;144(2):215-222. doi: 10.1097/AOG.0000000000005632. Epub 2024 Jun 6. PMID: 38843526; PMCID: PMC11250101.
Kharbanda EO, DeSilva MB, Lipkind HS, Romitti PA, Zhu J, Vesco KK, Boyce TG, Daley MF, Fuller CC, Getahun D, Jackson LA, Williams JTB, Zerbo O, Weintraub ES, Vazquez-Benitez G. COVID-19 Vaccination in the First Trimester and Major Structural Birth Defects Among Live Births. JAMA Pediatr. 2024 Aug 1;178(8):823-829. doi: 10.1001/jamapediatrics.2024.1917. PMID: 38949821; PMCID: PMC11217887.
Ahrens KA, Palmsten K, Lipkind HS, Ackerman-Banks CM, Grantham CO. Does reversible postpartum contraception reduce the risk of pregnancy condition recurrence? A longitudinal claims-based study from Maine. Ann Epidemiol. 2024 Aug;96:58-65. doi: 10.1016/j.annepidem.2024.06.001. Epub 2024 Jun 15. PMID: 38885800; PMCID: PMC11283344.
Son M, Riley LE, Staniczenko AP, Cron J, Yen S, Thomas C, Sholle E, Osborne LM, Lipkind HS. Nonadjuvanted Bivalent Respiratory Syncytial Virus Vaccination and Perinatal Outcomes. JAMA Netw Open. 2024 Jul 1;7(7):e2419268. doi: 10.1001/jamanetworkopen.2024.19268. PMID: 38976271; PMCID: PMC11231799.
Vesco KK, Denoble AE, Lipkind HS, Kharbanda EO, DeSilva MB, Daley MF, Getahun D, Zerbo O, Naleway AL, Jackson L, Williams JTB, Boyce TG, Fuller CC, Weintraub ES, Vazquez-Benitez G. Obstetric Complications and Birth Outcomes After Antenatal Coronavirus Disease 2019 (COVID-19) Vaccination. Obstet Gynecol. 2024 Jun 1;143(6):794-802. doi: 10.1097/AOG.0000000000005583. Epub 2024 Apr 17. PMID: 38626447; PMCID: PMC11090513.
Ackerman-Banks CM, Palmsten K, Lipkind HS, Ahrens KA. Association between gestational diabetes and cardiovascular disease within 24 months postpartum. Am J Obstet Gynecol MFM. 2024 Jun;6(6):101366. doi: 10.1016/j.ajogmf.2024.101366. Epub 2024 Apr 3. PMID: 38580094.
Brooks N, Irving SA, Kauffman TL, Vesco KK, Slaughter M, Smith N, Tepper NK, Olson CK, Weintraub ES, Naleway AL; Vaccine Safety Datalink Menstrual Irregularities Working Group. Abnormal uterine bleeding diagnoses and care following COVID-19 vaccination. Am J Obstet Gynecol. 2024 May;230(5):540.e1-540.e13. doi: 10.1016/j.ajog.2024.01.006. Epub 2024 Jan 12. PMID: 38219855.
Weingarten SJ, Brockhoff EJ, Spielman E, Lipkind HS, Scholl JE. Implementation of virtual group prenatal genetic counseling: a pilot study. Am J Obstet Gynecol MFM. 2024 Apr;6(4):101327. doi: 10.1016/j.ajogmf.2024.101327. Epub 2024 Mar 4. PMID: 38447675.
Ahrens KA, Palmsten K, Grantham CO, Lipkind HS, Ackerman-Banks CM. Acute health care utilization in the first 24 months postpartum by rurality and pregnancy complications: A prospective cohort study. Health Serv Res. 2024 Feb;59(1):e14247. doi: 10.1111/1475-6773.14247. Epub 2023 Oct 12. PMID: 37827521; PMCID: PMC10771903.
Kauffman TL, Irving SA, Brooks N, Vesco KK, Slaughter M, Smith N, Tepper NK, Olson CK, Weintraub ES, Naleway AL; Vaccine Safety Datalink Menstrual Irregularities Workgroup. Postmenopausal bleeding after COVID-19 vaccination. Am J Obstet Gynecol. 2024 Jan;230(1):71.e1-71.e14. doi: 10.1016/j.ajog.2023.09.007. Epub 2023 Sep 17. PMID: 37726057.

2023

Ackerman-Banks CM, Bhinder J, Eder M, Heerdt P, Sugeng L, Testani J, Alian A, Lipkind H, Velazquez E, Reddy U, Chou JC. Continuous non-invasive hemodynamic monitoring in early onset severe preeclampsia. Pregnancy Hypertens. 2023 Dec;34:27-32. doi: 10.1016/j.preghy.2023.09.003. Epub 2023 Sep 30. PMID: 37783090.
White KJ, Tortal D, Callahan K, Eng K, Hyland M, Underwood E, Senter L, León-Martínez D, Son M, Lipkind H. Using a Patient Educational Video to Improve Knowledge of Maternal Mortality Warning Signs: A Randomized Controlled Trial. Obstet Gynecol. 2023 Nov 1;142(5):1139-1147. doi: 10.1097/AOG.0000000000005368. Epub 2023 Sep 13. PMID: 37708502.
Vazquez-Benitez G, Haapala JL, Lipkind HS, DeSilva MB, Zhu J, Daley MF, Getahun D, Klein NP, Vesco KK, Irving SA, Nelson JC, Williams JTB, Hambidge SJ, Donahue J, Fuller CC, Weintraub ES, Olson C, Kharbanda EO. COVID-19 Vaccine Safety Surveillance in Early Pregnancy in the United States: Design Factors Affecting the Association Between Vaccine and Spontaneous Abortion. Am J Epidemiol. 2023 Aug 4;192(8):1386-1395. doi: 10.1093/aje/kwad059. PMID: 36928091; PMCID: PMC10466212.
Gelsinger C, Palmsten K, Lipkind HS, Pfeiffer M, Ackerman-Banks C, Hutcheon JA, Ahrens KA. Provision of Postpartum Contraception Before and After the Start of the COVID-19 Pandemic in Maine. Public Health Rep. 2023 Jul-Aug;138(4):655-663. doi: 10.1177/00333549231170198. Epub 2023 May 2. PMID: 37129355; PMCID: PMC10280119.
DeSilva MB, Haapala J, Vazquez-Benitez G, Boyce TG, Fuller CC, Daley MF, Getahun D, Hambidge SJ, Lipkind HS, Naleway AL, Nelson JC, Vesco KK, Weintraub ES, Williams JTB, Zerbo O, Kharbanda EO. Medically Attended Acute Adverse Events in Pregnant People After Coronavirus Disease 2019 (COVID-19) Booster Vaccination. Obstet Gynecol. 2023 Jul 1;142(1):125-129. doi: 10.1097/AOG.0000000000005241. Epub 2023 May 9. PMID: 37167612; PMCID: PMC10278564.
Ahrens KA, Palmsten K, Lipkind HS, Pfeiffer M, Gelsinger C, Ackerman-Banks C. Mental Health Within 24 Months After Delivery Among Women with Common Pregnancy Conditions. J Womens Health (Larchmt). 2023 Jul;32(7):787-800. doi: 10.1089/jwh.2022.0367. Epub 2023 May 15. PMID: 37192449; PMCID: PMC10354313.
Ackerman-Banks CM, Lipkind HS, Palmsten K, Ahrens KA. Association between hypertensive disorders of pregnancy and cardiovascular diseases within 24 months after delivery. Am J Obstet Gynecol. 2023 Jul;229(1):65.e1-65.e15. doi: 10.1016/j.ajog.2023.04.006. Epub 2023 Apr 7. PMID: 37031763; PMCID: PMC10330109.
Pfeiffer M, Gelsinger C, Palmsten K, Lipkind HS, Ackerman-Banks C, Ahrens KA. Rural-urban residence and sequelae of hypertensive disorders of pregnancy in the first year postpartum, 2007 – 2019. Pregnancy Hypertens. 2023 Jun;32:10-17. doi: 10.1016/j.preghy.2023.02.002. Epub 2023 Feb 14. PMID: 36822069; PMCID: PMC10219842.
Greenberg V, Vazquez-Benitez G, Kharbanda EO, Daley MF, Fu Tseng H, Klein NP, Naleway AL, Williams JTB, Donahue J, Jackson L, Weintraub E, Lipkind H, DeSilva MB. Tdap vaccination during pregnancy and risk of chorioamnionitis and related infant outcomes. Vaccine. 2023 May 22;41(22):3429-3435. doi: 10.1016/j.vaccine.2023.04.043. Epub 2023 Apr 26. PMID: 37117057; PMCID: PMC10466272.
Ackerman-Banks CM, Lipkind HS, Palmsten K, Pfeiffer M, Gelsinger C, Ahrens KA. Association of Prenatal Depression With New Cardiovascular Disease Within 24 Months Postpartum. J Am Heart Assoc. 2023 May 2;12(9):e028133. doi: 10.1161/JAHA.122.028133. Epub 2023 Apr 19. PMID: 37073814; PMCID: PMC10227220.
Kharbanda EO, Haapala J, Lipkind HS, DeSilva MB, Zhu J, Vesco KK, Daley MF, Donahue JG, Getahun D, Hambidge SJ, Irving SA, Klein NP, Nelson JC, Weintraub ES, Williams JTB, Vazquez-Benitez G. COVID-19 Booster Vaccination in Early Pregnancy and Surveillance for Spontaneous Abortion. JAMA Netw Open. 2023 May 1;6(5):e2314350. doi: 10.1001/jamanetworkopen.2023.14350. PMID: 37204791; PMCID: PMC10199343.
Hosier H, Lipkind HS, Rasheed H, DeWan AT, Rogne T. Dyslipidemia and Risk of Preeclampsia: A Multiancestry Mendelian Randomization Study. Hypertension. 2023 May;80(5):1067-1076. doi: 10.1161/HYPERTENSIONAHA.122.20426. Epub 2023 Mar 8. PMID: 36883459.
Grechukhina O, Lipkind HS, Lundsberg LS, Merriam AA, Raab C, Leon-Martinez D, Campbell KH. Severe Maternal Morbidity Review and Preventability Assessment in a Large Academic Center. Obstet Gynecol. 2023 Apr 1;141(4):857-860. doi: 10.1097/AOG.0000000000005116. Epub 2023 Mar 9. PMID: 36897178.
Ackerman-Banks CM, Pudwell J, Lundsberg L, Lipkind HS, Smith GN. Use of family history of cardiovascular disease or chronic hypertension to better identify who needs postpartum cardiovascular risk screening. Am J Obstet Gynecol MFM. 2023 Mar;5(3):100850. doi: 10.1016/j.ajogmf.2022.100850. Epub 2023 Jan 11. PMID: 36640863.
Johnstone AM, Pudwell J, Ackerman-Banks CM, Lundsberg LS, Lipkind HS, Smith GN. High-sensitivity C-reactive protein use in cardiovascular risk screening at 6 to 12 months postpartum following hypertensive disorders of pregnancy. Am J Obstet Gynecol MFM. 2023 Jan;5(1):100776. doi: 10.1016/j.ajogmf.2022.100776. Epub 2022 Oct 20. PMID: 36273813.

2022

DeSilva M, Haapala J, Vazquez-Benitez G, Vesco KK, Daley MF, Getahun D, Zerbo O, Naleway A, Nelson JC, Williams JTB, Hambidge SJ, Boyce TG, Fuller CC, Lipkind HS, Weintraub E, McNeil MM, Kharbanda EO. Evaluation of Acute Adverse Events after Covid-19 Vaccination during Pregnancy. N Engl J Med. 2022 Jul 14;387(2):187-189. doi: 10.1056/NEJMc2205276. Epub 2022 Jun 22. PMID: 35731916; PMCID: PMC9258750.
Jeffery MM, Ahadpour M, Allen S, Araojo R, Bellolio F, Chang N, Ciaccio L, Emanuel L, Fillmore J, Gilbert GH, Koussis P, Lee C, Lipkind H, Mallama C, Meyer T, Moncur M, Nuckols T, Pacanowski MA, Page DB, Papadopoulos E, Ritchie JD, Ross JS, Shah ND, Soukup M, St Clair CO, Tamang S, Torbati S, Wallace DW, Zhao Y, Heckmann R. Acute pain pathways: protocol for a prospective cohort study. BMJ Open. 2022 Jul 5;12(7):e058782. doi: 10.1136/bmjopen-2021-058782. PMID: 35790333; PMCID: PMC9258513.
Tita AT, Szychowski JM, Boggess K, Dugoff L, Sibai B, Lawrence K, Hughes BL, Bell J, Aagaard K, Edwards RK, Gibson K, Haas DM, Plante L, Metz T, Casey B, Esplin S, Longo S, Hoffman M, Saade GR, Hoppe KK, Foroutan J, Tuuli M, Owens MY, Simhan HN, Frey H, Rosen T, Palatnik A, Baker S, August P, Reddy UM, Kinzler W, Su E, Krishna I, Nguyen N, Norton ME, Skupski D, El-Sayed YY, Ogunyemi D, Galis ZS, Harper L, Ambalavanan N, Geller NL, Oparil S, Cutter GR, Andrews WW; Chronic Hypertension and Pregnancy (CHAP) Trial Consortium. Treatment for Mild Chronic Hypertension during Pregnancy. N Engl J Med. 2022 May 12;386(19):1781-1792. doi: 10.1056/NEJMoa2201295. Epub 2022 Apr 2. PMID: 35363951; PMCID: PMC9575330.
Ackerman-Banks CM, Grechukhina O, Spatz E, Lundsberg L, Chou J, Smith G, Greenberg VR, Reddy UM, Xu X, O’Bryan J, Smith S, Perley L, Lipkind HS. Seizing the Window of Opportunity Within 1 Year Postpartum: Early Cardiovascular Screening. J Am Heart Assoc. 2022 Apr 19;11(8):e024443. doi: 10.1161/JAHA.121.024443. Epub 2022 Apr 12. PMID: 35411781; PMCID: PMC9238464.
Forray A, Mele A, Byatt N, Londono Tobon A, Gilstad-Hayden K, Hunkle K, Hong S, Lipkind H, Fiellin DA, Callaghan K, Yonkers KA. Support Models for Addiction Related Treatment (SMART) for pregnant women: Study protocol of a cluster randomized trial of two treatment models for opioid use disorder in prenatal clinics. PLoS One. 2022 Jan 13;17(1):e0261751. doi: 10.1371/journal.pone.0261751. PMID: 35025898; PMCID: PMC8758001.
Lipkind HS, Vazquez-Benitez G, DeSilva M, Vesco KK, Ackerman-Banks C, Zhu J, Boyce TG, Daley MF, Fuller CC, Getahun D, Irving SA, Jackson LA, Williams JTB, Zerbo O, McNeil MM, Olson CK, Weintraub E, Kharbanda EO. Receipt of COVID-19 Vaccine During Pregnancy and Preterm or Small-for-Gestational-Age at Birth – Eight Integrated Health Care Organizations, United States, December 15, 2020-July 22, 2021. MMWR Morb Mortal Wkly Rep. 2022 Jan 7;71(1):26-30. doi: 10.15585/mmwr.mm7101e1. PMID: 34990445; PMCID: PMC8735559.

2021

Kharbanda EO, Haapala J, DeSilva M, Vazquez-Benitez G, Vesco KK, Naleway AL, Lipkind HS. Spontaneous Abortion Following COVID-19 Vaccination During Pregnancy. JAMA. 2021 Oct 26;326(16):1629-1631. doi: 10.1001/jama.2021.15494. Erratum in: JAMA. 2021 Oct 5;326(13):1331. doi: 10.1001/jama.2021.16235. PMID: 34495304; PMCID: PMC8427483.
Zheng Y, Wen X, Bian J, Zhao J, Lipkind HS, Hu H. Racial, Ethnic, and Geographic Disparities in Cardiovascular Health Among Women of Childbearing Age in the United States. J Am Heart Assoc. 2021 Sep 7;10(17):e020138. doi: 10.1161/JAHA.120.020138. Epub 2021 Aug 25. PMID: 34431309; PMCID: PMC8649299.
Platner MH, Ackerman CM, Howland RE, Illuzzi J, Reddy UM, Bourjeily G, Xu X, Lipkind HS. Severe maternal morbidity and mortality during delivery hospitalization of class I, II, III, and super obese women. Am J Obstet Gynecol MFM. 2021 Sep;3(5):100420. doi: 10.1016/j.ajogmf.2021.100420. Epub 2021 Jun 19. PMID: 34157439; PMCID: PMC9667816.
Zheng Y, Wen X, Bian J, Lipkind H, Hu H. Associations between the chemical composition of PM2.5 and gestational diabetes mellitus. Environ Res. 2021 Jul;198:110470. doi: 10.1016/j.envres.2020.110470. Epub 2020 Nov 18. PMID: 33217440.
Razzaghi H, Meghani M, Pingali C, Crane B, Naleway A, Weintraub E, Kenigsberg TA, Lamias MJ, Irving SA, Kauffman TL, Vesco KK, Daley MF, DeSilva M, Donahue J, Getahun D, Glenn S, Hambidge SJ, Jackson L, Lipkind HS, Nelson J, Zerbo O, Oduyebo T, Singleton JA, Patel SA. COVID-19 Vaccination Coverage Among Pregnant Women During Pregnancy – Eight Integrated Health Care Organizations, United States, December 14, 2020-May 8, 2021. MMWR Morb Mortal Wkly Rep. 2021 Jun 18;70(24):895-899. doi: 10.15585/mmwr.mm7024e2. PMID: 34138834; PMCID: PMC8220952.
Greenberg VR, Silasi M, Lundsberg LS, Culhane JF, Reddy UM, Partridge C, Lipkind HS. Perinatal outcomes in women with elevated blood pressure and stage 1 hypertension. Am J Obstet Gynecol. 2021 May;224(5):521.e1-521.e11. doi: 10.1016/j.ajog.2020.10.049. Epub 2020 Nov 4. PMID: 33157064.
Kharbanda EO, Vazquez-Benitez G, DeSilva MB, Naleway AL, Klein NP, Hechter RC, Glanz JM, Donahue JG, Jackson LA, Sheth SS, Greenberg V, Panagiotakopoulos L, Mba-Jonas A, Lipkind HS. Association of Inadvertent 9-Valent Human Papillomavirus Vaccine in Pregnancy With Spontaneous Abortion and Adverse Birth Outcomes. JAMA Netw Open. 2021 Apr 1;4(4):e214340. doi: 10.1001/jamanetworkopen.2021.4340. PMID: 33818618; PMCID: PMC8022219.
Buhimschi CS, Bahtiyar MO, Zhao G, Abdelghany O, Schneider L, Razeq SA, Dulay AT, Lipkind HS, Mieth S, Rogers L, Bhandari V, Buhimschi IA. Antenatal N-acetylcysteine to improve outcomes of premature infants with intra-amniotic infection and inflammation (Triple I): randomized clinical trial. Pediatr Res. 2021 Jan;89(1):175-184. doi: 10.1038/s41390-020-01106-w. Epub 2020 Aug 20. PMID: 32818949; PMCID: PMC7451831.

Lujan Lab

2025

Carter FE, Jarrett BY, Lee ND, Zaman N, Reich AM, Wilson KA, Oldfield AL, Vanden Brink H, Lujan ME. Changes in antral follicle dynamics following weight loss in women with polycystic ovary syndrome. Hum Reprod. 2025 Nov 1;40(11):2161-2171. doi: 10.1093/humrep/deaf169. PMID: 40929646; PMCID: PMC12584915.
Carter FE, Kalay AB, Jarrett BY, Oldfield AL, Brink HV, Lujan ME. Utility of Polycystic Ovarian Morphology on Ultrasonography Across Menstrual Cycle Phases to Aid in the Diagnosis of Polycystic Ovary Syndrome (PCOS). J Ultrasound Med. 2025 Aug 27. doi: 10.1002/jum.70040. Epub ahead of print. PMID: 40862524.
Carter FE, Jarrett BY, Oldfield AL, Vanden Brink H, Kim JY, Lujan ME. Impact of Hypocaloric Dietary Intervention on Phenotypic Presentations of Polycystic Ovary Syndrome (PCOS). Nutrients. 2025 Jul 4;17(13):2223. doi: 10.3390/nu17132223. PMID: 40647327; PMCID: PMC12251410
Vanden Brink H, McCormick KC, Lujan ME, Chang J, Ipp L, Mudrak EL, Alladeen A, Lamar H, Kim JY, Mendle J. Psychological symptoms in perimenarcheal adolescents: association with PCOS risk factors. Front Endocrinol (Lausanne). 2025 Jun 12;16:1551958. doi: 10.3389/fendo.2025.1551958. PMID: 40575266; PMCID: PMC12197959
Yano Maher JC, Zelinski MB, Oktay KH, Duncan FE, Segars JH, Lujan ME, Lou H, Yun BH, Hanfling SN, Schwartz LE, Laronda MM, Halvorson LM, O’Neill KE, Gomez-Lobo V. Classification system of human ovarian follicle morphology: recommendations of the National Institute of Child Health and Human Development – sponsored ovarian nomenclature workshop. Fertil Steril. 2025 May;123(5):761-778. doi: 10.1016/j.fertnstert.2024.11.016. Epub 2024 Nov 15. PMID: 39549739; PMCID: PMC12045743
Peña AS, Witchel SF, Boivin J, Burgert TS, Ee C, Hoeger KM, Lujan ME, Mousa A, Oberfield S, Tay CT, Teede H. International evidence-based recommendations for polycystic ovary syndrome in adolescents. BMC Med. 2025 Mar 11;23(1):151. doi: 10.1186/s12916-025-03901-w. PMID: 40069730; PMCID: PMC11899933.
van der Ham K, Barbagallo F, van Schilfgaarde E, Lujan ME, Laven JSE, Louwers YV. The additional value of ultrasound markers in the diagnosis of polycystic ovary syndrome. Fertil Steril. 2025 Feb;123(2):342-349. doi: 10.1016/j.fertnstert.2024.08.342. Epub 2024 Aug 31. PMID: 39218282.

2024

van der Ham K, Barbagallo F, van Schilfgaarde E, Lujan ME, Laven JSE, Louwers YV. The additional value of ultrasound markers in the diagnosis of polycystic ovary syndrome. Fertil Steril. 2024 Aug 31:S0015-0282(24)01995-2. doi: 10.1016/j.fertnstert.2024.08.342. Epub ahead of print. PMID: 39218282.
Vanden Brink H, Burgert TS, Barral R, Malik A, Gadiraju M, Lujan ME. Ovarian Morphology in Girls Longitudinal Cohort Study: Pilot Evaluation of Ovarian Morphology as a Biomarker of Reproductive and Metabolic Features during the First Gynecological Year. J Pediatr Adolesc Gynecol. 2024 Jun;37(3):315-322. doi: 10.1016/j.jpag.2024.02.004. Epub 2024 Feb 21. PMID: 38395192; PMCID: PMC11195913.
Oldfield AL, Carter FE, Reeves RE, Jarrett BY, Vanden Brink H, Lujan ME. Impact of a hypocaloric dietary intervention on antral follicle dynamics in eumenorrheic women with obesity. Hum Reprod. 2024 Apr 3;39(4):801-811. doi: 10.1093/humrep/deae017. PMID: 38335228; PMCID: PMC10988108.
Maitin-Shepard M, Werner EF, Feig LA, Chavarro JE, Mumford SL, Wylie B, Rando OJ, Gaskins AJ, Sakkas D, Arora M, Kudesia R, Lujan ME, Braun J, Mozaffarian D. Food, nutrition, and fertility: from soil to fork. Am J Clin Nutr. 2024 Feb;119(2):578-589. doi: 10.1016/j.ajcnut.2023.12.005. Epub 2023 Dec 13. PMID: 38101699.
Pea J, Bryan J, Wan C, Oldfield AL, Ganga K, Carter FE, Johnson LM, Lujan ME. Ultrasonographic criteria in the diagnosis of polycystic ovary syndrome: a systematic review and diagnostic meta-analysis. Hum Reprod Update. 2024 Jan 3;30(1):109-130. doi: 10.1093/humupd/dmad027. PMID: 37804097; PMCID: PMC10762001.

2023

Evans AT, Vanden Brink H, Lim JS, Jarrett BY, Lin AW, Lujan ME, Hoeger K. Overnight Melatonin Concentration and Sleep Quality Are Associated with the Clinical Features of Polycystic Ovary Syndrome. Biomedicines. 2023 Oct 12;11(10):2763. doi: 10.3390/biomedicines11102763. PMID: 37893137; PMCID: PMC10604825.
Teede HJ, Tay CT, Laven J, Dokras A, Moran LJ, Piltonen TT, Costello MF, Boivin J, M Redman L, A Boyle J, Norman RJ, Mousa A, Joham AE; International PCOS Network. Recommendations from the 2023 International Evidence-based Guideline for the Assessment and Management of Polycystic Ovary Syndrome. Fertil Steril. 2023 Oct;120(4):767-793. doi: 10.1016/j.fertnstert.2023.07.025. Epub 2023 Aug 14. PMID: 37589624.
Teede HJ, Tay CT, Laven J, Dokras A, Moran LJ, Piltonen TT, Costello MF, Boivin J, Redman LM, Boyle JA, Norman RJ, Mousa A, Joham AE; International PCOS Network. Recommendations from the 2023 International Evidence-based Guideline for the Assessment and Management of Polycystic Ovary Syndrome†. Hum Reprod. 2023 Sep 5;38(9):1655-1679. doi: 10.1093/humrep/dead156. PMID: 37580037; PMCID: PMC10477934.
Oldfield AL, Vanden Brink H, Carter FE, Jarrett BY, Lujan ME. Obesity is associated with alterations in antral follicle dynamics in eumenorrheic women. Hum Reprod. 2023 Mar 1;38(3):459-470. doi: 10.1093/humrep/dead007. PMID: 36708012; PMCID: PMC9977134.
O’Neill KE, Maher JY, Laronda MM, Duncan FE, LeDuc RD, Lujan ME, Oktay KH, Pouch AM, Segars JH, Tsui EL, Zelinski MB, Halvorson LM, Gomez-Lobo V. Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. Am J Obstet Gynecol. 2023 Mar;228(3):270-275.e4. doi: 10.1016/j.ajog.2022.09.040. Epub 2022 Sep 30. PMID: 36191605; PMCID: PMC9974561.
Vanden Brink H, Jarrett BY, Pereira N, Spandorfer SD, Hoeger KM, Lujan ME. Diagnostic Performance of Ovarian Morphology on Ultrasonography across Anovulatory Conditions-Impact of Body Mass Index. Diagnostics (Basel). 2023 Jan 19;13(3):374. doi: 10.3390/diagnostics13030374. PMID: 36766481; PMCID: PMC9914229.

2022

Kazemi M, Kim JY, Wan C, Xiong JD, Michalak J, Xavier IB, Ganga K, Tay CT, Grieger JA, Parry SA, Moran LJ, Lujan ME. Comparison of dietary and physical activity behaviors in women with and without polycystic ovary syndrome: a systematic review and meta-analysis of 39 471 women. Hum Reprod Update. 2022 Nov 2;28(6):910-955. doi: 10.1093/humupd/dmac023. Erratum in: Hum Reprod Update. 2023 Jan 5;29(1):155. doi: 10.1093/humupd/dmac036. PMID: 35639552; PMCID: PMC9629501.
Vanden Brink H, Nosrati A, Ortiz-Flores AE, Tam A, Jarrett BY, Johnson L, Peppin AK, Lujan ME. Reliability and Agreement of Ultrasonographic Measures of the Ovarian Stroma: Impact of Methodology. J Ultrasound Med. 2022 Sep;41(9):2307-2315. doi: 10.1002/jum.15917. Epub 2021 Dec 16. PMID: 34913507; PMCID: PMC9285645.
Joham AE, Piltonen T, Lujan ME, Kiconco S, Tay CT. Challenges in diagnosis and understanding of natural history of polycystic ovary syndrome. Clin Endocrinol (Oxf). 2022 Aug;97(2):165-173. doi: 10.1111/cen.14757. Epub 2022 May 30. PMID: 35593530; PMCID: PMC9541175.
Kazemi M, Kim JY, Wan C, Xiong JD, Parry SA, Azziz R, Lujan ME. Comprehensive evaluation of disparities in cardiometabolic and reproductive risk between Hispanic and White women with polycystic ovary syndrome in the United States: a systematic review and meta-analysis. Am J Obstet Gynecol. 2022 Feb;226(2):187-204.e15. doi: 10.1016/j.ajog.2021.07.032. Epub 2021 Aug 9. PMID: 34384776.

2021

Vanden Brink H, Pea J, Lujan ME. Ultrasonographic features of ovarian morphology capture nutritional and metabolic influences on the reproductive axis: implications for biomarker development in ovulatory disorders. Curr Opin Biotechnol. 2021 Aug;70:42-47. doi: 10.1016/j.copbio.2020.10.008. Epub 2020 Nov 25. PMID: 33248350; PMCID: PMC8144229.
Oldfield AL, Kazemi M, Lujan ME. Impact of Obesity on Anti-Mullerian Hormone (AMH) Levels in Women of Reproductive Age. J Clin Med. 2021 Jul 20;10(14):3192. doi: 10.3390/jcm10143192. PMID: 34300357; PMCID: PMC8306853.
Ding A, Guerin A, Lujan ME, Velez MP. Polycystic Ovary Syndrome and Incidental Diagnosis of Mosaic Turner Syndrome. J Obstet Gynaecol Can. 2021 Jun;43(6):756-759. doi: 10.1016/j.jogc.2020.08.020. Epub 2020 Sep 8. PMID: 33158769.
Kazemi M, Kim JY, Parry SA, Azziz R, Lujan ME. Disparities in cardio metabolic risk between Black and White women with polycystic ovary syndrome: a systematic review and meta-analysis. Am J Obstet Gynecol. 2021 May;224(5):428-444.e8. doi: 10.1016/j.ajog.2020.12.019. Epub 2020 Dec 13. PMID: 33316275.
Kazemi M, Thalacker-Mercer AE, Lujan ME. Response to Letter to the Editor from Smith et al: “Osteosarcopenia in Reproductive-Aged Women With Polycystic Ovary Syndrome: A Multicenter Case-Control Study”. J Clin Endocrinol Metab. 2021 Mar 8;106(3):e1500-e1501. doi: 10.1210/clinem/dgaa670. PMID: 32948874; PMCID: PMC9115323.
Vanden Brink H, Pisch AJ, Lujan ME. A comparison of two- and three-dimensional ultrasonographic methods for evaluation of ovarian follicle counts and classification of polycystic ovarian morphology. Fertil Steril. 2021 Mar;115(3):761-770. doi: 10.1016/j.fertnstert.2020.09.006. Epub 2021 Feb 20. PMID: 33618897.
Kazemi M, Hadi A, Pierson RA, Lujan ME, Zello GA, Chilibeck PD. Effects of Dietary Glycemic Index and Glycemic Load on Cardiometabolic and Reproductive Profiles in Women with Polycystic Ovary Syndrome: A Systematic Review and Meta-analysis of Randomized Controlled Trials. Adv Nutr. 2021 Feb 1;12(1):161-178. doi: 10.1093/advances/nmaa092. PMID: 32805007; PMCID: PMC7850057.
Lin AW, Siscovick D, Sternfeld B, Schreiner P, Lewis CE, Wang ET, Merkin SS, Wellons M, Steffen L, Calderon-Margalit R, Cassano PA, Lujan ME. Associations of diet, physical activity and polycystic ovary syndrome in the Coronary Artery Risk Development in Young Adults Women’s Study. BMC Public Health. 2021 Jan 6;21(1):35. doi: 10.1186/s12889-020-10028-5. PMID: 33407255; PMCID: PMC7789704.

Martin

2025

Kim ES, Lin MC, Lu CH, Casero D, Aguirre B, Brown J, Olagoke O, Martin CR, Wadehra M, Calkins KL, Chu A. Polyunsaturated fatty acid balance modulates microglial state in a murine model of oxygen-induced neovascularization. Res Sq [Preprint]. 2025 Sep 23:rs.3.rs-7491382. doi: 10.21203/rs.3.rs-7491382/v1. PMID: 41041571; PMCID: PMC12486074.
Martin CR, Polin RA. The Unfinished Science of Preterm Nutrition: Implementing Progress and Navigating Uncertainty Belong in the Neonatal Intensive Care Unit. J Pediatr. 2025 Sep;284:114668. doi: 10.1016/j.jpeds.2025.114668. Epub 2025 May 22. PMID: 40412471.
Martin CR. Confronting the fatty acid problem in preterm infants: biological needs, nutritional gaps. Am J Clin Nutr. 2025 Aug;122(2):379-381. doi: 10.1016/j.ajcnut.2025.06.012. Epub 2025 Jul 4. PMID: 40615345.
Andrews C, Vodapally S, Foster LP, Lawandy I, Murphy M, Castellanos M, Moncada D, Mourao ML, Bhushan B, Berger PK, Fichorova R, Monthé-Drèze C, Freedman SD, Angelidou A, Martin CR, Sen S. Cohort profile: Mother and Infant Metabolome and Microbiome (MIMM) study, a prospective cohort study of mothers and infants in Boston, Massachusetts. BMJ Open. 2025 Jun 18;15(6):e096957. doi: 10.1136/bmjopen-2024-096957. PMID: 40533202; PMCID: PMC12182119.
German K, Wood TR, Gogcu S, Heagerty PJ, Mayock DE, Comstock BA, Puia-Dumitrescu M, Kolnik S, Mietzsch U, Law J, Perez K, Valentine G, Bammler TK, Juul SE; PENUT Trial Consortium. Neurodevelopmental outcomes after red cell transfusion exposure in male versus female extremely preterm infants. Pediatr Res. 2025 Jun 2. doi: 10.1038/s41390-025-04149-z. Epub ahead of print. PMID: 40456918.
Ten Barge JA, van den Bosch GE, Allegaert K, Bhatt A, Brindley N, Byrne D, Campbell-Yeo M, Camprubi-Camprubi M, Cavallaro G, Durrmeyer X, Embleton N, Eriksson M, Flint RB, Garrido F, Giannì ML, Giannoni E, Kitt H, Klerk D, Kristjánsdóttir G, Amponsah AK, Lapillonne A, Martin CR, Matyas M, Norman E, Ohja S, Pirlotte S, Del Rio R, Roué JM, Sevivas C, Slater R, Smits A, de Pipaon MS, Tauzin M, Ukkonen T, Unal S, Villamor E, Molloy EJ, Simons SHP. Pain management in preterm infants with necrotizing enterocolitis: an international expert consensus statement. Eur J Pediatr. 2025 May 14;184(6):342. doi: 10.1007/s00431-025-06168-8. PMID: 40369136; PMCID: PMC12078406.
Cohen AJ, Chidester WR, Wray DT, Jessen N, Jones A, Bitsui C, Zhao J, Maschek JA, Cox JE, Martin CR, Joss-Moore LA. Docosahexaenoic Acid Supplementation in Postnatal Growth Restricted Rats Does Not Normalize Lung Function or PPARγ Activity. Biomolecules. 2025 Apr 9;15(4):551. doi: 10.3390/biom15040551. PMID: 40305361; PMCID: PMC12024927.
Harpavat S, Aucott SW, Karpen SJ, Shneider BL, Wang K; and the SECTION ON GASTROENTEROLOGY, HEPATOLOGY, AND NUTRITION; COMMITTEE ON FETUS AND NEWBORN; SECTION ON SURGERY. Guidance for the Primary Care Provider in Identifying Infants With Biliary Atresia by 2-4 Weeks of Life: Clinical Report. Pediatrics. 2025 Feb 18:e2024070077. doi: 10.1542/peds.2024-070077. Epub ahead of print. PMID: 39961332.

2024

Bhutani VK, Wong RJ, Turkewitz D, Rauch DA, Mowitz ME, Barfield WD; COMMITTEE ON FETUS & NEWBORN. Phototherapy to Prevent Severe Neonatal Hyperbilirubinemia in the Newborn Infant 35 or More Weeks of Gestation: Technical Report. Pediatrics. 2024 Sep 1;154(3):e2024068026. doi: 10.1542/peds.2024-068026. PMID: 39183672.
Sharma P, Luo G, Wang C, Brodsky D, Martin CR, Beam A, Beam K. Assessment of the clinical knowledge of ChatGPT-4 in neonatal-perinatal medicine: a comparative analysis with ChatGPT-3.5. J Perinatol. 2024 Sep;44(9):1365-1366. doi: 10.1038/s41372-024-01912-8. Epub 2024 Feb 24. PMID: 38402349.
Thomas J, Bunik M, Holmes A, Keels MA, Poindexter B, Meyer A, Gilliland A; SECTION ON BREASTFEEDING; SECTION ON ORAL HEALTH; COUNCIL ON QUALITY IMPROVEMENT AND PATIENT SAFETY; COMMITTEE ON FETUS & NEWBORN; SECTION ON OTOLARYNGOLOGY-HEAD AND NECK SURGERY. Identification and Management of Ankyloglossia and Its Effect on Breastfeeding in Infants: Clinical Report. Pediatrics. 2024 Aug 1;154(2):e2024067605. doi: 10.1542/peds.2024-067605. PMID: 39069819.
Buck CO, Santoro KL, Shabanova V, Martin CR, Taylor SN. Establishing feasibility and reliability of subcutaneous fat measurements by ultrasound in very preterm infants. Pediatr Res. 2024 Jul 28. doi: 10.1038/s41390-024-03439-2. Epub ahead of print. PMID: 39069538.
Ahmed S, Odumade OA, van Zalm P, Fatou B, Hansen R, Martin CR, Angelidou A, Steen H. Proteomics-Based Mapping of Bronchopulmonary Dysplasia-Associated Changes in Noninvasively Accessible Oral Secretions. J Pediatr. 2024 Jul;270:113774. doi: 10.1016/j.jpeds.2023.113774. Epub 2023 Oct 13. PMID: 37839510; PMCID: PMC11014893.
Holzapfel LF, Unger JP, Gordon P, Yang H, Cluette-Brown JE, Gollins LA, Hair AB, Martin CR. Fatty acid concentrations in preterm infants fed the exclusive human milk diet: a prospective cohort study. J Perinatol. 2024 May;44(5):680-686. doi: 10.1038/s41372-023-01841-y. Epub 2023 Dec 11. PMID: 38082071; PMCID: PMC11090710.
Sizemore N, Oliphant K, Zheng R, Martin CR, Claud EC, Chattopadhyay I. A digital twin of the infant microbiome to predict neurodevelopmental deficits. Sci Adv. 2024 Apr 12;10(15):eadj0400. doi: 10.1126/sciadv.adj0400. Epub 2024 Apr 10. PMID: 38598636; PMCID: PMC11006218.
Hingorani SR, Schmicker RH, Halloran B, Brophy P, Heagerty PJ, Juul S, Goldstein SL, Askenazi D; PENUT Investigators. Association Between Urinary Biomarkers and CKD in Extremely Low Gestational Age Neonates. Am J Kidney Dis. 2024 Apr;83(4):497-507. doi: 10.1053/j.ajkd.2023.09.008. Epub 2023 Nov 4. PMID: 37926336; PMCID: PMC10960703.
How HS, Malhotra A, Martin C. EBNEO commentary: Early human milk fortification in infants born extremely preterm: A randomised trial. Acta Paediatr. 2024 Mar;113(3):625-626. doi: 10.1111/apa.17110. Epub 2024 Jan 18. PMID: 38235608.
Nair J, Martin CR. Context of time on intestinal injury in preterm infants. Pediatr Res. 2024 Mar;95(4):873-874. doi: 10.1038/s41390-023-02844-3. Epub 2023 Oct 24. PMID: 37875727.

2023

Heras A, Chambers R, Solomon Z, Blatt L, Martin CR. Nutrition-based implications and therapeutics in the development and recovery of bronchopulmonary dysplasia. Semin Perinatol. 2023 Oct;47(6):151818. doi: 10.1016/j.semperi.2023.151818. Epub 2023 Sep 9. PMID: 37775366.
Beam K, Sharma P, Kumar B, Wang C, Brodsky D, Martin CR, Beam A. Performance of a Large Language Model on Practice Questions for the Neonatal Board Examination. JAMA Pediatr. 2023 Sep 1;177(9):977-979. doi: 10.1001/jamapediatrics.2023.2373. PMID: 37459084; PMCID: PMC10352922.
Frost B, Martin CR, Calkins KL. Dilemmas in the delivery of intravenous lipid emulsions and approach to hypertriglyceridemia in very preterm and low birth weight infants. J Perinatol. 2023 Sep;43(9):1189-1193. doi: 10.1038/s41372-023-01637-0. Epub 2023 Apr 8. PMID: 37031340.
Chan AP, Rostas S, Rogers S, Martin CR, Calkins KL. Parenteral Nutrition in the Neonatal Intensive Care Unit: Intravenous Lipid Emulsions. Clin Perinatol. 2023 Sep;50(3):575-589. doi: 10.1016/j.clp.2023.04.012. Epub 2023 Jun 1. PMID: 37536765.
Blanco CL, Smith V, Ramel SE, Martin CR. Dilemmas in parenteral glucose delivery and approach to glucose monitoring and interpretation in the neonate. J Perinatol. 2023 Sep;43(9):1200-1205. doi: 10.1038/s41372-023-01640-5. Epub 2023 Mar 24. PMID: 36964206.
Khan FA, Jancelewicz T, Kieran K, Islam S; COMMITTEE ON FETUS AND NEWBORN; SECTION ON SURGERY; SECTION ON UROLOGY. Assessment and Management of Inguinal Hernias in Children. Pediatrics. 2023 Jul 1;152(1):e2023062510. doi: 10.1542/peds.2023-062510. PMID: 37357733.
Davis BE, Leppert MO, German K, Lehmann CU, Adams-Chapman I; COUNCIL ON CHILDREN WITH DISABILITIES; COMMITTEE ON FETUS AND NEWBORN. Primary Care Framework to Monitor Preterm Infants for Neurodevelopmental Outcomes in Early Childhood. Pediatrics. 2023 Jul 1;152(1):e2023062511. doi: 10.1542/peds.2023-062511. PMID: 37357736.
Martin CR. Fatty acid supplementation and health outcomes in preterm infants: Hand-waving or true biological impact? Am J Clin Nutr. 2023 May;117(5):839-841. doi: 10.1016/j.ajcnut.2023.02.021. Epub 2023 Apr 19. PMID: 37137612.
Ramiro-Cortijo D, Herranz Carrillo G, Singh P, Rebollo-Hernanz M, Rodríguez-Rodríguez P, Ruvira S, Martín-Trueba M, Martin CR, Arribas SM. Maternal and Neonatal Factors Modulating Breast Milk Cytokines in the First Month of Lactation. Antioxidants (Basel). 2023 Apr 25;12(5):996. doi: 10.3390/antiox12050996. PMID: 37237863; PMCID: PMC10215605.
Ramiro-Cortijo D, Singh P, Herranz Carrillo G, Gila-Díaz A, Martín-Cabrejas MA, Martin CR, Arribas SM. Association of maternal body composition and diet on breast milk hormones and neonatal growth during the first month of lactation. Front Endocrinol (Lausanne). 2023 Mar 2;14:1090499. doi: 10.3389/fendo.2023.1090499. PMID: 36936154; PMCID: PMC10018215.
Tsikis ST, Fligor SC, Mitchell PD, Hirsch TI, Carbeau S, First E, Loring G, Rudie C, Freedman SD, Martin CR, Gura KM, Puder M. Fat digestion using RELiZORB in children with short bowel syndrome who are dependent on parenteral nutrition: Protocol for a 90-day, phase 3, open labeled study. PLoS One. 2023 Mar 1;18(3):e0282248. doi: 10.1371/journal.pone.0282248. PMID: 36857339; PMCID: PMC9977023.
Holzapfel LF, Hair AB, Preidis GA, Halder T, Yang H, Unger JP, Freedman S, Martin CR. Fecal Elastase in Preterm Infants to Predict Growth Outcomes. J Pediatr Gastroenterol Nutr. 2023 Feb 1;76(2):206-212. doi: 10.1097/MPG.0000000000003672. Epub 2022 Dec 1. PMID: 36705701; PMCID: PMC9886337.
Lu J, Martin CR, Claud EC. Neurodevelopmental outcome of infants who develop necrotizing enterocolitis: The gut-brain axis. Semin Perinatol. 2023 Feb;47(1):151694. doi: 10.1016/j.semperi.2022.151694. Epub 2022 Dec 20. PMID: 36572620; PMCID: PMC9974904.
Garcia MR, Comstock BA, Patel RM, Tolia VN, Josephson CD, Georgieff MK, Rao R, Monsell SE, Juul SE, Ahmad KA; PENUT Trial Consortium. Iron supplementation and the risk of bronchopulmonary dysplasia in extremely low gestational age newborns. Pediatr Res. 2023 Feb;93(3):701-707. doi: 10.1038/s41390-022-02160-2. Epub 2022 Jun 20. PMID: 35725917; PMCID: PMC9763546.

2022

Ramiro-Cortijo D, Herranz Carrillo G, Gila-Diaz A, Ruvira S, Singh P, Braojos C, Martin CR, Arribas SM. Association between Adherence to the Healthy Food Pyramid and Breast Milk Fatty Acids in the First Month of Lactation. Nutrients. 2022 Dec 11;14(24):5280. doi: 10.3390/nu14245280. PMID: 36558439; PMCID: PMC9780987.
Stewart DL, Elsayed Y, Fraga MV, Coley BD, Annam A, Milla SS; COMMITTEE ON FETUS AND NEWBORN AND SECTION ON RADIOLOGY; Section on Radiology Executive Committee, 2021–2022. Use of Point-of-Care Ultrasonography in the NICU for Diagnostic and Procedural Purposes. Pediatrics. 2022 Dec 1;150(6):e2022060053. doi: 10.1542/peds.2022-060053. PMID: 37154781.
Martin CR. Parenteral Protein in Extremely Preterm Infants – More Is Not Better. N Engl J Med. 2022 Nov 3;387(18):1712-1713. doi: 10.1056/NEJMe2212522. PMID: 36322851.
Hingorani S, Schmicker R, Ahmad KA, Frantz ID, Mayock DE, La Gamma EF, Baserga M, Khan JY, Gilmore MM, Robinson T, Brophy P, Heagerty PJ, Juul SE, Goldstein S, Askenazi D; PENUT Trial Consortium; PENUT Primary Investigators and coauthors. Prevalence and Risk Factors for Kidney Disease and Elevated BP in 2-Year-Old Children Born Extremely Premature. Clin J Am Soc Nephrol. 2022 Aug;17(8):1129-1138. doi: 10.2215/CJN.15011121. Epub 2022 Jul 19. PMID: 35853728; PMCID: PMC9435989.
Frazer LC, Yakah W, Martin CR. Decreased Acetic Acid in the Stool of Preterm Infants Is Associated with an Increased Risk of Bronchopulmonary Dysplasia. Nutrients. 2022 Jun 10;14(12):2412. doi: 10.3390/nu14122412. PMID: 35745141; PMCID: PMC9230097.
Santoro K, Martin CR. Lipids and Long Chain Polyunsaturated Fatty Acids in Preterm Infants. Clin Perinatol. 2022 Jun;49(2):381-391. doi: 10.1016/j.clp.2022.02.007. Epub 2022 Apr 21. PMID: 35659092; PMCID: PMC9177057.
Davenport P, Fan HH, Nolton E, Feldman HA, Lorenz V, Canas J, Acosta-Zaldívar M, Yakah W, Arthur C, Martin C, Stowell S, Koehler J, Mager D, Sola-Visner M. Platelet transfusions in a murine model of neonatal polymicrobial sepsis: Divergent effects on inflammation and mortality. Transfusion. 2022 Jun;62(6):1177-1187. doi: 10.1111/trf.16895. Epub 2022 May 6. PMID: 35522536; PMCID: PMC11465244.
Santoro KL, Yakah W, Singh P, Ramiro-Cortijo D, Medina-Morales E, Freedman SD, Martin CR. Acetaminophen and Xenobiotic Metabolites in Human Milk and the Development of Bronchopulmonary Dysplasia and Retinopathy of Prematurity in a Cohort of Extremely Preterm Infants. J Pediatr. 2022 May;244:224-229.e3. doi: 10.1016/j.jpeds.2022.01.030. Epub 2022 Jan 31. PMID: 35093319; PMCID: PMC9152735.
Taylor SN, Fenton TR, Groh-Wargo S, Gura K, Martin CR, Griffin IJ, Rozga M, Moloney L. Exclusive Maternal Milk Compared With Exclusive Formula on Growth and Health Outcomes in Very-Low-Birthweight Preterm Infants: Phase II of the Pre-B Project and an Evidence Analysis Center Systematic Review. Front Pediatr. 2022 Feb 25;9:793311. doi: 10.3389/fped.2021.793311. PMID: 35280446; PMCID: PMC8913886.
Taylor SN, Martin CR. Evidence-based Discharge Nutrition to Optimize Preterm Infant Outcomes. Neoreviews. 2022 Feb 1;23(2):e108-e116. doi: 10.1542/neo.23-2-e108. PMID: 35102382.
Juul SE, Wood TR, Comstock BA, Perez K, Gogcu S, Puia-Dumitrescu M, Berkelhamer S, Heagerty PJ; PENUT Consortium. Deaths in a Modern Cohort of Extremely Preterm Infants From the Preterm Erythropoietin Neuroprotection Trial. JAMA Netw Open. 2022 Feb 1;5(2):e2146404. doi: 10.1001/jamanetworkopen.2021.46404. PMID: 35129596; PMCID: PMC8822378.
Martin CR. Definitions of necrotizing enterocolitis: What are we defining and is machine learning the answer? Pediatr Res. 2022 Feb;91(3):488-489. doi: 10.1038/s41390-021-01687-0. Epub 2021 Aug 31. PMID: 34465874.
Fenton TR, Griffin IJ, Groh-Wargo S, Gura K, Martin CR, Taylor SN, Rozga M, Moloney L. Very Low Birthweight Preterm Infants: A 2020 Evidence Analysis Center Evidence-Based Nutrition Practice Guideline. J Acad Nutr Diet. 2022 Jan;122(1):182-206. doi: 10.1016/j.jand.2021.02.027. Epub 2021 Apr 2. PMID: 33820749.
Belfort MB, Ramel SE, Martin CR, Fichorova R, Kuban KCK, Heeren T, Fry RC, O’Shea TM. Systemic Inflammation in the First 2 Weeks after Birth as a Determinant of Physical Growth Outcomes in Hospitalized Infants with Extremely Low Gestational Age. J Pediatr. 2022 Jan;240:37-43.e1. doi: 10.1016/j.jpeds.2021.09.006. Epub 2021 Sep 8. PMID: 34508750; PMCID: PMC8712377.
Good M, Martin CR. A Promising Genetic Target for a Deadly Disease: Single Immunoglobulin Interleukin 1 (SIGIRR) Mutations in Necrotizing Enterocolitis. Cell Mol Gastroenterol Hepatol. 2022;13(2):674-675. doi: 10.1016/j.jcmgh.2021.10.011. Epub 2021 Nov 2. PMID: 34740617; PMCID: PMC8776998.
Lewis AN, de la Cruz D, Wynn JL, Frazer LC, Yakah W, Martin CR, Yang H, Itriago E, Unger J, Hair AB, Miele J, Sullivan BA, Husain A, Good M. Evaluation of the Neonatal Sequential Organ Failure Assessment and Mortality Risk in Preterm Infants with Necrotizing Enterocolitis. Neonatology. 2022;119(3):334-344. doi: 10.1159/000522560. Epub 2022 Mar 21. PMID: 35313308; PMCID: PMC9117503.
Frazer LC, Gura KM, Bines JE, Puder M, Martin CR. [Prevención y manejo de la colestasis asociada a la nutrición parenteral y la enfermedad hepática asociada a la insuficiencia intestinal en los lactantes críticamente enfermos]. World Rev Nutr Diet. 2022;122:408-430. Spanish. doi: 10.1159/000526555. Epub 2022 Sep 29. PMID: 36174529.
Bozzetti V, Martin CR. [Práctica de la nutrición enteral en lactantes de muy bajo y extremadamente bajo peso al nacer]. World Rev Nutr Diet. 2022;122:284-301. Spanish. doi: 10.1159/000526523. Epub 2022 Sep 29. PMID: 36174520.

2021

Mayock DE, Gogcu S, Puia-Dumitrescu M, Shaw DWW, Wright JN, Comstock BA, Heagerty PJ, Juul SE; Preterm Erythropoietin Neuroprotection (PENUT) Trial Consortium. Association between Term Equivalent Brain Magnetic Resonance Imaging and 2-Year Outcomes in Extremely Preterm Infants: A Report from the Preterm Erythropoietin Neuroprotection Trial Cohort. J Pediatr. 2021 Dec;239:117-125.e6. doi: 10.1016/j.jpeds.2021.08.040. Epub 2021 Aug 26. PMID: 34454953; PMCID: PMC9052881.
Frazer LC, Martin CR. Parenteral lipid emulsions in the preterm infant: current issues and controversies. Arch Dis Child Fetal Neonatal Ed. 2021 Nov;106(6):676-681. doi: 10.1136/archdischild-2020-319108. Epub 2021 Jan 29. PMID: 33514630; PMCID: PMC8319211.
Frazer LC, Martin CR. Reply to ‘Parenteral nutrition for preterm infants: correcting for arachidonic and docosahexaenoic acid may not suffice’. Arch Dis Child Fetal Neonatal Ed. 2021 Nov;106(6):683-684. doi: 10.1136/archdischild-2021-322370. Epub 2021 Jun 15. PMID: 34131040.
Fenton TR, Groh-Wargo S, Gura K, Martin CR, Taylor SN, Griffin IJ, Rozga M, Moloney L. Effect of Enteral Protein Amount on Growth and Health Outcomes in Very-Low-Birth-Weight Preterm Infants: Phase II of the Pre-B Project and an Evidence Analysis Center Systematic Review. J Acad Nutr Diet. 2021 Nov;121(11):2287-2300.e12. doi: 10.1016/j.jand.2020.11.002. Epub 2020 Dec 22. PMID: 33358688.
Enstad S, Cheema S, Thomas R, Fichorova R, Martin CR, O’Tierney-Ginn P, Wagner CL, Sen S. Response to messaging and methodological considerations when researching breastfeeding and obesity. Eur J Clin Nutr. 2021 Oct;75(10):1526-1527. doi: 10.1038/s41430-021-00900-x. Epub 2021 Apr 23. PMID: 33893448.
Vu PT, Ohls RK, Mayock DE, German KR, Comstock BA, Heagerty PJ, Juul SE; PENUT Consortium. Transfusions and neurodevelopmental outcomes in extremely low gestation neonates enrolled in the PENUT Trial: a randomized clinical trial. Pediatr Res. 2021 Jul;90(1):109-116. doi: 10.1038/s41390-020-01273-w. Epub 2021 Jan 11. PMID: 33432157; PMCID: PMC7797706.
Goodstein MH, Stewart DL, Keels EL, Moon RY; COMMITTEE ON FETUS AND NEWBORN, TASK FORCE ON SUDDEN INFANT DEATH SYNDROME. Transition to a Safe Home Sleep Environment for the NICU Patient. Pediatrics. 2021 Jul;148(1):e2021052046. doi: 10.1542/peds.2021-052046. Epub 2021 Jun 21. PMID: 34155135.
Poindexter B; COMMITTEE ON FETUS AND NEWBORN. Use of Probiotics in Preterm Infants. Pediatrics. 2021 Jun;147(6):e2021051485. doi: 10.1542/peds.2021-051485. Epub 2021 May 24. Erratum in: Pediatrics. 2021 Dec 1;148(6):e2021054370. doi: 10.1542/peds.2021-054370. PMID: 34031231.
Joung KE, Martin CR, Cherkerzian S, Kellogg M, Belfort MB. Human Milk Hormone Intake in the First Month of Life and Physical Growth Outcomes in Preterm Infants. J Clin Endocrinol Metab. 2021 May 13;106(6):1793-1803. doi: 10.1210/clinem/dgab001. PMID: 33544860.
Askenazi DJ, Heagerty PJ, Schmicker RH, Brophy P, Juul SE, Goldstein SL, Hingorani S; PENUT Trial Consortium. The Impact of Erythropoietin on Short- and Long-Term Kidney-Related Outcomes in Neonates of Extremely Low Gestational Age. Results of a Multicenter, Double-Blind, Placebo-Controlled Randomized Clinical Trial. J Pediatr. 2021 May;232:65-72.e7. doi: 10.1016/j.jpeds.2021.01.031. Epub 2021 Jan 20. PMID: 33484699; PMCID: PMC8093092.
Rao C, Coyte KZ, Bainter W, Geha RS, Martin CR, Rakoff-Nahoum S. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature. 2021 Mar;591(7851):633-638. doi: 10.1038/s41586-021-03241-8. Epub 2021 Feb 24. PMID: 33627867; PMCID: PMC7990694.
Fleiss N, Coggins SA, Lewis AN, Zeigler A, Cooksey KE, Walker LA, Husain AN, de Jong BS, Wallman-Stokes A, Alrifai MW, Visser DH, Good M, Sullivan B, Polin RA, Martin CR, Wynn JL. Evaluation of the Neonatal Sequential Organ Failure Assessment and Mortality Risk in Preterm Infants With Late-Onset Infection. JAMA Netw Open. 2021 Feb 1;4(2):e2036518. doi: 10.1001/jamanetworkopen.2020.36518. PMID: 33538825; PMCID: PMC7862993.
Yakah W, Singh P, Brown J, Stoll B, Burrin D, Premkumar MH, Otu HH, Gu X, Dillon ST, Libermann TA, Freedman SD, Martin CR. Parenteral lipid emulsions induce unique ileal fatty acid and metabolomic profiles but do not increase the risk of necrotizing enterocolitis in preterm pigs. Am J Physiol Gastrointest Liver Physiol. 2021 Feb 1;320(2):G227-G239. doi: 10.1152/ajpgi.00311.2020. Epub 2020 Nov 25. PMID: 33236951; PMCID: PMC7948117.
Yakah W, Ramiro-Cortijo D, Singh P, Brown J, Stoll B, Kulkarni M, Oosterloo BC, Burrin D, Maddipati KR, Fichorova RN, Freedman SD, Martin CR. Parenteral Fish-Oil Containing Lipid Emulsions Limit Initial Lipopolysaccharide-Induced Host Immune Responses in Preterm Pigs. Nutrients. 2021 Jan 12;13(1):205. doi: 10.3390/nu13010205. PMID: 33445698; PMCID: PMC7828127.
Embleton N, Berrington J, Bloomfield F, Martin C. Letter to the Editor: Effect on splanchnic oxygenation of breast milk, fortified breast milk and formula milk in preterm infants. Pediatr Res. 2021 Jan;89(1):4-5. doi: 10.1038/s41390-020-1043-y. Epub 2020 Jun 27. PMID: 32593166.
Bozzetti V, Martin CR. The Practice of Enteral Nutrition in Very Low and Extremely Low Birth Weight Infants. World Rev Nutr Diet. 2021;122:265-280. doi: 10.1159/000514743. Epub 2021 Aug 5. PMID: 34352759.
Frazer LC, Gura KM, Bines JE, Puder M, Martin CR. Prevention and Management of Parenteral Nutrition-Associated Cholestasis and Intestinal Failure-Associated Liver Disease in the Critically Ill Infant. World Rev Nutr Diet. 2021;122:379-399. doi: 10.1159/000514763. Epub 2021 Aug 5. PMID: 34352771.

Murphy, Kristin

2025

Park BJ, Hua S, Casler KD, Cefaloni E, Ayers MC, Lake RF, Murphy KE, Vertino PM, O’Connell MR, Murphy PJ. CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci. iScience. 2025 Nov 21;28(11):113757. doi: 10.1016/j.isci.2025.113757. eCollection 2025 Nov 21. PubMed PMID: 41234774; PubMed Central PMCID: PMC12605858.
McGrath KE, Olsen JL, Koniski AD, Murphy KE, Getman M, An HH, Schulz VP, Kim AR, Zhang B, Carlson TL, Papoin J, Blanc L, Kingsley PD, Westhoff CM, Gallagher PG, Chou ST, Steiner LA, Palis J. BMI1 regulates human erythroid self-renewal through both gene repression and gene activation. Nat Commun. 2025 Aug 15;16(1):7619. doi: 10.1038/s41467-025-62993-3. PubMed PMID: 40817093; PubMed Central PMCID: PMC12356964.
Murphy K, Getman M, Lv X, Murphy Z, Abid D, Rahman N, Bulger M, Steiner L. Histone H4 lysine 20 methylation marks genes dynamically regulated during erythroid maturation. Epigenetics Chromatin. 2025 Jul 26;18(1):48. doi: 10.1186/s13072-025-00609-2. PubMed PMID: 40713835; PubMed Central PMCID: PMC12296644.
Abid D, Murphy K, Murphy Z, Rahman N, Getman M, Steiner L. The Condensin II complex regulates essential gene expression programs during erythropoiesis. Development. 2025 May 15;152(10). doi: 10.1242/dev.204485. Epub 2025 May 19. PubMed PMID: 40260585; PubMed Central PMCID: PMC12148035

2023

Lv X, Murphy K, Murphy Z, Getman M, Rahman N, Nakamura Y, Blanc L, Gallagher PG, Palis J, Mohandas N, Steiner LA. HEXIM1 is an essential transcription regulator during human erythropoiesis. Blood. 2023 Dec 21;142(25):2198-2215. doi: 10.1182/blood.2022019495. PubMed PMID: 37738561; PubMed Central PMCID: PMC10733840.
Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development. 2023 Nov 1;150(21). doi: 10.1242/dev.202338. Epub 2023 Nov 8. PubMed PMID: 37938830; PubMed Central PMCID: PMC10651094.
Lim TY, Wilde BR, Thomas ML, Murphy KE, Vahrenkamp JM, Conway ME, Varley KE, Gertz J, Ayer DE. TXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic binding. PLoS Biol. 2023 Mar;21(3):e3001778. doi: 10.1371/journal.pbio.3001778. eCollection 2023 Mar. PubMed PMID: 36930677; PubMed Central PMCID: PMC10058090.

2021

Ruff GL, Murphy KE, Smith ZR, Vertino PM, Murphy PJ. Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation. BMC Cancer. 2021 Dec 18;21(1):1342. doi: 10.1186/s12885-021-09077-9. PubMed PMID: 34922480; PubMed Central PMCID: PMC8684129.

Murphy ZC, Murphy K, Myers J, Getman M, Couch T, Schulz VP, Lezon-Geyda K, Palumbo C, Yan H, Mohandas N, Gallagher PG, Steiner LA. Regulation of RNA polymerase II activity is essential for terminal erythroid maturation. Blood. 2021 Nov 4;138(18):1740-1756. doi: 10.1182/blood.2020009903. PubMed PMID: 34075391; PubMed Central PMCID: PMC8569412.

Nikitin Lab

2025

Flesken-Nikitin A, Pirtz MG, Ashe CS, Ellenson LH, Yemelyanova A, Cosgrove BD, Nikitin AY. Cell state dynamics during early stages of serous endometrial carcinoma. J Pathol. 2025 Nov;267(3):289-303. doi: 10.1002/path.6470. Epub 2025 Sep 9. PMID: 40923619.
Phuong DJ, Ralston CQ, Ezzat TM, Ashe CS, Armstrong AP, Flesken-Nikitin A, Yamulla RJ, Nikitin AY, Schimenti JC. Combinatorial organoid mutagenesis screen reveals gene constellations driving malignant transformation, pathology and chemosensitivity in high-grade serous ovarian carcinoma. bioRxiv [Preprint]. 2025 May 11:2025.03.10.642422. doi: 10.1101/2025.03.10.642422. PMID: 40654781; PMCID: PMC12248148.
Phuong DJ, Pirtz MG, Ralston CQ, Cosgrove BD, Schimenti JC, Flesken-Nikitin A, Nikitin AY. Aggressive Serous Carcinomas of the Female Reproductive Tract: Cancer-Prone Cell States and Genetic Drivers. Cancers (Basel). 2025 Feb 11;17(4):604. doi: 10.3390/cancers17040604. PMID: 40002199; PMCID: PMC11852459.

2024

Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Author Correction: Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Nov 20;15(1):10053. doi: 10.1038/s41467-024-54465-x. Erratum for: Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39567528; PMCID: PMC11579345.
Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39366996; PMCID: PMC11452611.

2023

Fu DJ, De Micheli AJ, Harlan BA, Bidarimath M, Ellenson LH, Cosgrove BD, Flesken-Nikitin A, Nikitin AY. Correction: Cells expressing PAX8 are the main source of homeostatic regeneration of adult mouse endometrial epithelium and give rise to serous endometrial carcinoma. Dis Model Mech. 2023 Oct 1;16(10):dmm050537. doi: 10.1242/dmm.050537. Epub 2023 Oct 23. Erratum for: doi: 10.1242/dmm.047035. PMID: 37870490; PMCID: PMC10618595.
Penfold L, Woods A, Pollard AE, Arizanova J, Pascual-Navarro E, Muckett PJ, Dore MH, Montoya A, Whilding C, Fets L, Mokochinski J, Constantin TA, Varela-Carver A, Leach DA, Bevan CL, Nikitin AY, Hall Z, Carling D. AMPK activation protects against prostate cancer by inducing a catabolic cellular state. Cell Rep. 2023 Apr 25;42(4):112396. doi: 10.1016/j.celrep.2023.112396. Epub 2023 Apr 15. PMID: 37061917; PMCID: PMC10576838.

O'Brien Lab

2025

Park CY, Barad A, Xu Y, Bender E, Thomas AK, Haller CM, Gu Z, Pressman EK, O’Brien KO. Dietary intake in East Asian and Northern European participants from the FeGenes study. Eur J Nutr. 2025 Jun 5;64(5):205. doi: 10.1007/s00394-025-03730-w. PMID: 40471375; PMCID: PMC12345378.
Weber DR, O’Brien KO, Ballester L, Rackovsky N, Graulich B, Schwartz GJ. Greater Urinary Calcium Excretion Is Associated With Diminished Bone Accrual in Youth With Type 1 Diabetes. J Clin Endocrinol Metab. 2025 May 19;110(6):e1802-e1810. doi: 10.1210/clinem/dgae660. PMID: 39302657; PMCID: PMC12086414.
Barad A, Xu Y, Bender E, Pressman EK, Gu Z, O’Brien KO. Differences in nonheme iron absorption between healthy adults of East Asian or Northern European ancestry from the Iron Genes in East Asian and Northern European Adults Study (FeGenes): A cross-sectional stable iron isotope study. Am J Clin Nutr. 2025 Feb;121(2):417-426. doi: 10.1016/j.ajcnut.2024.11.015. PMID: 39909711; PMCID: PMC11863334.
Barad A, Xu Y, Bender E, Pressman EK, Gu Z, O’Brien KO. Iron regulatory hormones and their associations with iron status biomarkers among healthy adults of East Asian or Northern European ancestry: A cross-sectional comparison from the Iron Genes in East Asian and Northern European Adults Study (FeGenes). Am J Clin Nutr. 2025 Feb;121(2):406-416. doi: 10.1016/j.ajcnut.2024.10.018. PMID: 39909710; PMCID: PMC11863331.
Barad A, Xu Y, Bender E, Kang W, Xu R, Gu Z, Pressman EK, O’Brien KO. Characterization of iron status biomarkers and hematological indices among young adults of East Asian or Northern European ancestry: A cross-sectional analysis from the Iron Genes in East Asian and Northern European Adults Study (FeGenes). Am J Clin Nutr. 2025 Feb;121(2):394-405. doi: 10.1016/j.ajcnut.2024.10.014. PMID: 39909709; PMCID: PMC11863323.

2024

Weber DR, O’Brien KO, Ballester L, Rackovsky N, Graulich B, Schwartz GJ. Greater urinary calcium excretion is associated with diminished bone accrual in youth with type 1 diabetes. J Clin Endocrinol Metab. 2024 Sep 20:dgae660. doi: 10.1210/clinem/dgae660. Epub ahead of print. PMID: 39302657.
Barad A, Clark AG, Pressman EK, O’Brien KO. Associations Between Genetically Predicted Iron Status and Cardiovascular Disease Risk: A Mendelian Randomization Study. J Am Heart Assoc. 2024 Jun 4;13(11):e034991. doi: 10.1161/JAHA.124.034991. Epub 2024 May 31. PMID: 38818967; PMCID: PMC11255641.
Gaffney-Stomberg E, Nakayama AT, Lutz LJ, McClung JP, O’Brien KO, Staab JS. Load carriage exercise increases calcium absorption and retention in healthy young women. J Bone Miner Res. 2024 Mar 4;39(1):39-49. doi: 10.1093/jbmr/zjad003. PMID: 38630876.
Archundia-Herrera MC, Nunes F, Barrios ID, Park CY, Bell RC, O’Brien KO. Development of a Database for the Estimation of Heme Iron and Nonheme Iron Content of Animal-Based Foods. Curr Dev Nutr. 2024 Mar 3;8(4):102130. doi: 10.1016/j.cdnut.2024.102130. PMID: 38545421; PMCID: PMC10963891.
O’Brien KO, Pressman EK. Reply to M Jefferds et al. Am J Clin Nutr. 2024 Jan;119(1):234-235. doi: 10.1016/j.ajcnut.2023.09.028. Epub 2023 Nov 27. PMID: 38176778; PMCID: PMC11347789.
Barad A, Guillet R, Pressman EK, Katzman PJ, Ganz T, Nemeth E, O’Brien KO. Placental ferroportin protein abundance is associated with neonatal erythropoietic activity and iron status in newborns at high risk for iron deficiency and anemia. Am J Clin Nutr. 2024 Jan;119(1):76-86. doi: 10.1016/j.ajcnut.2023.10.022. Epub 2023 Oct 27. PMID: 37890671; PMCID: PMC10808842.

2023

Evanchuk JL, Kozyrskyj A, Hanas N, Goruk S, Vaghef-Mehrabani E, Archundia-Herrera CM, O’Brien KO, Letourneau NL, Giesbrecht GF, Bell RC, Field CJ. Maternal Iron Status Is Dynamic Throughout Pregnancy and Might Predict Birth Outcomes in a Sex Dependent Manner: Results from the Alberta Pregnancy Outcomes and Nutrition (APrON) Cohort Study. J Nutr. 2023 Sep;153(9):2585-2597. doi: 10.1016/j.tjnut.2023.06.042. Epub 2023 Jun 29. PMID: 37393033.
O’Brien K, Wang Y. The Placenta: A Maternofetal Interface. Annu Rev Nutr. 2023 Aug 21;43:301-325. doi: 10.1146/annurev-nutr-061121-085246. PMID: 37603428.
Delaney KM, Barad A, Castillo LF, Hasund CM, Guillet R, Pressman EK, Katzman PJ, Ganz T, Nemeth E, O’Brien KO. Placental Erythroferrone and Erythropoietin mRNA Expression is not Associated with Maternal or Neonatal Iron Status in Adolescents Carrying Singletons and Adult Women Carrying Multiples. J Nutr. 2023 Jul;153(7):1950-1958. doi: 10.1016/j.tjnut.2023.05.023. Epub 2023 May 28. PMID: 37253412; PMCID: PMC10375499.
Kang W, Irvine C, Wang Y, Clark A, Gu Z, Pressman E, O’Brien KO. Hemoglobin distributions and prevalence of anemia in a multiethnic United States pregnant population. Am J Clin Nutr. 2023 Jun;117(6):1320-1330. doi: 10.1016/j.ajcnut.2023.01.022. Epub 2023 May 12. PMID: 37270292; PMCID: PMC10447485.

2022

Sangkhae V, Yu V, Coffey R, O’Brien KO, Ganz T, Nemeth E. Erythroferrone contributes to iron mobilization for embryo erythropoiesis in iron-deficient mouse pregnancies. Am J Hematol. 2022 Oct;97(10):1348-1358. doi: 10.1002/ajh.26680. Epub 2022 Aug 16. PMID: 36071577; PMCID: PMC9462668.
Cornes R, Sintes C, Peña A, Albin S, O’Brien KO, Abrams SA, Donangelo CM. Daily Intake of a Functional Synbiotic Yogurt Increases Calcium Absorption in Young Adult Women. J Nutr. 2022 Jul 6;152(7):1647-1654. doi: 10.1093/jn/nxac088. PMID: 35411924.
Wang Y, Guo X, Hong X, Wang G, Pearson C, Zuckerman B, Clark AG, O’Brien KO, Wang X, Gu Z. Association of mitochondrial DNA content, heteroplasmies and inter-generational transmission with autism. Nat Commun. 2022 Jul 1;13(1):3790. doi: 10.1038/s41467-022-30805-7. PMID: 35778412; PMCID: PMC9249801.
O’Brien KO. Maternal, fetal and placental regulation of placental iron trafficking. Placenta. 2022 Jul;125:47-53. doi: 10.1016/j.placenta.2021.12.018. Epub 2021 Dec 24. PMID: 34974896; PMCID: PMC9226198.
Delaney KM, Cao C, Guillet R, Pressman EK, O’Brien KO. Fetal iron uptake from recent maternal diet and the maternal RBC iron pool. Am J Clin Nutr. 2022 Apr 1;115(4):1069-1079. doi: 10.1093/ajcn/nqac020. PMID: 35102365; PMCID: PMC8971007.
Barad A, Guillet R, Pressman EK, Katzman PJ, Miller RK, Darrah TH, O’Brien KO. Placental Iron Content Is Lower than Previously Estimated and Is Associated with Maternal Iron Status in Women at Greater Risk of Gestational Iron Deficiency and Anemia. J Nutr. 2022 Mar 3;152(3):737-746. doi: 10.1093/jn/nxab416. PMID: 34875094.
Best CM, Sherwood R, Novotny JA, Zhang S, Pressman EK, O’Brien KO. Vitamin D kinetics in nonpregnant and pregnant women after a single oral dose of trideuterated vitamin D3. J Steroid Biochem Mol Biol. 2022 Feb;216:106034. doi: 10.1016/j.jsbmb.2021.106034. Epub 2021 Nov 26. PMID: 34843870; PMCID: PMC8749867.

2021

Kang W, Barad A, Clark AG, Wang Y, Lin X, Gu Z, O’Brien KO. Ethnic Differences in Iron Status. Adv Nutr. 2021 Oct 1;12(5):1838-1853. doi: 10.1093/advances/nmab035. PMID: 34009254; PMCID: PMC8483971.
Tussing-Humphreys L, LaBomascus B, O’Brien K, Nemeth E, Sangkhae V, Steffen AD, Castellanos K, DeMartelly V, Ruchob R, Welke L, Hemphill NO, Pezley L, McLeod A, Hirsch B, Elam G, Ferrans CE, Koenig MD. Prepregnancy Obesity Does Not Impact Placental Iron Trafficking. J Nutr. 2021 Sep 4;151(9):2646-2654. doi: 10.1093/jn/nxab191. PMID: 34132349; PMCID: PMC8417928.
Delaney KM, Guillet R, Pressman EK, Ganz T, Nemeth E, O’Brien KO. Umbilical Cord Erythroferrone Is Inversely Associated with Hepcidin, but Does Not Capture the Most Variability in Iron Status of Neonates Born to Teens Carrying Singletons and Women Carrying Multiples. J Nutr. 2021 Sep 4;151(9):2590-2600. doi: 10.1093/jn/nxab156. PMID: 34236433; PMCID: PMC8417932.
Rahmani R, Stevens E, Rackovsky N, O’Brien KO, Schwartz GJ, Weber DR. Female Sex and Obesity Are Risk Factors for Inadequate Calcium Intake in Youth With Type 1 Diabetes. Front Clin Diabetes Healthc. 2021 Sep;2:723855. doi: 10.3389/fcdhc.2021.723855. Epub 2021 Sep 6. PMID: 34713272; PMCID: PMC8547769.
Delaney KM, Guillet R, Pressman EK, Ganz T, Nemeth E, O’Brien KO. Serum Erythroferrone During Pregnancy Is Related to Erythropoietin but Does Not Predict the Risk of Anemia. J Nutr. 2021 Jul 1;151(7):1824-1833. doi: 10.1093/jn/nxab093. PMID: 33982118; PMCID: PMC8245876.
Kang W, Baer N, Ramsan M, Vermeylen F, Stoltzfus RJ, O’Brien KO. Iron supplementation in anemic Zanzibari toddlers is associated with greater loss in erythrocyte iron isotope enrichment. Am J Clin Nutr. 2021 Jul 1;114(1):330-337. doi: 10.1093/ajcn/nqab044. PMID: 33829247; PMCID: PMC8246609.
Wallace TC, Bailey RL, Lappe J, O’Brien KO, Wang DD, Sahni S, Weaver CM. Dairy intake and bone health across the lifespan: a systematic review and expert narrative. Crit Rev Food Sci Nutr. 2021;61(21):3661-3707. doi: 10.1080/10408398.2020.1810624. Epub 2020 Sep 14. PMID: 32924543.

Ophir Lab

2025

Basurto E, Ophir AG, Montoya B, Cano-Ramírez H, González-Flores O, Suárez-Rodríguez M, Hoffman K. Episodic memory and reproductive condition could independently influence the pair bond maintenance in the male prairie vole (Microtus ochrogaster): Ecological implications and translational relevance in the study of sub-clinical manifestations of schizophrenia. Behav Brain Res. 2025 Aug 24;492:115648. doi: 10.1016/j.bbr.2025.115648. Epub 2025 May 21. PMID: 40409376.

2024

Madrid JE, Pranic NM, Chu S, Bergstrom JJD, Singh R, Rabinovich J, Lopez KA, Ophir AG, Tschida KA. Effects of short-term isolation on social behaviors in prairie voles. PLoS One. 2024 Nov 11;19(11):e0313172. doi: 10.1371/journal.pone.0313172. PMID: 39527561; PMCID: PMC11554233.
Hiura LC, Lazaro VA, Ophir AG. Paternal absence and increased caregiving independently and interactively shape the development of male prairie voles at subadult and adult life stages. Horm Behav. 2024 Aug;164:105605. doi: 10.1016/j.yhbeh.2024.105605. Epub 2024 Jul 19. PMID: 39032207; PMCID: PMC11330720.
Sailer LL, Haghani A, Zoller JA, Li CZ, Ophir AG, Horvath S. Epigenetic aging studies of pair bonding in prairie voles. Sci Rep. 2024 Jul 29;14(1):17439. doi: 10.1038/s41598-024-67641-2. PMID: 39075111; PMCID: PMC11286801.
Forero SA, Liu S, Shetty N, Ophir AG. Re-wiring of the bonded brain: Gene expression among pair bonded female prairie voles changes as they transition to motherhood. Genes Brain Behav. 2024 Jun;23(3):e12906. doi: 10.1111/gbb.12906. PMID: 38861664; PMCID: PMC11166254.
Freeman AR, Arenas S, Lee DN, Singh B, Ophir AG. Characterization of oxytocin and vasopressin receptors in the Southern giant pouched rat and comparison to other rodents. Front Endocrinol (Lausanne). 2024 May 13;15:1390203. doi: 10.3389/fendo.2024.1390203. PMID: 38803478; PMCID: PMC11128605.
Sailer LL, Finton CJ, Patel PP, Bogdanowicz SM, Ophir AG. Dorsal CA1 lesions of the hippocampus impact mating tactics in prairie voles by shifting non-monogamous males’ use of space to resemble monogamous males. Front Behav Neurosci. 2024 Feb 26;18:1355807. doi: 10.3389/fnbeh.2024.1355807. PMID: 38468707; PMCID: PMC10925758.

2023

Forero SA, Ophir AG. Bonding against the odds: Male prairie vole response to the “widow effect” among females. Behav Processes. 2023 Nov;213:104968. doi: 10.1016/j.beproc.2023.104968. Epub 2023 Nov 19. PMID: 37984679.
Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O’Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science. 2023 Aug 11;381(6658):eabq5693. doi: 10.1126/science.abq5693. Epub 2023 Aug 11. PMID: 37561875; PMCID: PMC11180965.
Wu WY, Yiu E, Ophir AG, Smith DM. Effects of social context manipulation on dorsal and ventral hippocampal neuronal responses. Hippocampus. 2023 Jul;33(7):830-843. doi: 10.1002/hipo.23507. Epub 2023 Feb 15. PMID: 36789678; PMCID: PMC11127721.
Wallace KJ, Chun EK, Manns JR, Ophir AG, Kelly AM. A test of the social behavior network reveals differential patterns of neural responses to social novelty in bonded, but not non-bonded, male prairie voles. Horm Behav. 2023 Jun;152:105362. doi: 10.1016/j.yhbeh.2023.105362. Epub 2023 Apr 21. PMID: 37086574; PMCID: PMC10291480.
Forero SA, Sailer LL, Girčytė A, Madrid JE, Sullivan N, Ophir AG. Motherhood and DREADD manipulation of the nucleus accumbens weaken established pair bonds in female prairie voles. Horm Behav. 2023 May;151:105351. doi: 10.1016/j.yhbeh.2023.105351. Epub 2023 Mar 30. PMID: 37003159; PMCID: PMC10133177.
Hiura LC, Lazaro VA, Ophir AG. Plasticity in parental behavior and vasopressin: responses to co-parenting, pup age, and an acute stressor are experience-dependent. Front Behav Neurosci. 2023 Apr 24;17:1172845. doi: 10.3389/fnbeh.2023.1172845. PMID: 37168139; PMCID: PMC10164929.
Freeman AR, Lee DN, Allen JJ, Blank B, Jeffery D, Lerer A, Singh B, Southard T, Cheong SH, Ophir AG. Extreme plasticity of reproductive state in a female rodent. Curr Biol. 2023 Mar 27;33(6):R215-R216. doi: 10.1016/j.cub.2023.02.004. PMID: 36977379.

2022

Sailer LL, Park AH, Galvez A, Ophir AG. Lateral septum DREADD activation alters male prairie vole prosocial and antisocial behaviors, not partner preferences. Commun Biol. 2022 Nov 26;5(1):1299. doi: 10.1038/s42003-022-04274-z. PMID: 36435943; PMCID: PMC9701193.
Bentz EJ, Ophir AG. Chromosome-scale genome assembly of the African giant pouched rat (Cricetomys ansorgei) and evolutionary analysis reveals evidence of olfactory specialization. Genomics. 2022 Nov;114(6):110521. doi: 10.1016/j.ygeno.2022.110521. Epub 2022 Nov 8. PMID: 36351561.
Rice MA, Galindez SM, Garner JT, Ophir AG. Effects of social and environmental contexts on multi-male mating and mixed paternity in socially monogamous female prairie voles. R Soc Open Sci. 2022 Oct 5;9(10):220298. doi: 10.1098/rsos.220298. PMID: 36249338; PMCID: PMC9532998.
Sailer LL, Patel PP, Park AH, Moon J, Hanadari-Levy A, Ophir AG. Synergistic consequences of early-life social isolation and chronic stress impact coping and neural mechanisms underlying male prairie vole susceptibility and resilience. Front Behav Neurosci. 2022 Jul 25;16:931549. doi: 10.3389/fnbeh.2022.931549. PMID: 35957922; PMCID: PMC9358287.
Finton CJ, Ophir AG. Developmental exposure to intranasal vasopressin impacts adult prairie vole spatial memory. Psychoneuroendocrinology. 2022 Jul;141:105750. doi: 10.1016/j.psyneuen.2022.105750. Epub 2022 Mar 25. PMID: 35397260; PMCID: PMC9149121.
Lo B, Freeman AR, Singh B, Hanadari-Levy A, Berman J, Chaves A, Choudhry A, Ophir AG. Effects of a GnRH agonist on sex behavior in females of the southern giant pouched rat. Integr Comp Biol. 2022 May 19:icac037. doi: 10.1093/icb/icac037. Epub ahead of print. PMID: 35588370.
Prior NH, Bentz EJ, Ophir AG. Reciprocal processes of sensory perception and social bonding: an integrated social-sensory framework of social behavior. Genes Brain Behav. 2022 Mar;21(3):e12781. doi: 10.1111/gbb.12781. Epub 2021 Dec 14. PMID: 34905293; PMCID: PMC9744507.
Finton CJ, Kelly AM, Ophir AG. Support for the parental practice hypothesis: Subadult prairie voles exhibit similar behavioral and neural profiles when alloparenting kin and non-kin. Behav Brain Res. 2022 Jan 24;417:113571. doi: 10.1016/j.bbr.2021.113571. Epub 2021 Sep 6. PMID: 34499932; PMCID: PMC8578440.
Forero SA, Ophir AG. Multi-Level Effects Driving Cognitive and Behavioral Variability among Prairie Voles: Insights into Reproductive Decision-Making from Biological Levels of Organization. Brain Behav Evol. 2022;97(3-4):225-240. doi: 10.1159/000522109. Epub 2022 Jan 20. PMID: 35051922; PMCID: PMC9256755.

Osborne Lab

2025

Bergink V, Akbarian S, Byatt N, Chandra PS, Cirino N, Dazzan P, De Witte L, Di Florio A, Dolman C, Jones I, Kamperman A, Mahjani B, Meltzer-Brody S, Munk-Olsen T, Nagle-Yang S, Osborne LM, Rasgon N, Robakis T, Thippeswamy H, Vigod SN, Payne JL. Postpartum Psychosis and Bipolar Disorder: Review of Neurobiology and Expert Consensus Statement on classification. Biol Psychiatry. 2025 Oct 22:S0006-3223(25)01536-7. doi: 10.1016/j.biopsych.2025.10.016. Epub ahead of print. PMID: 41135771.
Osborne LM, Appelbaum P, Watson K, Yonkers K, Burnett-Zeigler I, Epperson CN, Monk C, Wisner KL. US Abortion Restrictions and the Neuropsychiatric Health of Pregnant Individuals and Families. JAMA Psychiatry. 2025 Oct 1;82(10):1025-1029. doi: 10.1001/jamapsychiatry.2025.1376. PMID: 40668571.
Solomonov N, Kerchner D, Dai Y, Kwon M, Callaghan DG, Schier MM, Zhang Y, Osborne LM, Benda NC. Prevalence and Trajectories of Perinatal Anxiety and Depression in a Large Urban Medical Center. JAMA Netw Open. 2025 Sep 2;8(9):e2533111. doi: 10.1001/jamanetworkopen.2025.33111. PMID: 40982279; PMCID: PMC12455385.
Temkin-Yu AB, Oh A, Siegel IE, Liu MX, Seewald MJ, Blicker E, Ayaz A, Hermann AD, Givrad S, Baez LM, Osborne LM, Green CM, Schier MM, Falk A, Bennett SM. A novel app-based cognitive behavioral perinatal skills program: A case series. Digit Health. 2025 Sep 29;11:20552076251382084. doi: 10.1177/20552076251382084. PMID: 41036437; PMCID: PMC12480806.
Abramowitz JS, Hellberg SN, Krasnow J, Friedman JB, Myers NS, Nestadt PS, Ojalehto HJ, Juel EK, Samuels J, Kimmel ME, Osborne LM, Storch EA, Nestadt G, Musci RJ. Prenatal obsessive beliefs predict postpartum obsessive-compulsive symptoms: a prospective study. Psychiatry Res. 2025 Sep;351:116620. doi: 10.1016/j.psychres.2025.116620. Epub 2025 Jun 30. PMID: 40628003; PMCID: PMC12321878.
Rast CE, Musci R, Abramowitz JS, Nestadt G, Nestadt P, Kimmel MC, Dibbs T, Osborne LM, Samuels J, Krasnow J, Storch EA. Psychometric evaluation of the Yale-Brown Obsessive-Compulsive Scale in pregnant women. Arch Womens Ment Health. 2025 Aug;28(4):919-926. doi: 10.1007/s00737-024-01548-9. Epub 2025 Jan 2. Erratum in: Arch Womens Ment Health. 2025 Aug;28(4):965. doi: 10.1007/s00737-025-01580-3. PMID: 39745521; PMCID: PMC12321150.
Abramowitz JS, Myers NS, Friedman JB, Juel EK, Nestadt G, Kimmel M, Osborne LM, Storch EA, Samuels J, Nestadt PS, Musci R. Psychometric properties of the OCI-4: a brief screening tool for perinatal obsessive-compulsive disorder. Arch Womens Ment Health. 2025 Aug;28(4):895-902. doi: 10.1007/s00737-024-01539-w. Epub 2024 Nov 30. PMID: 39613898; PMCID: PMC12303159.
Etyemez S, Mehta K, Iyer S, Özdemir İ, Osborne LM. Biomarkers of reproductive psychiatric disorders. Br J Psychiatry. 2025 Jun;226(6):352-368. doi: 10.1192/bjp.2025.134. Epub 2025 Jun 20. PMID: 40538358; PMCID: PMC12257282.
Osborne LM, Etyemez S, Pinna G, Alemani R, Standeven LR, Wang XQ, Payne JL. Correction: Neuroactive steroid biosynthesis during pregnancy predicts future postpartum depression: a role for the 3α and/or 3β-HSD neurosteroidogenic enzymes? Neuropsychopharmacology. 2025 May;50(6):1021. doi: 10.1038/s41386-025-02109-z. Erratum for: Neuropsychopharmacology. 2025 May;50(6):904-912. doi: 10.1038/s41386-025-02052-z. PMID: 40247014; PMCID: PMC12032098.
Okun ML, Payne JL, Osborne LM, Feliciano L, Lac A. Effects of Using a Smart Bassinet on the Mental Health of Military-Affiliated Pregnant Women: Protocol for a Randomized Controlled Sleep Health and Mood in Newly Expectant Military Mothers (SHINE) Trial. JMIR Res Protoc. 2025 Apr 10;14:e66439. doi: 10.2196/66439. PMID: 40209215; PMCID: PMC12022534.
Rast CE, Dibbs T, Pinciotti CM, Jagannathan N, Abramowitz JS, Kimmel MC, Musci R, Nestadt G, Nestadt P, Osborne LM, Samuels J, Storch EA. Psychometric properties of the postpartum thoughts and behaviors checklist. J Obsessive Compuls Relat Disord. 2025 Apr;45:100939. doi: 10.1016/j.jocrd.2025.100939. Epub 2025 Feb 19. PMID: 40831602; PMCID: PMC12360429.
Schoretsanitis G, Osborne LM, Sundström-Poromaa I, Wenzel ES, Payne JL, Barbui C, Gastaldon C, Deligiannidis KM. Peripartum allopregnanolone blood concentrations and depressive symptoms: a systematic review and individual participant data meta-analysis. Mol Psychiatry. 2025 Mar;30(3):1148-1160. doi: 10.1038/s41380-024-02747-7. Epub 2024 Nov 7. PMID: 39511449; PMCID: PMC11835716.
Hantsoo L, Osborne LM, Susser LC. Editorial: Psychiatric illness across the menstrual cycle. Front Psychiatry. 2025 Feb 12;16:1568088. doi: 10.3389/fpsyt.2025.1568088. PMID: 40012716; PMCID: PMC11862688.
Drexhage HA, Bergink V, Poletti S, Benedetti F, Osborne LM. Conventional and new immunotherapies for immune system dysregulation in postpartum mood disorders: comparisons to immune system dysregulations in bipolar disorder, major depression, and postpartum autoimmune thyroid disease. Expert Rev Clin Immunol. 2025 Feb;21(2):113-135. doi: 10.1080/1744666X.2024.2420053. Epub 2024 Oct 29. PMID: 39441185; PMCID: PMC11786996.
Surkan PJ, Park S, Sheng Z, Zaidi A, Atif N, Osborne LM, Rahman A, Malik A. Effects of a Prenatal Anxiety Randomized Controlled Trial Intervention on Infant Development in Pakistan. Acad Pediatr. 2025 Jan-Feb;25(1):102551. doi: 10.1016/j.acap.2024.07.018. Epub 2024 Aug 2. PMID: 39097000; PMCID: PMC11833752.
Temkin-Yu AB, Ayaz A, Blicker E, Liu MX, Oh A, Siegel IE, Seewald MJ, Hermann AD, Givrad S, Baez LM, Osborne LM, Green CM, Schier MM, Davis AM, Zhu S, Falk A, Bennett SM. Feasibility of a Mobile App-Based Cognitive-Behavioral Perinatal Skills Program: Protocol for Nonrandomized Pilot Trial. JMIR Res Protoc. 2025 Jan 28;14:e59461. doi: 10.2196/59461. PMID: 39874578; PMCID: PMC11815301.
Hart A, Weiss-Goldman N, Halpern J, Bennett F, White LA, Birndorf C, Van Nortwick N, Osborne LM, Robakis TK. Attachment classification and early adversity predict perinatal partial hospital treatment response. J Affect Disord. 2025 Jan 15;369:182-187. doi: 10.1016/j.jad.2024.09.139. Epub 2024 Sep 24. PMID: 39326587.

2024

Schoretsanitis G, Osborne LM, Sundström-Poromaa I, Wenzel ES, Payne JL, Barbui C, Gastaldon C, Deligiannidis KM. Peripartum allopregnanolone blood concentrations and depressive symptoms: a systematic review and individual participant data meta-analysis. Mol Psychiatry. 2024 Nov 7. doi: 10.1038/s41380-024-02747-7. Epub ahead of print. PMID: 39511449.
Barone JC, Ho A, Osborne LM, Eisenlohr-Moul TA, Morrow AL, Payne JL, Epperson CN, Hantsoo L. Luteal phase sertraline treatment of premenstrual dysphoric disorder (PMDD): Effects on markers of hypothalamic pituitary adrenal (HPA) axis activation and inflammation. Psychoneuroendocrinology. 2024 Nov;169:107145. doi: 10.1016/j.psyneuen.2024.107145. Epub 2024 Jul 24. PMID: 39096755; PMCID: PMC11381144.
Drexhage HA, Bergink V, Poletti S, Benedetti F, Osborne LM. Conventional and new immunotherapies for immune system dysregulation in postpartum mood disorders: comparisons to immune system dysregulations in bipolar disorder, major depression, and postpartum autoimmune thyroid disease. Expert Rev Clin Immunol. 2024 Oct 29:1-23. doi: 10.1080/1744666X.2024.2420053. Epub ahead of print. PMID: 39441185.
Standeven LR, Bajaj M, McEvoy K, Shirinian D, Voegtline K, Osborne LM, Payne JL, Hantsoo L. The link between childhood traumatic events and the continuum of premenstrual disorders. Front Psychiatry. 2024 Oct 9;15:1443352. doi: 10.3389/fpsyt.2024.1443352. PMID: 39444627; PMCID: PMC11496889.
Osborne LM, Monk C. Perinatal mental health: Research that moves the agenda forward. Semin Perinatol. 2024 Oct;48(6):151952. doi: 10.1016/j.semperi.2024.151952. Epub 2024 Jul 14. PMID: 39034178.
Hart A, Weiss-Goldman N, Halpern J, Bennett F, White LA, Birndorf C, Van Nortwick N, Osborne LM, Robakis TK. Attachment classification and early adversity predict perinatal partial hospital treatment response. J Affect Disord. 2024 Sep 24;369:182-187. doi: 10.1016/j.jad.2024.09.139. Epub ahead of print. PMID: 39326587.
Etyemez S, Mehta K, Tutino E, Zaidi A, Atif N, Rahman A, Malik A, Voegtline KM, Surkan PJ, Osborne LM. The immune phenotype of perinatal anxiety in an anxiety-focused behavioral intervention program in Pakistan. Brain Behav Immun. 2024 Aug;120:141-150. doi: 10.1016/j.bbi.2024.05.028. Epub 2024 May 21. PMID: 38777289.
Sha Q, Escobar Galvis ML, Madaj ZB, Keaton SA, Smart L, Edgerly YM, Anis E, Leach R, Osborne LM, Achtyes E, Brundin L. Dysregulated placental expression of kynurenine pathway enzymes is associated with inflammation and depression in pregnancy. Brain Behav Immun. 2024 Jul;119:146-153. doi: 10.1016/j.bbi.2024.03.042. Epub 2024 Mar 29. PMID: 38555986; PMCID: PMC11210184.
Son M, Riley LE, Staniczenko AP, Cron J, Yen S, Thomas C, Sholle E, Osborne LM, Lipkind HS. Nonadjuvanted Bivalent Respiratory Syncytial Virus Vaccination and Perinatal Outcomes. JAMA Netw Open. 2024 Jul 1;7(7):e2419268. doi: 10.1001/jamanetworkopen.2024.19268. PMID: 38976271; PMCID: PMC11231799.
DeMairo J, Rimsky L, Moses A, Birndorf C, Bellenbaum P, Van Nortwick N, Osborne LM, Robakis TK. Outcomes at the Motherhood Center: A Comparison of Virtual and On-Site Versions of a Specialized Perinatal Partial Hospitalization Program. Matern Child Health J. 2024 May;28(5):828-835. doi: 10.1007/s10995-023-03836-9. Epub 2023 Nov 15. PMID: 37964152.
Smirnova L, Modafferi S, Schlett C, Osborne LM, Payne JL, Sabunciyan S. Blood extracellular vesicles carrying brain-specific mRNAs are potential biomarkers for detecting gene expression changes in the female brain. Mol Psychiatry. 2024 Apr;29(4):962-973. doi: 10.1038/s41380-023-02384-6. Epub 2024 Jan 11. PMID: 38212371.
Weingarten SJ, Osborne LM. Review of the Assessment and Management of Perinatal Mood and Anxiety Disorders. Focus (Am Psychiatr Publ). 2024 Jan;22(1):16-24. doi: 10.1176/appi.focus.20230023. Epub 2024 Jan 12. PMID: 38694149; PMCID: PMC11058917.

2023

Carlini SV, Osborne LM, Deligiannidis KM. Current pharmacotherapy approaches and novel GABAergic antidepressant development in postpartum depression. Dialogues Clin Neurosci. 2023 Dec;25(1):92-100. doi: 10.1080/19585969.2023.2262464. Epub 2023 Oct 5. PMID: 37796239; PMCID: PMC10557560.
Hannan K, Sherer ML, Osborne LM. Vitamin D levels and anxiety symptomatology in pregnancy and the postpartum. Arch Womens Ment Health. 2023 Dec;26(6):857-861. doi: 10.1007/s00737-023-01358-5. Epub 2023 Aug 11. PMID: 37566124.
Osborne LM, Jan RK, Kulkarni J. Editorial: Highlights in women’s mental health 2021/22. Front Glob Womens Health. 2023 Nov 8;4:1323318. doi: 10.3389/fgwh.2023.1323318. PMID: 38025981; PMCID: PMC10664563.
Etyemez S, Miller KN, Voegtline KM, Özdemir İ, Standeven LR, Santovito LS, Pinna G, Payne JL, Osborne LM. Metabolites of progesterone in pregnancy: Associations with perinatal anxiety. Psychoneuroendocrinology. 2023 Oct;156:106327. doi: 10.1016/j.psyneuen.2023.106327. Epub 2023 Jun 29. PMID: 37423029; PMCID: PMC10530426.
Riddle JN, Jager LR, Sherer M, Pangtey M, Osborne LM. Anxiety in pregnancy and stress responsiveness: An exploratory study of heart rate variability, cortisol, and alpha-amylase in the third trimester. J Neuroendocrinol. 2023 Jul;35(7):e13238. doi: 10.1111/jne.13238. Epub 2023 Mar 3. PMID: 36866835.
Riddle JN, Yau B, Baller E, Bradshaw P, Leistikow N, Ross DA, Osborne LM. The Other Postpartum: Pregnancy Loss and Mental Illness. Biol Psychiatry. 2023 May 15;93(10):e31-e32. doi: 10.1016/j.biopsych.2023.01.003. Epub 2023 Mar 6. PMID: 36890043.
Sherer ML, Malik A, Osborne LM, Rowther AA, Zaidi A, Atif N, Rahman A, Kahloon LE, Salman M, Yenokyan G, Surkan PJ. Biological Mechanisms in Pregnant Women With Anxiety (Happy Mother-Healthy Baby Supplement Study): Protocol for a Longitudinal Mixed Methods Observational Study. JMIR Res Protoc. 2023 Apr 11;12:e43193. doi: 10.2196/43193. PMID: 37040167; PMCID: PMC10132042.
Hage B, Watson E, Shenai N, Osborne L, Hutner L, Waltner-Toews R, Gopalan P. A Peer-to-Peer, Longitudinal Reproductive Psychiatry Educational Curriculum for Obstetrics/Gynecology Residents. Acad Psychiatry. 2023 Feb;47(1):43-47. doi: 10.1007/s40596-022-01710-4. Epub 2022 Sep 20. PMID: 36127485.
Erdly C, Etyemez S, Standeven LR, Nagle-Yang S, Osborne LM. Setting Common Standards for Reproductive Psychiatry Education: Effectiveness of the National Curriculum in Reproductive Psychiatry. Acad Psychiatry. 2023 Feb;47(1):63-68. doi: 10.1007/s40596-022-01663-8. Epub 2022 Jun 1. PMID: 35648379.

2022

Bradshaw PJ, Baller EB, Riddle JN, Leistikow N, Ross DA, Osborne LM. From Forgotten to Ignored: Herstory of Involutional Melancholia, Menopause, and Cognition. Biol Psychiatry. 2022 Nov 1;92(9):e37-e39. doi: 10.1016/j.biopsych.2022.08.018. PMID: 36202544.
Sherer ML, Voegtline KM, Park HS, Miller KN, Shuffrey LC, Klein SL, Osborne LM. The immune phenotype of perinatal anxiety. Brain Behav Immun. 2022 Nov;106:280-288. doi: 10.1016/j.bbi.2022.09.005. Epub 2022 Sep 14. PMID: 36115543.
Osborne LM, Payne JL, Sherer ML, Sabunciyan S. Altered extracellular mRNA communication in postpartum depression is associated with decreased autophagy. Mol Psychiatry. 2022 Nov;27(11):4526-4535. doi: 10.1038/s41380-022-01794-2. Epub 2022 Sep 22. PMID: 36138128.
Leistikow N, Baller EB, Bradshaw PJ, Riddle JN, Ross DA, Osborne LM. Prescribing Sleep: An Overlooked Treatment for Postpartum Depression. Biol Psychiatry. 2022 Aug 1;92(3):e13-e15. doi: 10.1016/j.biopsych.2022.03.006. Epub 2022 Mar 16. PMID: 35400485; PMCID: PMC10243364.
Boland RJ, Dingle AD, Travis MJ, Osborne LM, Shapiro MA, Madaan V, Ahmed I. Using the Psychiatry Resident-In-Training Examination (PRITE) to Assess the Psychiatry Medical Knowledge Milestones in Psychiatry. Acad Psychiatry. 2022 Jun;46(3):331-337. doi: 10.1007/s40596-021-01537-5. Epub 2021 Oct 8. PMID: 34623622.
Pawluski JL, Apter G, Kulkarni J, Osborne LM. Editorial: Neurobiology of Peripartum Mental Illness. Front Glob Womens Health. 2022 May 27;3:888088. doi: 10.3389/fgwh.2022.888088. PMID: 35712234; PMCID: PMC9197121.
Hudepohl N, MacLean JV, Osborne LM. Perinatal Obsessive-Compulsive Disorder: Epidemiology, Phenomenology, Etiology, and Treatment. Curr Psychiatry Rep. 2022 Apr;24(4):229-237. doi: 10.1007/s11920-022-01333-4. Epub 2022 Apr 6. PMID: 35384553; PMCID: PMC10323687.
Standeven LR, Osborne LM, Betz JF, Yenokyan G, Voegtline K, Hantsoo L, Payne JL. Allopregnanolone and depression and anxiety symptoms across the peripartum: an exploratory study. Arch Womens Ment Health. 2022 Apr;25(2):521-526. doi: 10.1007/s00737-021-01186-5. Epub 2021 Oct 29. PMID: 34714413; PMCID: PMC9113043.

2021

Voegtline K, Payne JL, Standeven LR, Sundel B, Pangtey M, Osborne LM. Using the Penn State Worry Questionnaire in the Peripartum. J Womens Health (Larchmt). 2021 Dec;30(12):1761-1768. doi: 10.1089/jwh.2020.8669. Epub 2021 Jan 12. PMID: 33434445; PMCID: PMC8721499.
Osborne LM, Voegtline K, Standeven LR, Sundel B, Pangtey M, Hantsoo L, Payne JL. High worry in pregnancy predicts postpartum depression. J Affect Disord. 2021 Nov 1;294:701-706. doi: 10.1016/j.jad.2021.07.009. Epub 2021 Jul 19. PMID: 34343928; PMCID: PMC8442474.
Hutner LA, Yeaton-Massey A, Toscano M, Coulehan J, Hage B, Gopalan P, Doyle MA, Olgun M, Frew J, Nagle-Yang S, Osborne LM, Miller ES. Cultivating mental health education in obstetrics and gynecology: a call to action. Am J Obstet Gynecol MFM. 2021 Nov;3(6):100459. doi: 10.1016/j.ajogmf.2021.100459. Epub 2021 Aug 14. PMID: 34403822.
Standeven LR, Payne JL, Pangtey M, Osborne LM. Lack of psychotropic medication changes among mood disordered women across the peripartum period. Hum Psychopharmacol. 2021 Sep;36(5):e2786. doi: 10.1002/hup.2786. Epub 2021 Mar 7. PMID: 33682220; PMCID: PMC8416692.
Gross MS, Ju H, Osborne LM, Jelin EB, Sekar P, Jelin AC. Indeterminate Prenatal Ultrasounds and Maternal Anxiety: A Prospective Cohort Study. Matern Child Health J. 2021 May;25(5):802-812. doi: 10.1007/s10995-020-03042-x. Epub 2021 Jan 3. PMID: 33392932; PMCID: PMC8062287.
Standeven LR, Olson E, Leistikow N, Payne JL, Osborne LM, Hantsoo L. Polycystic Ovary Syndrome, Affective Symptoms, and Neuroactive Steroids: a Focus on Allopregnanolone. Curr Psychiatry Rep. 2021 Apr 21;23(6):36. doi: 10.1007/s11920-021-01244-w. PMID: 33881645; PMCID: PMC8060230.
Osborne LM, Kimmel MC, Surkan PJ. The Crisis of Perinatal Mental Health in the Age of Covid-19. Matern Child Health J. 2021 Mar;25(3):349-352. doi: 10.1007/s10995-020-03114-y. Epub 2021 Feb 4. PMID: 33543374; PMCID: PMC7861156.
Leistikow N, Smith MH, Payne JL, Osborne LM. Is Valproate Reasonable? Am J Psychiatry. 2021 Jan 1;178(1):99. doi: 10.1176/appi.ajp.2020.20030350. PMID: 33384011; PMCID: PMC8015434.

Permar Lab

2025

Connors MR, Karthigeyan KP, Fuller AS, Mitchell L, Preston H, Ananyev S, Crooks CM, Stanton R, Anderson DE, Permar SR. Specificity and functional humoral immune responses induced by the VBI-1501A eVLP HCMV gB vaccine compared to the gB/MF59 vaccine. Hum Vaccin Immunother. 2025 Dec;21(1):2564555. doi: 10.1080/21645515.2025.2564555. Epub 2025 Sep 24. PMID: 40990374; PMCID: PMC12461891.
McGinty EE, Bitton A, Permar SR. Medicaid Cuts and U.S. Children’s Health – Fixing a Broken System. N Engl J Med. 2025 Nov 6;393(18):1766-1769. doi: 10.1056/NEJMp2509878. Epub 2025 Nov 1. PMID: 41181905.
Obregon-Perko V, Awasthi A, Barfield R, Berendam SJ, Yagnik B, Styles T, Tharp G, Gupta PM, Mensah G, Neja M, Kumar M, Fray E, Bu F, Pollara J, Tuyishime M, Ferrari G, Siliciano JD, Siliciano RF, Mavigner M, Silvestri G, Amara RR, Bosinger S, Fouda GG, Permar SR, Chan C, Chahroudi A. Identifying correlates of viral rebound timing and viral control in SHIV-infected infant macaques after ART interruption. Sci Transl Med. 2025 Oct 29;17(822):eadq1965. doi: 10.1126/scitranslmed.adq1965. Epub 2025 Oct 29. PMID: 41160668.
Anronikov S, Meikle C, Milligan EC, Chen H, Mukherjee N, Bjornson Z, Gaudillière B, Jiang S, Permar SR, Van Rompay KKA, Nolan GP, De Paris K, McIlwain DR. Comparative single-cell immune responses in peripheral blood and lymph node of immunized SARS-CoV-2 challenged infant rhesus macaques. Front Immunol. 2025 Sep 15;16:1599408. doi: 10.3389/fimmu.2025.1599408. PMID: 41030442; PMCID: PMC12477255.
Giorgi EE, Abrahams MR, Fouda G, John-Stewart G, Goga A, Mullins JI, Permar SR, Janes HE, Martin TM. Characterization of Early Viral Populations in Infants Acquiring HIV Through Perinatal and Breastmilk Transmission: A Review of what is Currently Known and the Gaps that Need to be Addressed to Guide Passive HIV Immunization of Breastfeeding Infants. Curr HIV Res. 2025 Sep 4. doi: 10.2174/011570162X357975250902104402. Epub ahead of print. PMID: 40916416.
Hills LB, Bhat N, Hurst JH, Myers A, Burke TW, McClain MT, Petzold E, Rotta AT, Turner NA, Grifoni A, Weiskopf D, Dogariu Y, Fouda GG, Permar SR, Sette A, Woods CW, Kelly MS, Crotty S. Pediatric T cell and B cell responses to SARS-CoV-2 infection. JCI Insight. 2025 Sep 4;10(20):e196032. doi: 10.1172/jci.insight.196032. PMID: 40906527; PMCID: PMC12581660.
Fouda GG, Singh A, Nelson A, Janes H, Martin T, Levy O, Wu D, Zou F, Jean-Philippe P, De Paris K, Van Rompay KKA, Permar SR. Integration of Preclinical and Clinical Vaccine Safety and Immunogenicity Testing for Development of a Pediatric HIV Vaccine to Achieve Protective HIV Immunity Prior to Adolescence. Curr HIV Res. 2025 Aug 8. doi: 10.2174/011570162X366522250721113420. Epub ahead of print. PMID: 40798950.
Permar SR, Wilson PC. Evolving rare B cell lineages for an effective HIV vaccine. Science. 2025 Jul 31;389(6759):455-457. doi: 10.1126/science.adz6436. Epub 2025 Jul 31. PMID: 40743359.
Karthigeyan KP, Connors M, Binuya CR, Gross M, Fuller AS, Crooks CM, Wang H-Y, Sponholtz MR, Byrne PO, Herbek S, Andy C, Gerber LM, Campbell JD, Williams CA, Mitchell E, van der Maas L, Miller I, Yu D, Bottomley MJ, McLellan JS, Permar SR. A human cytomegalovirus prefusion-like glycoprotein B subunit vaccine elicits humoral immunity similar to that of postfusion gB in mice. J Virol. 2025 Jun 17;99(6):e0217824. doi: 10.1128/jvi.02178-24. Epub 2025 May 8. PMID: 40338082; PMCID: PMC12172439.
Williams CA, Murphy EA, Gross M, Herbek S, Mohammed I, Sukhu AC, Salvatore CM, Prabhu M, Johnston CD, Riley LE, Permar SR, Yang YJ. SARS-CoV-2 Vaccine-Elicited Antibody Responses in Human Milk. J Pediatric Infect Dis Soc. 2025 Jun 16;14(6):piae086. doi: 10.1093/jpids/piae086. PMID: 39238169; PMCID: PMC12399877.
Issah YA, Hu X, Isaac J, Shen X, Davis D, Ozorowski G, Sewall LM, Zhang S, Kang E, Vuong K, Dennis M, Chen JL, Ramos JM, Yasmeen A, Eudailey J, Cupo A, Weinbaum C, Gao H, Stanfield-Oakley S, Ferrari G, Klasse PJ, Fouda G, Hudgens M, Ward AB, Montefiori DC, Sanders RW, Moore JP, Van Rompay KKA, De Paris K, Permar SR, Nelson AN. Germline-targeting HIV Envelope SOSIP immunization more frequently elicits broadly-neutralizing antibody precursor responses in infant compared to juvenile rhesus macaques. bioRxiv [Preprint]. 2025 May 30:2025.05.27.656273. doi: 10.1101/2025.05.27.656273. PMID: 40501834; PMCID: PMC12154809.
Jiang D, Soo N, Tan CY, Dankwa S, Wang HY, Theriot BS, Xue K, Hill D, Ardeshir A, Bain JR, Heston SM, Hurst JH, Siddiqui NY, Van Rompay KKA, Cervantes-Barragan L, Smith JP, Song R, Roper J, Kelly MS, Hudgens MG, Paris K, Permar SR, Goswami R, Surana NK. Commensal bacteria inhibit viral infections via a tryptophan metabolite. bioRxiv [Preprint]. 2025 May 12:2024.04.21.589969. doi: 10.1101/2024.04.21.589969. PMID: 38659737; PMCID: PMC11042330.
Bahadir Z, Narayan P, Wolters R, Permar SR, Fouda G, Hessell AJ, Haigwood NL. Monoclonal Antibodies for Pediatric Viral Disease Prevention and Treatment. Pediatrics. 2025 May 1;155(5):e2024068690. doi: 10.1542/peds.2024-068690. PMID: 40174915.
Langel SN, Otero CE, Steppe JT, Williams CA, Travieso T, Chang J, Webster H, Williamson LE, Crowe JE Jr, Greenberg HB, Wu H, Hornik CP, Mansouri K, Edwards RJ, Stalls V, Acharya P, Blasi M, Permar SR. Breast milk delivery of an engineered dimeric IgA protects neonates against rotavirus. Mucosal Immunol. 2025 Apr;18(2):441-452. doi: 10.1016/j.mucimm.2025.01.002. Epub 2025 Jan 20. PMID: 39842610; PMCID: PMC11982437.
Alba C, Malhotra S, Horsfall S, Barnhart ME, Bekker A, Chapman K, Cunningham CK, Fast PE, Fouda GG, Freedberg KA, Goga A, Ghazaryan LR, Leroy V, Mann C, McCluskey MM, McFarland EJ, Muturi-Kioi V, Permar SR, Shapiro R, Sok D, Stranix-Chibanda L, Weinstein MC, Ciaranello AL, Dugdale CM. Cost-effectiveness of broadly neutralizing antibodies for HIV prophylaxis for infants born in settings with high HIV burdens. PLoS One. 2025 Mar 19;20(3):e0318940. doi: 10.1371/journal.pone.0318940. PMID: 40106399; PMCID: PMC11922280.
Wang HY, Taher H, Kreklywich CN, Schmidt KA, Scheef EA, Barfield R, Otero CE, Valencia SM, Zhang K, Callahan C, Monticolo F, Qiao Y, Gilbride RM, Crooks CM, Mirza A, Knight K, Moström MJ, Manuel TD, Sprehe L, Kendall S, Burgt NV, Kowalik TF, Barry PA, Hansen SG, Shu J, Tarantal AF, Chan C, Streblow DN, Picker LJ, Kaur A, Früh K, Permar SR, Malouli D. The pentameric complex is not required for congenital CMV transmission in seronegative rhesus macaques. Sci Transl Med. 2025 Mar 12;17(789):eadm8961. doi: 10.1126/scitranslmed.adm8961. Epub 2025 Mar 12. PMID: 40073152; PMCID: PMC12208562.
Stark A, Crooks CM, Permar SR, Weimer KED. Neonatal Cytomegalovirus Infection: Advocacy, Legislation, and Changing Practice. Clin Perinatol. 2025 Mar;52(1):115-132. doi: 10.1016/j.clp.2024.10.008. Epub 2024 Dec 21. PMID: 39892947.
Miller IG, Mahant AM, Jenks JA, Semmes EC, Rochat E, Herbek SL, Andy C, Rodgers NS, Pollara J, Gerber LM, Herold BC, Permar SR. Influence of Distinct Maternal Cytomegalovirus-Specific Neutralizing and Fc Receptor-Binding Responses on Congenital Cytomegalovirus Transmission in HIV-Exposed Neonates. Viruses. 2025 Feb 26;17(3):325. doi: 10.3390/v17030325. PMID: 40143253; PMCID: PMC11946089.
Serota DE, Crooks CM, McGinty EE, Permar SR, Riley L. Policy strategies for inclusion of pregnant and lactating women in vaccine research. Health Aff Sch. 2025 Feb 19;3(3):qxaf035. doi: 10.1093/haschl/qxaf035. PMID: 40065780; PMCID: PMC11891035.
Manuel T, Moström M, Crooks CM, Davalos A, Barfield R, Scheef E, Kendall S, Midkiff CC, Sprehe L, Trexler M, Boquet F, Shroyer M, Danner V, Doyle-Myers L, Weinbaum C, Mirza A, Lammi S, Otero C, Lee MR, Rogers LW, Granek J, Owzar K, Malouli D, Früh K, Kowalik T, Chan C, Permar SR, Blair RV, Kaur A. A nonhuman primate model mirrors human congenital cytomegalovirus infection and reveals a spectrum of vertical transmission outcomes. bioRxiv [Preprint]. 2025 Jan 21:2025.01.16.633406. doi: 10.1101/2025.01.16.633406. PMID: 40492197; PMCID: PMC12148051.
Permar SR, Schleiss MR, Plotkin SA. A vaccine against cytomegalovirus: how close are we? J Clin Invest. 2025 Jan 2;135(1):e182317. doi: 10.1172/JCI182317. PMID: 39744948; PMCID: PMC11684802.

2024

Karthigeyan KP, Binuya C, Vuong K, Permar SR, Nelson AN. Research on Maternal Vaccination for HIV Prevention. Clin Perinatol. 2024 Dec;51(4):769-782. doi: 10.1016/j.clp.2024.08.007. Epub 2024 Sep 11. PMID: 39487019; PMCID: PMC11531644.
Semmes EC, Nettere DR, Nelson AN, Hurst JH, Cain DW, Burt TD, Kurtzberg J, Reeves RK, Coyne CB, Fouda GG, Pollara J, Permar SR, Walsh KM. In utero human cytomegalovirus infection expands NK-like FcγRIII+ CD8+ T cells that mediate Fc antibody functions. J Clin Invest. 2024 Nov 12:e181342. doi: 10.1172/JCI181342. Epub ahead of print. PMID: 39531313.
Dankwa S, Kosman C, Dennis M, Giorgi EE, Vuong K, Pahountis I, Garza A, Binuya C, McCarthy J, Mayer BT, Ngo JT, Enemuo CA, Carnathan DG, Stanfield-Oakley S, Berendam SJ, Weinbaum C, Engelman K, Magnani DM, Chan C, Ferrari G, Silvestri G, Amara RR, Chahroudi A, Permar SR, Fouda GG, Goswami R. A novel HIV triple broadly neutralizing antibody (bNAb) combination-based passive immunization of infant rhesus macaques achieves durable protective plasma neutralization levels and mediates anti-viral effector functions. PLoS One. 2024 Nov 11;19(11):e0312411. doi: 10.1371/journal.pone.0312411. PMID: 39527587; PMCID: PMC11554116.
Jasset OJ, Lopez Zapana PA, Bahadir Z, Shook L, Dennis M, Gilbert E, Liu ZA, Yinger RV, Bald C, Bradford CG, Silfen AH, Klein SL, Pekosz A, Permar S, Konnikova L, Yonker LM, Lauffenburger D, Nelson A, Elovitz MA, Edlow AG. Enhanced placental antibody transfer efficiency with longer interval between maternal RSV vaccination and birth. Am J Obstet Gynecol. 2024 Nov 6:S0002-9378(24)01125-6. doi: 10.1016/j.ajog.2024.10.053. Epub ahead of print. PMID: 39515450.
Alwine J, Goodrum F, Banfield B, Bloom D, Britt WJ, Broadbent AJ, Campos SK, Casadevall A, Chan GC, Cliffe AR, Dermody T, Duprex P, Enquist LW, Frueh K, Geballe AP, Gaglia M, Goldstein S, Greninger AL, Gronvall GK, Jung JU, Kamil JP, Lakdawala S, Liu S-L, Luftig M, Moore JP, Moscona A, Neuman BW, Nikolich JŽ, O’Connor C, Pekosz A, Permar S, Pfeiffer J, Purdy J, Rasmussen A, Semler B, Smith GA, Stein DA, Van Doorslaer K, Weller SK, Whelan SPJ, Yurochko A. The harms of promoting the lab leak hypothesis for SARS-CoV-2 origins without evidence. J Virol. 2024 Sep 17;98(9):e0124024. doi: 10.1128/jvi.01240-24. Epub 2024 Aug 1. PMID: 39087765; PMCID: PMC11406950.
Sperling JB, Roth NEW, Welsh WE, McElvaine AT, Permar SR, Gbadegesin RA. Supporting students from underrepresented minority backgrounds in graduate school: A mixed-methods formative study to inform post-baccalaureate design. J Clin Transl Sci. 2024 Sep 16;8(1):e124. doi: 10.1017/cts.2024.590. PMID: 39345705; PMCID: PMC11428063.
Sponholtz MR, Byrne PO, Lee AG, Ramamohan AR, Goldsmith JA, McCool RS, Zhou L, Johnson NV, Hsieh CL, Connors M, Karthigeyan KP, Crooks CM, Fuller AS, Campbell JD, Permar SR, Maynard JA, Yu D, Bottomley MJ, McLellan JS. Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation. Proc Natl Acad Sci U S A. 2024 Sep 10;121(37):e2404250121. doi: 10.1073/pnas.2404250121. Epub 2024 Sep 4. PMID: 39231203; PMCID: PMC11406251.
Williams CA, Murphy EA, Gross M, Herbek S, Mohammed I, Sukhu AC, Salvatore C, Prabhu M, Riley LE, Permar SR, Yang YJ. SARS-CoV-2 Vaccine Elicited Antibody Responses in Human Milk. J Pediatric Infect Dis Soc. 2024 Sep 6:piae086. doi: 10.1093/jpids/piae086. Epub ahead of print. PMID: 39238169.
Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Conway JM, Chan C. Assessing the impact of autologous virus neutralizing antibodies on viral rebound time in postnatally SHIV-infected ART-treated infant rhesus macaques. Epidemics. 2024 Sep;48:100780. doi: 10.1016/j.epidem.2024.100780. Epub 2024 Jun 27. PMID: 38964130; PMCID: PMC11518701.
Nelson AN, Shen X, Vekatayogi S, Zhang S, Ozorowski G, Dennis M, Sewall LM, Milligan E, Davis D, Cross KA, Chen Y, van Schooten J, Eudailey J, Isaac J, Memon S, Weinbaum C, Gao H, Stanfield-Oakley S, Byrd A, Chutkan S, Berendam S, Cronin K, Yasmeen A, Alam S, LaBranche CC, Rogers K, Shirreff L, Cupo A, Derking R, Villinger F, Klasse PJ, Ferrari G, Williams WB, Hudgens MG, Ward AB, Montefiori DC, Van Rompay KKA, Wiehe K, Moore JP, Sanders RW, De Paris K, Permar SR. Immunization with germ line-targeting SOSIP trimers elicits broadly neutralizing antibody precursors in infant macaques. Sci Immunol. 2024 Aug 30;9(98):eadm7097. doi: 10.1126/sciimmunol.adm7097. Epub 2024 Aug 30. PMID: 39213340.
Hu X, Karthigeyan KP, Herbek S, Valencia SM, Jenks JA, Webster H, Miller IG, Connors M, Pollara J, Andy C, Gerber LM, Walter EB, Edwards KM, Bernstein DI, Hou J, Koch M, Panther L, Carfi A, Wu K, Permar SR. Human Cytomegalovirus mRNA-1647 Vaccine Candidate Elicits Potent and Broad Neutralization and Higher Antibody-Dependent Cellular Cytotoxicity Responses Than the gB/MF59 Vaccine. J Infect Dis. 2024 Aug 16;230(2):455-466. doi: 10.1093/infdis/jiad593. PMID: 38324766; PMCID: PMC11326847.
Woodyear S, Chandler TL, Kawagishi T, Lonergan TM, Patel VA, Williams CA, Permar SR, Ding S, Caddy SL. Chimeric Viruses Enable Study of Antibody Responses to Human Rotaviruses in Mice. Viruses. 2024 Jul 16;16(7):1145. doi: 10.3390/v16071145. PMID: 39066309; PMCID: PMC11281508.
Lantos PM, Gantt S, Janko M, Dionne F, Permar SR, Fowler K. A Geographically Weighted Cost-effectiveness Analysis of Newborn Cytomegalovirus Screening. Open Forum Infect Dis. 2024 Jun 7;11(6):ofae311. doi: 10.1093/ofid/ofae311. PMID: 38933739; PMCID: PMC11200186.
Dalapati T, Williams CA, Giorgi EE, Hurst JH, Herbek S, Chen JL, Kosman C, Rotta AT, Turner NA, Pulido N, Aquino JN, Pfeiffer TS, Rodriguez J, Fouda GG, Permar SR, Kelly MS. Immunogenicity of Monovalent mRNA-1273 and BNT162b2 Vaccines in Children <5 Years of Age. Pediatrics. 2024 Jun 1;153(6):e2024066190. doi: 10.1542/peds.2024-066190. PMID: 38548700; PMCID: PMC11153324.
Nelson A, Lam J, Permar SR, Abramson E. COVID-19 Research Delays Disproportionately Affected Pediatrician-Scientists from Backgrounds Under-Represented in Medicine. J Pediatr. 2024 Jun;269:113865. doi: 10.1016/j.jpeds.2023.113865. Epub 2023 Dec 5. PMID: 38061423; PMCID: PMC11096066.
Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu S-L, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O’Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A. Virology-the path forward. J Virol. 2024 Jan 23;98(1):e0179123. doi: 10.1128/jvi.01791-23. Epub 2024 Jan 3. Erratum in: J Virol. 2024 Mar 19;98(3):e0007424. doi: 10.1128/jvi.00074-24. PMID: 38168672; PMCID: PMC10804978.
Singh T, Miller IG, Venkatayogi S, Webster H, Heimsath HJ, Eudailey JA, Dudley DM, Kumar A, Mangan RJ, Thein A, Aliota MT, Newman CM, Mohns MS, Breitbach ME, Berry M, Friedrich TC, Wiehe K, O’Connor DH, Permar SR. Prior dengue virus serotype 3 infection modulates subsequent plasmablast responses to Zika virus infection in rhesus macaques. mBio. 2024 Mar 13;15(3):e0316023. doi: 10.1128/mbio.03160-23. Epub 2024 Feb 13. PMID: 38349142; PMCID: PMC10936420.
Wang HY, Li L, Nelson CS, Barfield R, Valencia S, Chan C, Muramatsu H, Lin PJC, Pardi N, An Z, Weissman D, Permar SR. Multivalent cytomegalovirus glycoprotein B nucleoside modified mRNA vaccines did not demonstrate a greater antibody breadth. NPJ Vaccines. 2024 Feb 20;9(1):38. doi: 10.1038/s41541-024-00821-3. PMID: 38378950; PMCID: PMC10879498.
Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu S-L, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O’Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A. Correction for Rasmussen et al., “Virology-the path forward”. J Virol. 2024 Mar 19;98(3):e0007424. doi: 10.1128/jvi.00074-24. Epub 2024 Feb 9. Erratum for: J Virol. 2024 Jan 23;98(1):e0179123. doi: 10.1128/jvi.01791-23. PMID: 38334328; PMCID: PMC10949460.

2023

Jiang D, Goswami R, Dennis M, Heimsath H, Kozlowski PA, Ardeshir A, Van Rompay KKA, De Paris K, Permar SR, Surana NK. Sutterella and its metabolic pathways positively correlate with vaccine-elicited antibody responses in infant rhesus macaques. Front Immunol. 2023 Dec 6;14:1283343. doi: 10.3389/fimmu.2023.1283343. PMID: 38124733; PMCID: PMC10731017.
Nettere D, Unnithan S, Rodgers N, Nohara J, Cray P, Berry M, Jones C, Armand L, Li SH, Berendam SJ, Fouda GG, Cain DW, Spence TN, Granek JA, Davenport CA, Edwards RJ, Wiehe K, Van Rompay KKA, Moody MA, Permar SR, Pollara J. Conjugation of HIV-1 envelope to hepatitis B surface antigen alters vaccine responses in rhesus macaques. NPJ Vaccines. 2023 Nov 24;8(1):183. doi: 10.1038/s41541-023-00775-y. PMID: 38001122; PMCID: PMC10673864.
Otero CE, Barfield R, Scheef E, Nelson CS, Rodgers N, Wang HY, Moström MJ, Manuel TD, Sass J, Schmidt K, Taher H, Papen C, Sprehe L, Kendall S, Davalos A, Barry PA, Früh K, Pollara J, Malouli D, Chan C, Kaur A, Permar SR. Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model. PLoS Pathog. 2023 Oct 23;19(10):e1011378. doi: 10.1371/journal.ppat.1011378. PMID: 37871009; PMCID: PMC10621917.
Valencia SM, Rochat E, Harnois MJ, Dennis M, Webster HS, Hora B, Kumar A, Wang HS, Li L, Freed D, Zhang N, An Z, Wang D, Permar SR. Vaccination with a replication-defective cytomegalovirus vaccine elicits a glycoprotein B-specific monoclonal antibody repertoire distinct from natural infection. NPJ Vaccines. 2023 Oct 10;8(1):154. doi: 10.1038/s41541-023-00749-0. PMID: 37816743; PMCID: PMC10564777.
Chandler TL, Yang A, Otero CE, Permar SR, Caddy SL. Protective mechanisms of nonneutralizing antiviral antibodies. PLoS Pathog. 2023 Oct 5;19(10):e1011670. doi: 10.1371/journal.ppat.1011670. PMID: 37796829; PMCID: PMC10553219.
Moström MJ, Yu S, Tran D, Saccoccio FM, Versoza CJ, Malouli D, Mirza A, Valencia S, Gilbert M, Blair RV, Hansen S, Barry P, Früh K, Jensen JD, Pfeifer SP, Kowalik TF, Permar SR, Kaur A. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. PLoS Pathog. 2023 Oct 5;19(10):e1011646. doi: 10.1371/journal.ppat.1011646. PMID: 37796819; PMCID: PMC10553354.
Gong Y, Moström M, Otero C, Valencia S, Tarantal AF, Kaur A, Permar SR, Chan C. Mathematical Modeling of Rhesus Cytomegalovirus Transplacental Transmission in Seronegative Rhesus Macaques. Viruses. 2023 Oct 1;15(10):2040. doi: 10.3390/v15102040. PMID: 37896817; PMCID: PMC10611067.
Mahant AM, Trejo FE, Aguilan JT, Sidoli S, Permar SR, Herold BC. Antibody attributes, Fc receptor expression, gestation and maternal SARS-CoV-2 infection modulate HSV IgG placental transfer. iScience. 2023 Aug 15;26(9):107648. doi: 10.1016/j.isci.2023.107648. PMID: 37670782; PMCID: PMC10475509.
Semmes EC, Miller IG, Rodgers N, Phan CT, Hurst JH, Walsh KM, Stanton RJ, Pollara J, Permar SR. ADCC-activating antibodies correlate with decreased risk of congenital human cytomegalovirus transmission. JCI Insight. 2023 Jul 10;8(13):e167768. doi: 10.1172/jci.insight.167768. PMID: 37427588; PMCID: PMC10371338.
Crooks CM, Chan C, Permar SR. Leveraging preclinical study designs to close gaps in vaccine development for perinatal pathogens. J Exp Med. 2023 Jul 3;220(7):e20230184. doi: 10.1084/jem.20230184. Epub 2023 Jun 8. PMID: 37289272; PMCID: PMC10250551.
Toor RK, Semmes EC, Walsh KM, Permar SR, Giulino-Roth L. Does congenital cytomegalovirus infection contribute to the development of acute lymphoblastic leukemia in children? Curr Opin Virol. 2023 Jun;60:101325. doi: 10.1016/j.coviro.2023.101325. Epub 2023 Apr 17. PMID: 37075577.
Ruel T, Penazzato M, Zech JM, Archary M, Cressey TR, Goga A, Harwell J, Landovitz RJ, Lain MG, Lallemant M, Namusoke-Magongo E, Mukui I, Permar SR, Prendergast AJ, Shapiro R, Abrams EJ. Novel Approaches to Postnatal Prophylaxis to Eliminate Vertical Transmission of HIV. Glob Health Sci Pract. 2023 Apr 28;11(2):e2200401. doi: 10.9745/GHSP-D-22-00401. PMID: 37116934; PMCID: PMC10141432.
Rosenberg YJ, Ordonez T, Khanwalkar US, Barnette P, Pandey S, Backes IM, Otero CE, Goldberg BS, Crowley AR, Leib DA, Shapiro MB, Jiang X, Urban LA, Lees J, Hessell AJ, Permar S, Haigwood NL, Ackerman ME. Evidence for the Role of a Second Fc-Binding Receptor in Placental IgG Transfer in Nonhuman Primates. mBio. 2023 Apr 25;14(2):e0034123. doi: 10.1128/mbio.00341-23. Epub 2023 Mar 22. PMID: 36946726; PMCID: PMC10127586.
Schleiss MR, Permar SR, John CC. What are the key pediatric public policy priorities as the COVID-19 pandemic persists? Pediatr Res. 2023 May;93(6):1451-1455. doi: 10.1038/s41390-023-02529-x. Epub 2023 Feb 25. PMID: 36841882; PMCID: PMC9958307.
Semmes EC, Permar SR. Human Cytomegalovirus Infection Primes Fetal Natural Killer Cells for Fc-Mediated Antiviral Defense. J Infect Dis. 2023 Mar 28;227(6):739-741. doi: 10.1093/infdis/jiac308. PMID: 35876548.
Hansen SG, Womack JL, Perez W, Schmidt KA, Marshall E, Iyer RF, Cleveland Rubeor H, Otero CE, Taher H, Vande Burgt NH, Barfield R, Randall KT, Morrow D, Hughes CM, Selseth AN, Gilbride RM, Ford JC, Caposio P, Tarantal AF, Chan C, Malouli D, Barry PA, Permar SR, Picker LJ, Früh K. Late gene expression-deficient cytomegalovirus vectors elicit conventional T cells that do not protect against SIV. JCI Insight. 2023 Mar 22;8(6):e164692. doi: 10.1172/jci.insight.164692. PMID: 36749635; PMCID: PMC10070102.
Milligan EC, Olstad K, Williams CA, Mallory M, Cano P, Cross KA, Munt JE, Garrido C, Lindesmith L, Watanabe J, Usachenko JL, Hopkins L, Immareddy R, Shaan Lakshmanappa Y, Elizaldi SR, Roh JW, Sammak RL, Pollard RE, Yee JL, Herbek S, Scobey T, Miehlke D, Fouda G, Ferrari G, Gao H, Shen X, Kozlowski PA, Montefiori D, Hudgens MG, Edwards DK, Carfi A, Corbett KS, Graham BS, Fox CB, Tomai M, Iyer SS, Baric R, Reader R, Dittmer DP, Van Rompay KKA, Permar SR, De Paris K. Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge 1 year later. Sci Transl Med. 2023 Mar;15(685):eadd6383. doi: 10.1126/scitranslmed.add6383. Epub 2023 Mar 1. PMID: 36454813; PMCID: PMC9765459.
Prabhu M, Yang YJ, Johnston CD, Murphy EA, Ketas TJ, Diaz-Tapia R, Jurkiewicz M, Racine-Brzostek S, Mohammed I, Sukhu AC, Singh S, Forlenza K, Iyer S, Yee J, Eng D, Marks K, Zhao Z, Klasse PJ, Permar S, Moore JP, Riley LE. Longitudinal antibody response kinetics following SARS-CoV-2 messenger RNA vaccination in pregnant and nonpregnant persons. Am J Obstet Gynecol MFM. 2023 Feb;5(2):100796. doi: 10.1016/j.ajogmf.2022.100796. Epub 2022 Nov 2. PMID: 36334723; PMCID: PMC9626404.
Sass J, Awasthi A, Obregon-Perko V, McCarthy J, Lloyd AL, Chahroudi A, Permar S, Chan C. A simple model for viral decay dynamics and the distribution of infected cell life spans in SHIV-infected infant rhesus macaques. Math Biosci. 2023 Feb;356:108958. doi: 10.1016/j.mbs.2022.108958. Epub 2022 Dec 22. PMID: 36567003; PMCID: PMC9918703.
Jenks JA, Amin S, Sponholtz MR, Kumar A, Wrapp D, Venkatayogi S, Tu JJ, Karthigeyan K, Valencia SM, Connors M, Harnois MJ, Hora B, Rochat E, McLellan JS, Wiehe K, Permar SR. A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus. PLoS Pathog. 2023 Jan 20;19(1):e1011107. doi: 10.1371/journal.ppat.1011107. PMID: 36662906; PMCID: PMC9891502.
Dugdale CM, Ufio O, Alba C, Permar SR, Stranix-Chibanda L, Cunningham CK, Fouda GG, Myer L, Weinstein MC, Leroy V, McFarland EJ, Freedberg KA, Ciaranello AL. Cost-effectiveness of broadly neutralizing antibody prophylaxis for HIV-exposed infants in sub-Saharan African settings. J Int AIDS Soc. 2023 Jan;26(1):e26052. doi: 10.1002/jia2.26052. PMID: 36604316; PMCID: PMC9816086.

2022

Singh T, Hwang KK, Miller AS, Jones RL, Lopez CA, Dulson SJ, Giuberti C, Gladden MA, Miller I, Webster HS, Eudailey JA, Luo K, Von Holle T, Edwards RJ, Valencia S, Burgomaster KE, Zhang S, Mangold JF, Tu JJ, Dennis M, Alam SM, Premkumar L, Dietze R, Pierson TC, Ooi EE, Lazear HM, Kuhn RJ, Permar SR, Bonsignori M. A Zika virus-specific IgM elicited in pregnancy exhibits ultrapotent neutralization. Cell. 2022 Dec 8;185(25):4826-4840.e17. doi: 10.1016/j.cell.2022.10.023. Epub 2022 Nov 18. PMID: 36402135; PMCID: PMC9742325.
Langel SN, Garrido C, Phan C, Travieso T, Kirshner H, DeMarco T, Ma ZM, Reader JR, Olstad KJ, Sammak RL, Shaan Lakshmanappa Y, Roh JW, Watanabe J, Usachenko J, Immareddy R, Pollard R, Iyer SS, Permar S, Miller LA, Van Rompay KKA, Blasi M. Dam-Infant Rhesus Macaque Pairs to Dissect Age-Dependent Responses to SARS-CoV-2 Infection. Immunohorizons. 2022 Dec 1;6(12):851-863. doi: 10.4049/immunohorizons.2200075. PMID: 36547390; PMCID: PMC10538284.
Anwar IJ, Ezekian B, DeLaura I, Manook M, Schroder P, Yoon J, Curfman V, Branum E, Messina J, Harnois M, Permar SR, Farris AB, Kwun J, Knechtle SJ. Addition of interleukin-6 receptor blockade to carfilzomib-based desensitization in a highly sensitized nonhuman primate model. Am J Transplant. 2022 Dec;22 Suppl 4(Suppl 4):1-11. doi: 10.1111/ajt.17208. PMID: 36239200; PMCID: PMC9722597.
Harnois MJ, Dennis M, Stöhr D, Valencia SM, Rodgers N, Semmes EC, Webster HS, Jenks JA, Barfield R, Pollara J, Chan C, Sinzger C, Permar SR. Characterization of Plasma Immunoglobulin G Responses in Elite Neutralizers of Human Cytomegalovirus. J Infect Dis. 2022 Nov 1;226(9):1667-1677. doi: 10.1093/infdis/jiac341. PMID: 35970817; PMCID: PMC10205896.
Mukhopadhyay S, Itell HL, Hartman E, Woodford E, Dhudasia MB, Steppe JT, Valencia S, Roark H, Wade KC, Weimer KED, Permar SR, Puopolo KM. Breast Milk and Saliva for Postnatal Cyto†megalovirus Screening among Very Low Birth Weight Infants. Pediatr Infect Dis J. 2022 Nov 1;41(11):904-910. doi: 10.1097/INF.0000000000003671. Epub 2022 Aug 23. PMID: 36102681.
Hu X, Wang HY, Otero CE, Jenks JA, Permar SR. Lessons from Acquired Natural Immunity and Clinical Trials to Inform Next-Generation Human Cytomegalovirus Vaccine Development. Annu Rev Virol. 2022 Sep 29;9(1):491-520. doi: 10.1146/annurev-virology-100220-010653. Epub 2022 Jun 15. PMID: 35704747; PMCID: PMC10154983.
Chen JL, Fries CN, Berendam SJ, Rodgers NS, Roe EF, Wu Y, Li SH, Jain R, Watts B, Eudailey J, Barfield R, Chan C, Moody MA, Saunders KO, Pollara J, Permar SR, Collier JH, Fouda GG. Self-assembling peptide nanofiber HIV vaccine elicits robust vaccine-induced antibody functions and modulates Fc glycosylation. Sci Adv. 2022 Sep 23;8(38):eabq0273. doi: 10.1126/sciadv.abq0273. Epub 2022 Sep 23. PMID: 36149967; PMCID: PMC9506727.
Smithgall MC, Murphy EA, Rand S, Sukhu A, Singh S, Schatz-Siemers N, Matrai C, Tu J, Salvatore CM, Prabhu M, Permar S, Riley LE, Robinson BD, Baergen RN, Yang YJ. Placental pathology, neonatal birth weight, and Apgar score in acute and distant SARS-CoV-2 infection. J Clin Transl Res. 2022 Sep 7;8(5):351-359. PMID: 36518545; PMCID: PMC9741934.
Permar SR, Kaur A, Fruh K. Derisking Human Cytomegalovirus Vaccine Clinical Development in Relevant Preclinical Models. J Infect Dis. 2022 Sep 4;226(4):563-565. doi: 10.1093/infdis/jiac131. PMID: 35415750; PMCID: PMC9441196.
Price Rapoza M, McElvaine A, Conroy MB, Okuyemi K, Rouphael N, Teach SJ, Widlansky M, Williams C, Permar SR; National R38 Consortium investigators. Early Outcomes of a New NIH Program to Support Research in Residency. Acad Med. 2022 Sep 1;97(9):1305-1310. doi: 10.1097/ACM.0000000000004643. Epub 2022 Mar 1. PMID: 35234717.
Yang L, Semmes EC, Ovies C, Megli C, Permar S, Gilner JB, Coyne CB. Innate immune signaling in trophoblast and decidua organoids defines differential antiviral defenses at the maternal-fetal interface. Elife. 2022 Aug 17;11:e79794. doi: 10.7554/eLife.79794. PMID: 35975985; PMCID: PMC9470165.
Semmes EC, Miller IG, Wimberly CE, Phan CT, Jenks JA, Harnois MJ, Berendam SJ, Webster H, Hurst JH, Kurtzberg J, Fouda GG, Walsh KM, Permar SR. Maternal Fc-mediated non-neutralizing antibody responses correlate with protection against congenital human cytomegalovirus infection. J Clin Invest. 2022 Aug 15;132(16):e156827. doi: 10.1172/JCI156827. PMID: 35763348; PMCID: PMC9374380.
De Paris K, Permar SR. Routine SARS-CoV-2 vaccination for all children. Immunol Rev. 2022 Aug;309(1):90-96. doi: 10.1111/imr.13108. Epub 2022 Jul 7. PMID: 35799475; PMCID: PMC9339529.
Nelson AN, Dennis M, Mangold JF, Li K, Saha PT, Cronin K, Cross KA, Kumar A, Mangan RJ, Shaw GM, Bar KJ, Haynes B, Moody AM, Munir Alam S, Pollara J, Hudgens MG, Van Rompay KKA, De Paris K, Permar SR. Leveraging antigenic seniority for maternal vaccination to prevent mother-to-child transmission of HIV-1. NPJ Vaccines. 2022 Jul 30;7(1):87. doi: 10.1038/s41541-022-00505-w. PMID: 35907918; PMCID: PMC9338948.
Dudley DM, Koenig MR, Stewart LM, Semler MR, Newman CM, Shepherd PM, Yamamoto K, Breitbach ME, Schotzko M, Kohn S, Antony KM, Qiu H, Tunga P, Anderson DM, Guo W, Dennis M, Singh T, Rybarczyk S, Weiler AM, Razo E, Mitzey A, Zeng X, Eickhoff JC, Mohr EL, Simmons HA, Fritsch MK, Mejia A, Aliota MT, Friedrich TC, Golos TG, Kodihalli S, Permar SR, O’Connor DH. Human immune globulin treatment controls Zika viremia in pregnant rhesus macaques. PLoS One. 2022 Jul 14;17(7):e0266664. doi: 10.1371/journal.pone.0266664. PMID: 35834540; PMCID: PMC9282477.
Berendam SJ, Nelson AN, Yagnik B, Goswami R, Styles TM, Neja MA, Phan CT, Dankwa S, Byrd AU, Garrido C, Amara RR, Chahroudi A, Permar SR, Fouda GG. Challenges and Opportunities of Therapies Targeting Early Life Immunity for Pediatric HIV Cure. Front Immunol. 2022 Jul 13;13:885272. doi: 10.3389/fimmu.2022.885272. PMID: 35911681; PMCID: PMC9325996.
Bilgilier C, Schneider M, Kührer K, Kilb N, Hartl R, Topakian T, Kastner MT, Herz T, Nelson CS, Permar SR, Roth G, Steininger C. Heterosubtypic, cross-reactive immunity to human Cytomegalovirus glycoprotein B. Clin Exp Immunol. 2022 Jun 11;208(2):245-254. doi: 10.1093/cei/uxac031. PMID: 35395673; PMCID: PMC9188346.
Tu JJ, Kumar A, Giorgi EE, Eudailey J, LaBranche CC, Martinez DR, Fouda GG, Moreau Y, Thomas A, Montefiori D, Gao F, Sagar M, Permar SR. Vertical HIV-1 Transmission in the Setting of Maternal Broad and Potent Antibody Responses. J Virol. 2022 Jun 8;96(11):e0023122. doi: 10.1128/jvi.00231-22. Epub 2022 May 10. PMID: 35536018; PMCID: PMC9175633.
Lucier A, Fong Y, Li SH, Dennis M, Eudailey J, Nelson A, Saunders K, Cunningham CK, McFarland E, McKinney R, Moody MA, LaBranche C, Montefiori D, Permar SR, Fouda GG. Frequent Development of Broadly Neutralizing Antibodies in Early Life in a Large Cohort of Children With Human Immunodeficiency Virus. J Infect Dis. 2022 May 16;225(10):1731-1740. doi: 10.1093/infdis/jiab629. PMID: 34962990; PMCID: PMC9113503.
Langel SN, Blasi M, Permar SR. Maternal immune protection against infectious diseases. Cell Host Microbe. 2022 May 11;30(5):660-674. doi: 10.1016/j.chom.2022.04.007. PMID: 35550669.
Vijayan KKV, Cross KA, Curtis AD 2nd, Van Rompay KKA, Pollara J, Fox CB, Tomai M, Hanke T, Fouda G, Hudgens MG, Permar SR, De Paris K. Early Post-Vaccination Gene Signatures Correlate With the Magnitude and Function of Vaccine-Induced HIV Envelope-Specific Plasma Antibodies in Infant Rhesus Macaques. Front Immunol. 2022 Apr 27;13:840976. doi: 10.3389/fimmu.2022.840976. PMID: 35572573; PMCID: PMC9094446.
Semmes EC, Li SH, Hurst JH, Yang Z, Niedzwiecki D, Fouda GG, Kurtzberg J, Walsh KM, Permar SR. Congenital Human Cytomegalovirus Infection Is Associated With Decreased Transplacental IgG Transfer Efficiency Due to Maternal Hypergammaglobulinemia. Clin Infect Dis. 2022 Apr 9;74(7):1131-1140. doi: 10.1093/cid/ciab627. PMID: 34260701; PMCID: PMC8994583.
Rouse DJ, Fette LM, Hughes BL, Saade GR, Dinsmoor MJ, Reddy UM, Pass R, Allard D, Mallett G, Clifton RG, Saccoccio FM, Permar SR, Gyamfi-Bannerman C, Varner MW, Goodnight WH, Tita ATN, Costantine MM, Swamy GK, Heyborne KD, Chien EK, Chauhan SP, El-Sayed YY, Casey BM, Parry S, Simhan HN, Napolitano PG, Macones GA; for the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network. Noninvasive Prediction of Congenital Cytomegalovirus Infection After Maternal Primary Infection. Obstet Gynecol. 2022 Mar 1;139(3):400-406. doi: 10.1097/AOG.0000000000004691. PMID: 35115450; PMCID: PMC8857032.
Gatta LA, Rochat E, Weber JM, Valencia S, Erkanli A, Dotters-Katz SK, Permar S, Hughes BL. Clinical factors associated with cytomegalovirus shedding among seropositive pregnant women. Am J Obstet Gynecol MFM. 2022 Mar;4(2):100560. doi: 10.1016/j.ajogmf.2021.100560. Epub 2022 Jan 4. PMID: 34990874; PMCID: PMC9942897.
Curtis AD 2nd, Saha PT, Dennis M, Berendam SJ, Ramasubramanian P, Cross KA, Alam SM, Ferrari G, Kozlowski PA, Fouda GG, Hudgens MG, Van Rompay KKA, Pollara J, Permar SR, De Paris K. Vaccine-Induced, High-Magnitude HIV Env-Specific Antibodies with Fc-Mediated Effector Functions Are Insufficient to Protect Infant Rhesus Macaques against Oral SHIV Infection. mSphere. 2022 Feb 23;7(1):e0083921. doi: 10.1128/msphere.00839-21. Epub 2022 Feb 23. PMID: 35196125; PMCID: PMC8865927.
Langel SN, Kelly FL, Brass DM, Nagler AE, Carmack D, Tu JJ, Travieso T, Goswami R, Permar SR, Blasi M, Palmer SM. E-cigarette and food flavoring diacetyl alters airway cell morphology, inflammatory and antiviral response, and susceptibility to SARS-CoV-2. Cell Death Discov. 2022 Feb 15;8(1):64. doi: 10.1038/s41420-022-00855-3. PMID: 35169120; PMCID: PMC8847558.
Nguyen-Tran H, Park SW, Messacar K, Dominguez SR, Vogt MR, Permar S, Permaul P, Hernandez M, Douek DC, McDermott AB, Metcalf CJE, Grenfell B, Spaulding AB. Enterovirus D68: a test case for the use of immunological surveillance to develop tools to mitigate the pandemic potential of emerging pathogens. Lancet Microbe. 2022 Feb;3(2):e83-e85. doi: 10.1016/S2666-5247(21)00312-8. Epub 2022 Jan 7. PMID: 35036969; PMCID: PMC8741221.

2021

Berendam SJ, Morgan-Asiedu PK, Mangan RJ, Li SH, Heimsath H, Luo K, Curtis AD 2nd, Eudailey JA, Fox CB, Tomai MA, Phillips B, Itell HL, Kunz E, Hudgens M, Cronin K, Wiehe K, Alam SM, Van Rompay KKA, De Paris K, Permar SR, Moody MA, Fouda GG. Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. PLoS One. 2021 Dec 31;16(12):e0256885. doi: 10.1371/journal.pone.0256885. PMID: 34972105; PMCID: PMC8719683.
Goswami R, Russell VS, Tu JJ, Thomas C, Hughes P, Kelly F, Langel SN, Steppe J, Palmer SM, Haystead T, Blasi M, Permar SR. Oral Hsp90 inhibitor SNX-5422 attenuates SARS-CoV-2 replication and dampens inflammation in airway cells. iScience. 2021 Dec 17;24(12):103412. doi: 10.1016/j.isci.2021.103412. Epub 2021 Nov 10. PMID: 34786537; PMCID: PMC8579697.
Permar S, Creech CB, Edwards KM, Walter EB. Proposals to Accelerate Novel Vaccine Development for Children. Pediatrics. 2021 Dec 10:e2021054593. doi: 10.1542/peds.2021-054593. Epub ahead of print. PMID: 34889454.
Obregon-Perko V, Bricker KM, Mensah G, Uddin F, Rotolo L, Vanover D, Desai Y, Santangelo PJ, Jean S, Wood JS, Connor-Stroud FC, Ehnert S, Berendam SJ, Liang S, Vanderford TH, Bar KJ, Shaw GM, Silvestri G, Kumar A, Fouda GG, Permar SR, Chahroudi A. Dynamics and origin of rebound viremia in SHIV-infected infant macaques following interruption of long-term ART. JCI Insight. 2021 Dec 8;6(23):e152526. doi: 10.1172/jci.insight.152526. PMID: 34699383; PMCID: PMC8675190.
Hurst JH, Heston SM, Chambers HN, Cunningham HM, Price MJ, Suarez L, Crew CG, Bose S, Aquino JN, Carr ST, Griffin SM, Smith SH, Jenkins K, Pfeiffer TS, Rodriguez J, DeMarco CT, De Naeyer NA, Gurley TC, Louzao R, Zhao C, Cunningham CK, Steinbach WJ, Denny TN, Lugo DJ, Moody MA, Permar SR, Rotta AT, Turner NA, Walter EB, Woods CW, Kelly MS. Severe Acute Respiratory Syndrome Coronavirus 2 Infections Among Children in the Biospecimens from Respiratory Virus-Exposed Kids (BRAVE Kids) Study. Clin Infect Dis. 2021 Nov 2;73(9):e2875-e2882. doi: 10.1093/cid/ciaa1693. PMID: 33141180; PMCID: PMC7665428.
Permar S, Creech CB, Edwards KM, Walter EB. Proposals to Accelerate Novel Vaccine Development for Children. Pediatrics. 2021 Oct 22;149(1):e2021054593. doi: 10.1542/peds.2021-054593. Epub ahead of print. PMID: 34686571; PMCID: PMC9645699.
Garrido C, Hurst JH, Lorang CG, Aquino JN, Rodriguez J, Pfeiffer TS, Singh T, Semmes EC, Lugo DJ, Rotta AT, Turner NA, Burke TW, McClain MT, Petzold EA, Permar SR, Moody MA, Woods CW, Kelly MS, Fouda GG. Asymptomatic or mild symptomatic SARS-CoV-2 infection elicits durable neutralizing antibody responses in children and adolescents. JCI Insight. 2021 Sep 8;6(17):e150909. doi: 10.1172/jci.insight.150909. PMID: 34228642; PMCID: PMC8492306.
Schleiss MR, John CC, Permar SR. Children are the key to the Endgame: A case for routine pediatric COVID vaccination. Vaccine. 2021 Sep 7;39(38):5333-5336. doi: 10.1016/j.vaccine.2021.08.005. Epub 2021 Aug 12. PMID: 34393021; PMCID: PMC8358829.
Webster H, Valencia S, Kumar A, Chan C, Dennis M, Roark H, Woods A, John S, Carfi A, Permar SR. Pre-existing immunity to cytomegalovirus in macaques influences human CMV vaccine responses in preclinical models. Vaccine. 2021 Sep 7;39(38):5358-5367. doi: 10.1016/j.vaccine.2021.08.011. Epub 2021 Aug 13. PMID: 34393017.
Fong Y, Permar SR, Tomaras GD. Four-parameter paired response curve for serial dilution assays. J Biopharm Stat. 2021 Sep 3;31(5):634-649. doi: 10.1080/10543406.2021.1931271. Epub 2021 Jun 7. PMID: 34097580; PMCID: PMC8570978.
Weimer KED, Roark H, Fisher K, Cotten CM, Kaufman DA, Bidegain M, Permar SR. Breast Milk and Saliva Lactoferrin Levels and Postnatal Cytomegalovirus Infection. Am J Perinatol. 2021 Aug;38(10):1070-1077. doi: 10.1055/s-0040-1701609. Epub 2020 Feb 18. PMID: 32069486; PMCID: PMC9851802.
Fries CN, Chen JL, Dennis ML, Votaw NL, Eudailey J, Watts BE, Hainline KM, Cain DW, Barfield R, Chan C, Moody MA, Haynes BF, Saunders KO, Permar SR, Fouda GG, Collier JH. HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth. Sci Rep. 2021 Jul 14;11(1):14494. doi: 10.1038/s41598-021-93702-x. PMID: 34262096; PMCID: PMC8280189.
Li M, Brokaw A, Furuta AM, Coler B, Obregon-Perko V, Chahroudi A, Wang HY, Permar SR, Hotchkiss CE, Golos TG, Rajagopal L, Adams Waldorf KM. Non-human Primate Models to Investigate Mechanisms of Infection-Associated Fetal and Pediatric Injury, Teratogenesis and Stillbirth. Front Genet. 2021 Jul 5;12:680342. doi: 10.3389/fgene.2021.680342. PMID: 34290739; PMCID: PMC8287178.
Marichannegowda MH, Mengual M, Kumar A, Giorgi EE, Tu JJ, Martinez DR, Romero-Severson EO, Li X, Feng L, Permar SR, Gao F. Different evolutionary pathways of HIV-1 between fetus and mother perinatal transmission pairs indicate unique immune selection in fetuses. Cell Rep Med. 2021 Jun 16;2(7):100315. doi: 10.1016/j.xcrm.2021.100315. PMID: 34337555; PMCID: PMC8324465.
Garrido C, Curtis AD 2nd, Dennis M, Pathak SH, Gao H, Montefiori D, Tomai M, Fox CB, Kozlowski PA, Scobey T, Munt JE, Mallory ML, Saha PT, Hudgens MG, Lindesmith LC, Baric RS, Abiona OM, Graham B, Corbett KS, Edwards D, Carfi A, Fouda G, Van Rompay KKA, De Paris K, Permar SR. SARS-CoV-2 vaccines elicit durable immune responses in infant rhesus macaques. Sci Immunol. 2021 Jun 15;6(60):eabj3684. doi: 10.1126/sciimmunol.abj3684. PMID: 34131024; PMCID: PMC8774290.
Wang HY, Valencia SM, Pfeifer SP, Jensen JD, Kowalik TF, Permar SR. Common Polymorphisms in the Glycoproteins of Human Cytomegalovirus and Associated Strain-Specific Immunity. Viruses. 2021 Jun 9;13(6):1106. doi: 10.3390/v13061106. PMID: 34207868; PMCID: PMC8227702.
Manook M, Flores WJ, Schmitz R, Fitch Z, Yoon J, Bae Y, Shaw B, Kirk A, Harnois M, Permar S, Farris AB, Magnani DM, Kwun J, Knechtle S. Measuring the Impact of Targeting FcRn-Mediated IgG Recycling on Donor-Specific Alloantibodies in a Sensitized NHP Model. Front Immunol. 2021 Jun 2;12:660900. doi: 10.3389/fimmu.2021.660900. PMID: 34149698; PMCID: PMC8207189.
Stark A, Cantrell S, Greenberg RG, Permar SR, Weimer KED. Long-term Outcomes after Postnatal Cytomegalovirus Infection in Low Birthweight Preterm Infants: A Systematic Review. Pediatr Infect Dis J. 2021 Jun 1;40(6):571-581. doi: 10.1097/INF.0000000000003072. PMID: 33902071.
McElvaine AT, Hawkins-Salsbury JA, Arora VM, Gladwin MT, Goldenring JR, Huston DP, Krakow D, Rhee K, Solway J, Steinman RA, Towler DA, Utz PJ, Yokoyama WM, Simpson RL, Muglia LJ, Permar SR, Gbadegesin RA. Innovations in MD-only physician-scientist training: experiences from the Burroughs Wellcome Fund physician-scientist institutional award initiative. J Clin Invest. 2021 May 17;131(10):e149948. doi: 10.1172/JCI149948. PMID: 33998594; PMCID: PMC8121502.
Mangold JF, Goswami R, Nelson AN, Martinez DR, Fouda GG, Permar SR. Maternal Intervention to Prevent Mother-to-Child Transmission of HIV: Moving Beyond Antiretroviral Therapy. Pediatr Infect Dis J. 2021 May 1;40(5S):S5-S10. doi: 10.1097/INF.0000000000002774. PMID: 34042904; PMCID: PMC9215267.
Chahroudi A, Permar S. Will We Have the Tools to Address a Reemergent Zika Virus Epidemic? Ann Intern Med. 2021 May;174(5):708-709. doi: 10.7326/M21-0397. Epub 2021 Feb 16. PMID: 33587689.
Kumar A, Giorgi EE, Tu JJ, Martinez DR, Eudailey J, Mengual M, Honnayakanahalli Marichannegowda M, Van Dyke R, Gao F, Permar SR. Mutations that confer resistance to broadly-neutralizing antibodies define HIV-1 variants of transmitting mothers from that of non-transmitting mothers. PLoS Pathog. 2021 Apr 2;17(4):e1009478. doi: 10.1371/journal.ppat.1009478. PMID: 33798244; PMCID: PMC8055002.
Fries CN, Curvino EJ, Chen JL, Permar SR, Fouda GG, Collier JH. Advances in nanomaterial vaccine strategies to address infectious diseases impacting global health. Nat Nanotechnol. 2021 Apr;16(4):1-14. doi: 10.1038/s41565-020-0739-9. Epub 2020 Aug 17. PMID: 32807876.
D’Agostino EM, Armstrong SC, Humphreys L, Coffman S, Sinclair G, Permar SR, Akinboyo IC. Symptomatic SARS-CoV-2 Transmission in Youth and Staff Attending Day Camps. Pediatrics. 2021 Apr;147(4):e2020042416. doi: 10.1542/peds.2020-042416. Epub 2021 Feb 3. PMID: 33536332.
Itell HL, Berenz A, Mangan RJ, Permar SR, Kaufman DA. Systemic and mucosal levels of lactoferrin in very low birth weight infants supplemented with bovine lactoferrin. Biochem Cell Biol. 2021 Feb;99(1):25-34. doi: 10.1139/bcb-2020-0238. Epub 2020 Aug 25. PMID: 32841570.
Kaufman DA, Berenz A, Itell HL, Conaway M, Blackman A, Nataro JP, Permar SR. Dose escalation study of bovine lactoferrin in preterm infants: getting the dose right. Biochem Cell Biol. 2021 Feb;99(1):7-13. doi: 10.1139/bcb-2020-0217. Epub 2020 Aug 26. PMID: 32846100.
Semmes EC, Chen JL, Goswami R, Burt TD, Permar SR, Fouda GG. Understanding Early-Life Adaptive Immunity to Guide Interventions for Pediatric Health. Front Immunol. 2021 Jan 21;11:595297. doi: 10.3389/fimmu.2020.595297. PMID: 33552052; PMCID: PMC7858666.
Berendam SJ, Styles TM, Morgan-Asiedu PK, Tenney D, Kumar A, Obregon-Perko V, Bar KJ, Saunders KO, Santra S, De Paris K, Tomaras GD, Chahroudi A, Permar SR, Amara RR, Fouda GG. Systematic Assessment of Antiviral Potency, Breadth, and Synergy of Triple Broadly Neutralizing Antibody Combinations against Simian-Human Immunodeficiency Viruses. J Virol. 2021 Jan 13;95(3):e01667-20. doi: 10.1128/JVI.01667-20. PMID: 33177194; PMCID: PMC7925105.

Place Lab

2025

Place NJ, Price PL, Henry ME. Two different immunoassays produced highly discordant results when used to measure anti-Müllerian hormone in feline blood serum and urine. J Vet Diagn Invest. 2025 Nov;37(6):927-932. doi: 10.1177/10406387251373083. Epub 2025 Sep 20. PMID: 40974248; PMCID: PMC12450206.
Pinn-Woodcock TL, Llanos-Soto SG, Ivanek R, Goodrich E, Frye E, Wells A, Mullen K, Arbittier E, Hughes L, Berryhill E, Brosnahan P, Buslinger L, Schnabel L, DeNotta S, Mallicote M, Peek S, Place NJ. Seasonal elevation in equine adrenocorticotropic hormone occurs throughout the contiguous United States and is influenced by latitude and age. J Am Vet Med Assoc. 2025 Aug 1;263(11):1380-1389. doi: 10.2460/javma.25.04.0223. PMID: 40749730.
Bovell RTM, Comizzoli P, Nagashima JB, Santiestevan J, Crosier AE, Place NJ. Anti-Müllerian hormone concentration measured before gonadotropin stimulation is associated with quality of subsequent ovarian response in the cheetah (Acinonyx jubatus) and domestic cat (Felis catus)†. Biol Reprod. 2025 Apr 13;112(4):754-766. doi: 10.1093/biolre/ioaf025. PMID: 39903683.

2024

Josefson CC, Fitzwater BM, Beltran RS, Costa DP, Fornara JH, Garland T Jr, Harris BN, Hinde K, Hood WR, Hunt E, Kenagy GJ, Liebl AL, Litmer AR, Lopes PC, Misra D, Meuti M, Place NJ, Powers LE, Saltzman W, Orr TJ. Balancing Act: An Interdisciplinary Exploration of Trade-offs in Reproducing Females. Integr Comp Biol. 2024 Dec 20;64(6):1734-1756. doi: 10.1093/icb/icae092. PMID: 38982258.
Place NJ, Peck DT. Testing the Adaptive Sterilization Hypothesis in Mice Inoculated with Chlamydia muridarum. Integr Comp Biol. 2024 Dec 20;64(6):1661-1666. doi: 10.1093/icb/icae010. PMID: 38587825.
Conley AJ, Berger T, Caruso CJ, Cotterman RF, Jones T, Christensen BW, Hollinshead FK, Place NJ. Population-based anti-Müllerian hormone reference intervals help define gonadal status in the bitch. J Am Vet Med Assoc. 2024 Sep 11:1-8. doi: 10.2460/javma.24.06.0405. Epub ahead of print. PMID: 39260407.
Josefson CC, Fitzwater BM, Beltran RS, Costa DP, Fornara JH, Garland T Jr, Harris BN, Hinde K, Hood WR, Hunt E, Kenagy GJ, Liebl AL, Litmer AR, Lopes PC, Misra D, Meuti M, Place NJ, Powers LE, Saltzman W, Orr TJ. Balancing Act: an Interdisciplinary Exploration of Trade-offs in Reproducing Females. Integr Comp Biol. 2024 Jul 9:icae092. doi: 10.1093/icb/icae092. Epub ahead of print. PMID: 38982258.
Place NJ, Peck DT. Testing the Adaptive Sterilization Hypothesis in mice inoculated with Chlamydia muridarum. Integr Comp Biol. 2024 Apr 8:icae010. doi: 10.1093/icb/icae010. Epub ahead of print. PMID: 38587825.

2023

Prieto JM, Carney PC, Smith SM, Miller ML, Rishniw M, Randolph JF, Salerno VJ, Lamb SV, Place NJ, Farace G, Peterson S, Peterson ME. Biological variation of serum thyrotropin and thyroid hormones concentrations determined at 8-week intervals for 1 year in clinically healthy cats. Vet Clin Pathol. 2023 Sep;52(3):493-502. doi: 10.1111/vcp.13251. Epub 2023 Aug 1. PMID: 37528445.
Brieño-Enríquez MA, Faykoo-Martinez M, Goben M, Grenier JK, McGrath A, Prado AM, Sinopoli J, Wagner K, Walsh PT, Lopa SH, Laird DJ, Cohen PE, Wilson MD, Holmes MM, Place NJ. Postnatal oogenesis leads to an exceptionally large ovarian reserve in naked mole-rats. Nat Commun. 2023 Feb 21;14(1):670. doi: 10.1038/s41467-023-36284-8. PMID: 36810851; PMCID: PMC9944903.

2022

McCormick SK, Holekamp KE, Smale L, Weldele ML, Glickman SE, Place NJ. Sex Differences in Spotted Hyenas. Cold Spring Harb Perspect Biol. 2022 Jun 14;14(6):a039180. doi: 10.1101/cshperspect.a039180. PMID: 34649923; PMCID: PMC9248831.
Buffenstein R, Amoroso V, Andziak B, Avdieiev S, Azpurua J, Barker AJ, Bennett NC, Brieño-Enríquez MA, Bronner GN, Coen C, Delaney MA, Dengler-Crish CM, Edrey YH, Faulkes CG, Frankel D, Friedlander G, Gibney PA, Gorbunova V, Hine C, Holmes MM, Jarvis JUM, Kawamura Y, Kutsukake N, Kenyon C, Khaled WT, Kikusui T, Kissil J, Lagestee S, Larson J, Lauer A, Lavrenchenko LA, Lee A, Levitt JB, Lewin GR, Lewis Hardell KN, Lin TD, Mason MJ, McCloskey D, McMahon M, Miura K, Mogi K, Narayan V, O’Connor TP, Okanoya K, O’Riain MJ, Park TJ, Place NJ, Podshivalova K, Pamenter ME, Pyott SJ, Reznick J, Ruby JG, Salmon AB, Santos-Sacchi J, Sarko DK, Seluanov A, Shepard A, Smith M, Storey KB, Tian X, Vice EN, Viltard M, Watarai A, Wywial E, Yamakawa M, Zemlemerova ED, Zions M, Smith ESJ. The naked truth: a comprehensive clarification and classification of current ‘myths’ in naked mole-rat biology. Biol Rev Camb Philos Soc. 2022 Feb;97(1):115-140. doi: 10.1111/brv.12791. Epub 2021 Sep 3. PMID: 34476892; PMCID: PMC9277573.

2021

Place NJ, Prado AM, Faykoo-Martinez M, Brieño-Enriquez MA, Albertini DF, Holmes MM. Germ cell nests in adult ovaries and an unusually large ovarian reserve in the naked mole-rat. Reproduction. 2021 Jan;161(1):89-98. doi: 10.1530/REP-20-0304. PMID: 33151901; PMCID: PMC7770031.

Ren Lab

2025

Favakeh A, Mokhtare A, Zhang H, Ren YA, Abbaspourrad A. On-chip oocyte cumulus removal using vibration-induced flow. Lab Chip. 2025 Oct 22;25(21):5551-5562. doi: 10.1039/d5lc00414d. PMID: 40977337.
Zhang H, Dhillon J, Soloway PD, Shui B, Lee S, Grenier JK, Munn PR, Ljungberg MC, Williams RB, Lanz RB, Liao YH, Ren YA. Semaphorin 3E-Plexin-D1 Pathway Downstream of the Luteinizing Hormone Surge Regulates Ovulation, Granulosa Cell Luteinization, and Ovarian Angiogenesis in Mice. Adv Sci (Weinh). 2025 Aug;12(29):e17163. doi: 10.1002/advs.202417163. Epub 2025 May 20. PMID: 40391781; PMCID: PMC12362816.
Zhang H, Lanz RB, Dhillon J, Soloway PD, Shui B, Ren YA. CCAAT/Enhancer-Binding Proteins α and β Regulate Ovulation and Gene Expression via Dose- and Stage-Dependent Mechanisms. Endocrinology. 2025 May 19;166(7):bqaf081. doi: 10.1210/endocr/bqaf081. PMID: 40294160; PMCID: PMC12086141.

2024

Chang WJ, Baker MS, Laritsky E, Gunasekara CJ, Maduranga U, Galliou JC, McFadden JW, Waltemyer JR, Berggren-Thomas B, Tate BN, Zhang H, Rosen BD, Van Tassell CP, Liu GE, Coarfa C, Ren YA, Waterland RA. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol. 2024 Jul 15;25(1):185. doi: 10.1186/s13059-024-03307-6. PMID: 39004763; PMCID: PMC11247883.
Mantri M, Zhang HH, Spanos E, Ren YA, De Vlaminck I. A spatiotemporal molecular atlas of the ovulating mouse ovary. Proc Natl Acad Sci U S A. 2024 Jan 30;121(5):e2317418121. doi: 10.1073/pnas.2317418121. Epub 2024 Jan 22. PMID: 38252830; PMCID: PMC10835069.

Rizzuto Lab

2025

Oh JH, Rizzuto G, Elkin R, Weistuch C, Norton L, Dveksler G, Deasy JO. Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients. Brief Funct Genomics. 2025 Jan 15;24. doi: 10.1093/bfgp/elaf004. PubMed PMID: 40257008; PubMed Central PMCID: PMC12010166.
Rizzuto G. B Cell Responses to the Placenta and Fetus. Annu Rev Pathol. 2025 Jan;20(1):33-58. doi: 10.1146/annurev-pathmechdis-111523-023459. Epub 2025 Jan 2. Review. PubMed PMID: 39264989; PubMed Central PMCID: PMC11912550.
Liu YL, Praiss AM, Chiang S, Devereaux K, Huang J, Rizzuto G, Al-Rawi D, Weigelt B, Jewell E, Abu-Rustum NR, Aghajanian C. Gestational trophoblastic neoplasm: Patient outcomes and clinical pearls from a multidisciplinary referral center. Gynecol Oncol. 2025 Jan;192:171-177. doi: 10.1016/j.ygyno.2024.12.009. Epub 2024 Dec 13. PubMed PMID: 39674133; PubMed Central PMCID: PMC11761376.

2023

Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight. 2023 Dec 8;8(23). doi: 10.1172/jci.insight.174976. PubMed PMID: 37934865; PubMed Central PMCID: PMC10795829.
Haber LA, Dhaliwal G, Lo L, Rizzuto G. Evaluating a low anion gap: A practical approach. Cleve Clin J Med. 2023 Oct 2;90(10):619-623. doi: 10.3949/ccjm.90a.23035. Review. PubMed PMID: 37783490; PubMed Central PMCID: PMC11924111.
Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M. A spatially resolved timeline of the human maternal-fetal interface. Nature. 2023 Jul;619(7970):595-605. doi: 10.1038/s41586-023-06298-9. Epub 2023 Jul 19. PubMed PMID: 37468587; PubMed Central PMCID: PMC10356615.
Glasner A, Rose SA, Sharma R, Gudjonson H, Chu T, Green JA, Rampersaud S, Valdez IK, Andretta ES, Dhillon BS, Schizas M, Dikiy S, Mendoza A, Hu W, Wang ZM, Chaudhary O, Xu T, Mazutis L, Rizzuto G, Quintanal-Villalonga A, Manoj P, de Stanchina E, Rudin CM, Pe’er D, Rudensky AY. Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. Nat Immunol. 2023 Jun;24(6):1020-1035. doi: 10.1038/s41590-023-01504-2. Epub 2023 May 1. PubMed PMID: 37127830; PubMed Central PMCID: PMC10232368.
Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities. bioRxiv. 2023 Apr 7;. doi: 10.1101/2023.04.07.535899. PubMed PMID: 37066405; PubMed Central PMCID: PMC10104109.
Lo WL, Kuhlmann M, Rizzuto G, Ekiz HA, Kolawole EM, Revelo MP, Andargachew R, Li Z, Tsai YL, Marson A, Evavold BD, Zehn D, Weiss A. A single-amino acid substitution in the adaptor LAT accelerates TCR proofreading kinetics and alters T-cell selection, maintenance and function. Nat Immunol. 2023 Apr;24(4):676-689. doi: 10.1038/s41590-023-01444-x. Epub 2023 Mar 13. PubMed PMID: 36914891; PubMed Central PMCID: PMC10063449.

2022

Rizzuto G, Erlebacher A. Trophoblast antigens, fetal blood cell antigens, and the paradox of fetomaternal tolerance. J Exp Med. 2022 May 2;219(5). doi: 10.1084/jem.20211515. Epub 2022 Apr 13. PubMed PMID: 35416936; PubMed Central PMCID: PMC9011327.
Rizzuto G, Brooks JF, Tuomivaara ST, McIntyre TI, Ma S, Rideaux D, Zikherman J, Fisher SJ, Erlebacher A. Establishment of fetomaternal tolerance through glycan-mediated B cell suppression. Nature. 2022 Mar;603(7901):497-502. doi: 10.1038/s41586-022-04471-0. Epub 2022 Mar 2. PubMed PMID: 35236989; PubMed Central PMCID: PMC9592526.

2021

Hirschhorn D, Betof Warner A, Maniyar R, Chow A, Mangarin LM, Cohen AD, Hamadene L, Rizzuto GA, Budhu S, Suek N, Liu C, Houghton AN, Merghoub T, Wolchok JD. Cyclophosphamide enhances the antitumor potency of GITR engagement by increasing oligoclonal cytotoxic T cell fitness. JCI Insight. 2021 Oct 22;6(20). doi: 10.1172/jci.insight.151035. PubMed PMID: 34676831; PubMed Central PMCID: PMC8564916.
Castel P, Dharmaiah S, Sale MJ, Messing S, Rizzuto G, Cuevas-Navarro A, Cheng A, Trnka MJ, Urisman A, Esposito D, Simanshu DK, McCormick F. RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity. Proc Natl Acad Sci U S A. 2021 Aug 17;118(33). doi: 10.1073/pnas.2103261118. PubMed PMID: 34380736; PubMed Central PMCID: PMC8379911.

Schimenti Lab

2025

Singh V, Schimenti JC. Relevance, strategies, and added value of mouse models in androgenetics. Andrology. 2025 Jul;13(5):1158-1169. doi: 10.1111/andr.13761. Epub 2024 Sep 19. PMID: 39300831.
James RC, Wang JK, Bhatt SR, Shadid SE, Phuong DJ, Schimenti JC. Embryonic Stem Cell-Specific Responses to DNA Replication Stress. bioRxiv [Preprint]. 2025 May 18:2025.05.16.654332. doi: 10.1101/2025.05.16.654332. PMID: 40463205; PMCID: PMC12132374.
Li L, Ding X, Sheft AP, Schimenti JC. WITHDRAWN: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development. bioRxiv [Preprint]. 2025 May 13:2024.02.26.582097. doi: 10.1101/2024.02.26.582097. PMID: 38463983; PMCID: PMC10925113.
Munisha M, Huang R, Khan J, Schimenti JC. Chronic replication stress-mediated genomic instability disrupts placenta development in mice. bioRxiv [Preprint]. 2025 May 12:2025.02.28.640689. doi: 10.1101/2025.02.28.640689. PMID: 40093167; PMCID: PMC11908151.
Phuong DJ, Ralston CQ, Ezzat TM, Ashe CS, Armstrong AP, Flesken-Nikitin A, Yamulla RJ, Nikitin AY, Schimenti JC. Combinatorial organoid mutagenesis screen reveals gene constellations driving malignant transformation, pathology and chemosensitivity in high-grade serous ovarian carcinoma. bioRxiv [Preprint]. 2025 May 11:2025.03.10.642422. doi: 10.1101/2025.03.10.642422. PMID: 40654781; PMCID: PMC12248148.
Li L, Gao J, Yi D, Sheft AP, Schimenti JC, Ding X. Scalable primordial germ cell-like-cell platform for functional genomics identifies epigenetic fertility modifiers. bioRxiv [Preprint]. 2025 May 2:2024.02.15.580543. doi: 10.1101/2024.02.15.580543. PMID: 38405756; PMCID: PMC10888945.
Phuong DJ, Pirtz MG, Ralston CQ, Cosgrove BD, Schimenti JC, Flesken-Nikitin A, Nikitin AY. Aggressive Serous Carcinomas of the Female Reproductive Tract: Cancer-Prone Cell States and Genetic Drivers. Cancers (Basel). 2025 Feb 11;17(4):604. doi: 10.3390/cancers17040604. PMID: 40002199; PMCID: PMC11852459.

2024

Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Author Correction: Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Nov 20;15(1):10053. doi: 10.1038/s41467-024-54465-x. Erratum for: Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39567528; PMCID: PMC11579345.
Flesken-Nikitin A, Ralston CQ, Fu DJ, De Micheli AJ, Phuong DJ, Harlan BA, Ashe CS, Armstrong AP, McKellar DW, Ghuwalewala S, Ellenson LH, Schimenti JC, Cosgrove BD, Nikitin AY. Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma. Nat Commun. 2024 Oct 5;15(1):8641. doi: 10.1038/s41467-024-52984-1. PMID: 39366996; PMCID: PMC11452611.
Singh V, Schimenti JC. Relevance, strategies, and added value of mouse models in androgenetics. Andrology. 2024 Sep 19. doi: 10.1111/andr.13761. Epub ahead of print. PMID: 39300831.
Gao J, Qin Y, Schimenti JC. Gene regulation during meiosis. Trends Genet. 2024 Apr;40(4):326-336. doi: 10.1016/j.tig.2023.12.006. Epub 2024 Jan 4. PMID: 38177041; PMCID: PMC11003842.

2023

Hung YH, Capeling M, Villanueva JW, Kanke M, Shanahan MT, Huang S, Cubitt R, Rinaldi VD, Schimenti JC, Spence JR, Sethupathy P. Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model. BMC Genomics. 2023 Oct 26;24(1):641. doi: 10.1186/s12864-023-09743-1. PMID: 37884859; PMCID: PMC10601309.
Williams RM, Bloom JC, Robertus CM, Recknagel AK, Putnam D, Schimenti JC, Zipfel WR. Practical strategies for robust and inexpensive imaging of aqueous-cleared tissues. J Microsc. 2023 Sep;291(3):237-247. doi: 10.1111/jmi.13213. Epub 2023 Jul 11. PMID: 37413663.
Ding X, Singh P, Schimenti K, Tran TN, Fragoza R, Hardy J, Orwig KE, Olszewska M, Kurpisz MK, Yatsenko AN, Conrad DF, Yu H, Schimenti JC. In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes. Proc Natl Acad Sci U S A. 2023 Jul 25;120(30):e2219925120. doi: 10.1073/pnas.2219925120. Epub 2023 Jul 17. PMID: 37459509; PMCID: PMC10372637.
Ding X, Schimenti JC. Female infertility from oocyte maturation arrest: assembling the genetic puzzle. EMBO Mol Med. 2023 Jun 7;15(6):e17729. doi: 10.15252/emmm.202317729. Epub 2023 Apr 19. PMID: 37073822; PMCID: PMC10245026.

2022

Schimenti JC, Huang R, Li L, James R. Genome Maintenance in Mammalian Stem Cells. Annu Rev Genet. 2022 Nov 30;56:145-164. doi: 10.1146/annurev-genet-072920-022154. Epub 2022 Aug 17. PMID: 35977408.
Fulton SL, Wenderski W, Lepack AE, Eagle AL, Fanutza T, Bastle RM, Ramakrishnan A, Hays EC, Neal A, Bendl J, Farrelly LA, Al-Kachak A, Lyu Y, Cetin B, Chan JC, Tran TN, Neve RL, Roper RJ, Brennand KJ, Roussos P, Schimenti JC, Friedman AK, Shen L, Blitzer RD, Robison AJ, Crabtree GR, Maze I. Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome. Nat Commun. 2022 Oct 26;13(1):6384. doi: 10.1038/s41467-022-34200-0. PMID: 36289231; PMCID: PMC9606253.
Rooney AM, Ayobami OO, Kelly NH, Schimenti JC, Ross FP, van der Meulen MCH. Bone mass and adaptation to mechanical loading are sexually dimorphic in adult osteoblast-specific ERα knockout mice. Bone. 2022 May;158:116349. doi: 10.1016/j.bone.2022.116349. Epub 2022 Feb 3. PMID: 35123146.

2021

Munisha M, Schimenti JC. Genome maintenance during embryogenesis. DNA Repair (Amst). 2021 Oct;106:103195. doi: 10.1016/j.dnarep.2021.103195. Epub 2021 Jul 29. PMID: 34358805.
Singh P, Fragoza R, Blengini CS, Tran TN, Pannafino G, Al-Sweel N, Schimenti KJ, Schindler K, Alani EA, Yu H, Schimenti JC. Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging. Nat Commun. 2021 Aug 18;12(1):5005. doi: 10.1038/s41467-021-25028-1. PMID: 34408140; PMCID: PMC8373927.
Ding X, Schimenti JC. Strategies to Identify Genetic Variants Causing Infertility. Trends Mol Med. 2021 Aug;27(8):792-806. doi: 10.1016/j.molmed.2020.12.008. Epub 2021 Jan 8. PMID: 33431240; PMCID: PMC8263794.
Gao P, Lyu Q, Ghanam AR, Lazzarotto CR, Newby GA, Zhang W, Choi M, Slivano OJ, Holden K, Walker JA 2nd, Kadina AP, Munroe RJ, Abratte CM, Schimenti JC, Liu DR, Tsai SQ, Long X, Miano JM. Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression. Genome Biol. 2021 Mar 16;22(1):83. doi: 10.1186/s13059-021-02304-3. PMID: 33722289; PMCID: PMC7962346.
Schimenti JC. Conditional surrender in one generation: determining the reproductive roles of mouse embryo lethal genes by embryo complementation. Biol Reprod. 2021 Jan 4;104(1):8-10. doi: 10.1093/biolre/ioaa193. PMID: 33057575.

Seandel Lab

2023

Luo Y, Yamada M, N’Tumba-Byn T, Asif H, Gao M, Hu Y, Marangoni P, Liu Y, Evans T, Rafii S, Klein OD, Voss HU, Hadjantonakis AK, Elemento O, Martin LA, Seandel M. SPRY4-dependent ERK negative feedback demarcates functional adult stem cells in the male mouse germline†. Biol Reprod. 2023 Oct 13;109(4):533-551. doi: 10.1093/biolre/ioad089. PMID: 37552049; PMCID: PMC10577279.
Yamada M, Luo Y, Seandel M. Viral Transduction of Mammalian Spermatogonial Stem Cells. Methods Mol Biol. 2023;2656:211-225. doi: 10.1007/978-1-0716-3139-3_12. PMID: 37249874.

Selvaraj Lab

2025

Koganti PP, Zhao AH, Kern MC, Fassinou ACR, Selvaraj V. STAR/STARD1: A mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy. Proc Natl Acad Sci U S A. 2025 Oct 14;122(41):e2508809122. doi: 10.1073/pnas.2508809122. Epub 2025 Oct 7. PMID: 41055982; PMCID: PMC12541442.
Zhao AH, Koganti PP, Qian M, Garcia A, O’Day P, Auchus RJ, Covey DF, Selvaraj V. Target validation uncouples TSPO from 19-Atriol-mediated inhibition of steroidogenesis and reveals true enzymatic targets. bioRxiv [Preprint]. 2025 Sep 25:2025.09.25.678677. doi: 10.1101/2025.09.25.678677. PMID: 41040383; PMCID: PMC12485943.
Smith CR, Tu LN, Koganti PP, Selvaraj V. TSPO deficiency reveals a novel role for porphyrins in regulating white adipose tissue lipid metabolism. bioRxiv [Preprint]. 2025 Sep 17:2025.09.14.676078. doi: 10.1101/2025.09.14.676078. PMID: 41000793; PMCID: PMC12458925.
Vijayan Pillai V, Koganti PP, Gurung S, Cheong SH, Selvaraj V. Transformed bovine trophoblast stem cell lines, characterization, gene editing and secretions. Biol Reprod. 2025 Sep 13:ioaf212. doi: 10.1093/biolre/ioaf212. Epub ahead of print. PMID: 40971496.
Koganti PP, Selvaraj V. Single cell resolution of neurosteroidogenesis in the murine brain: de novo biosynthesis. J Endocrinol. 2025 May 7;265(3):e240318. doi: 10.1530/JOE-24-0318. PMID: 40261711; PMCID: PMC12377410.
Koganti PP, Selvaraj V. Single cell resolution of neurosteroidogenesis in the murine brain: intermediary biosynthesis. J Endocrinol. 2025 May 7;265(3):e240333. doi: 10.1530/JOE-24-0333. PMID: 40261706; PMCID: PMC12413686.
Koganti PP, Zhao AH, Kern MC, Fassinou ACR, Selvaraj V. STAR/STARD1: a mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy. bioRxiv [Preprint]. 2025 Apr 10:2025.04.03.647084. doi: 10.1101/2025.04.03.647084. Update in: Proc Natl Acad Sci U S A. 2025 Oct 14;122(41):e2508809122. doi: 10.1073/pnas.2508809122. PMID: 40236021; PMCID: PMC11996515.

2024

Selvaraj V, Won E. Transforming aquaculture with insect-based feed: restraining factors. Anim Front. 2024 Sep 5;14(4):24-27. doi: 10.1093/af/vfae011. PMID: 39246843; PMCID: PMC11377066.
Schalich KM, Koganti PP, Castillo JM, Reiff OM, Cheong SH, Selvaraj V. The uterine secretory cycle: recurring physiology of endometrial outputs that setup the uterine luminal microenvironment. Physiol Genomics. 2024 Jan 1;56(1):74-97. doi: 10.1152/physiolgenomics.00035.2023. Epub 2023 Sep 11. PMID: 37694291.

2023

Sushadi PS, Kuwabara M, Maung EEW, Mohamad Mohtar MS, Sakamoto K, Selvaraj V, Asano A. Arresting calcium-regulated sperm metabolic dynamics enables prolonged fertility in poultry liquid semen storage. Sci Rep. 2023 Dec 8;13(1):21775. doi: 10.1038/s41598-023-48550-2. PMID: 38066036; PMCID: PMC10709635.

2022

Koganti PP, Tu LN, Selvaraj V. Functional metabolite reserves and lipid homeostasis revealed by the MA-10 Leydig cell metabolome. PNAS Nexus. 2022 Sep 27;1(4):pgac215. doi: 10.1093/pnasnexus/pgac215. PMID: 36714831; PMCID: PMC9802464.
Jimenez IA, Stilin AP, Morohaku K, Hussein MH, Koganti PP, Selvaraj V. Mitochondrial translocator protein deficiency exacerbates pathology in acute experimental ulcerative colitis. Front Physiol. 2022 Aug 19;13:896951. doi: 10.3389/fphys.2022.896951. PMID: 36060674; PMCID: PMC9437295.
Koganti PP, Zhao AH, Selvaraj V. Exogenous cholesterol acquisition signaling in LH-responsive MA-10 Leydig cells and in adult mice. J Endocrinol. 2022 Aug 17;254(3):187-199. doi: 10.1530/JOE-22-0043. PMID: 35900012; PMCID: PMC9840751.
Bishop CV, Selvaraj V, Townson DH, Pate JL, Wiltbank MC. History, insights, and future perspectives on studies into luteal function in cattle. J Anim Sci. 2022 Jul 1;100(7):skac143. doi: 10.1093/jas/skac143. PMID: 35772753; PMCID: PMC9246667.
Schalich KM, Selvaraj V. Contradictions on colostrum IgG levels and Brix values are real and can be explained. Response to letter by Lombard et al. (2022). J Anim Sci. 2022 Apr 1;100(4):skac120. doi: 10.1093/jas/skac120. PMID: 35483038; PMCID: PMC9049248.
Pillai VV, Kei TG, Gurung S, Das M, Siqueira LGB, Cheong SH, Hansen PJ, Selvaraj V. RhoA/ROCK signaling antagonizes bovine trophoblast stem cell self-renewal and regulates preimplantation embryo size and differentiation. Development. 2022 Apr 1;149(7):dev200115. doi: 10.1242/dev.200115. Epub 2022 Mar 31. PMID: 35297991.

2021

Pillai VV, Koganti PP, Kei TG, Gurung S, Butler WR, Selvaraj V. Efficient induction and sustenance of pluripotent stem cells from bovine somatic cells. Biol Open. 2021 Oct 15;10(10):bio058756. doi: 10.1242/bio.058756. Epub 2021 Nov 1. PMID: 34719702; PMCID: PMC8565620.
Schalich KM, Reiff OM, Nguyen BT, Lamb CL, Mondoza CR, Selvaraj V. Temporal kinetics of bovine mammary IgG secretion into colostrum and transition milk. J Anim Sci. 2021 May 1;99(5):skab083. doi: 10.1093/jas/skab083. PMID: 33715013; PMCID: PMC8139318.

Smith-Raska

2024

Richter F, Rutherford KD, Cooke AJ, Meshkati M, Eddy-Abrams V, Greene D, Kosowsky J, Park Y, Aggarwal S, Burke RJ, Chang W, Connors J, Giannone PJ, Hays T, Khattar D, Polak M, Senaldi L, Smith-Raska M, Sridhar S, Steiner L, Swanson JR, Tauber KA, Barbosa M, Guttmann KF, Turro E. A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease. Am J Kidney Dis. 2024 Jun;83(6):829-833. doi: 10.1053/j.ajkd.2023.12.011. Epub 2024 Jan 10. PMID: 38211685; PMCID: PMC11116050.

2021

Cullen SM, Hassan N, Smith-Raska M. Erratum to: Effects of noninherited ancestral genotypes on offspring phenotypes. Biol Reprod. 2021 Nov 15;105(5):1365. doi: 10.1093/biolre/ioab167. Erratum for: Biol Reprod. 2021 Sep 14;105(3):747-760. doi: 10.1093/biolre/ioab120. PMID: 34515296.
Cullen SM, Hassan N, Smith-Raska M. Effects of noninherited ancestral genotypes on offspring phenotypes†. Biol Reprod. 2021 Sep 14;105(3):747-760. doi: 10.1093/biolre/ioab120. Erratum in: Biol Reprod. 2021 Nov 15;105(5):1365. doi: 10.1093/biolre/ioab167. PMID: 34159361.

Smolka Lab

2025

Yang C, Du H, Lee GB, Uematsu M, He W, Doré E, Yu W, Sanford EJ, Smolka MB, Boilard E, Baskin JM, Hao L, Hu F. sPLA2-IIA modifies progranulin deficiency phenotypes in mouse models. Mol Neurodegener. 2025 Jun 17;20(1):72. doi: 10.1186/s13024-025-00863-8. PMID: 40528203; PMCID: PMC12175356.
Cao Y, Wang Y, Badar J, Palek M, Jaber K, Faça VM, Huang TC, Çelik E, Macurek L, Smolka MB. An ATM-PPM1D Circuit Controls the Processing and Restart of DNA Replication Forks. bioRxiv [Preprint]. 2025 May 15:2025.05.13.652823. doi: 10.1101/2025.05.13.652823. PMID: 40462982; PMCID: PMC12132398.
Smolka M, Comstock W, Navarro M, Maybee D, Rho Y, Wagner M, Wang Y. Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling. Res Sq [Preprint]. 2025 Mar 27:rs.3.rs-6220494. doi: 10.21203/rs.3.rs-6220494/v1. PMID: 40196009; PMCID: PMC11975022.
Comstock WJ, Navarro MV, Maybee DV, Rho Y, Wagner M, Wang Y, Smolka MB. Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling. bioRxiv [Preprint]. 2025 Mar 13:2024.12.16.628391. doi: 10.1101/2024.12.16.628391. PMID: 39764013; PMCID: PMC11702526.
Comstock WJ, Bhattarai S, Sanford EJ, Navarro MVAS, Smolka MB. Profiling Tel1 signaling reveals a non-canonical motif targeting DNA repair and telomere control machineries. J Biol Chem. 2025 Mar;301(3):108194. doi: 10.1016/j.jbc.2025.108194. Epub 2025 Jan 16. PMID: 39826692; PMCID: PMC11875207.
Hall PM, Mayse LA, Bai L, Smolka MB, Pugh BF, Wang MD. High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation. bioRxiv [Preprint]. 2025 Jan 4:2024.10.11.617876. doi: 10.1101/2024.10.11.617876. PMID: 39416127; PMCID: PMC11482950.

2024

Du H, Yang C, Nana AL, Seeley WW, Smolka M, Hu F. WITHDRAWN: Progranulin inhibits phospholipase sPLA2-IIA to control neuroinflammation. bioRxiv [Preprint]. 2024 Dec 13:2023.04.06.535844. doi: 10.1101/2023.04.06.535844. Update in: Mol Neurodegener. 2025 Jun 17;20(1):72. doi: 10.1186/s13024-025-00863-8. PMID: 37066328; PMCID: PMC10104136.
Wan M, Minelli ME, Zhao Q, Marshall S, Yu H, Smolka M, Mao Y. Phosphoribosyl modification of poly-ubiquitin chains at the Legionella-containing vacuole prohibiting autophagy adaptor recognition. Nat Commun. 2024 Aug 30;15(1):7481. doi: 10.1038/s41467-024-51273-1. PMID: 39214972; PMCID: PMC11364841.
Cao X, Huang S, Wagner MM, Cho YT, Chiu DC, Wartchow KM, Lazarian A, McIntire LB, Smolka MB, Baskin JM. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization. Nat Cell Biol. 2024 Oct;26(10):1804-1816. doi: 10.1038/s41556-024-01495-8. Epub 2024 Aug 29. PMID: 39209962; PMCID: PMC11559143.
Marshall S, Navarro MVAS, Ascenҫão CFR, Dibitetto D, Smolka MB. In-depth mapping of DNA-PKcs signaling uncovers noncanonical features of its kinase specificity. J Biol Chem. 2024 Aug;300(8):107513. doi: 10.1016/j.jbc.2024.107513. Epub 2024 Jun 28. PMID: 38945450; PMCID: PMC11327452.
Xie B, Sanford EJ, Hung SH, Wagner M, Heyer WD, Smolka MB. Multi-step control of homologous recombination via Mec1/ATR suppresses chromosomal rearrangements. EMBO J. 2024 Jul;43(14):3027-3043. doi: 10.1038/s44318-024-00139-9. Epub 2024 Jun 5. PMID: 38839993; PMCID: PMC11251156.
Ascenção C, Sims JR, Dziubek A, Comstock W, Fogarty EA, Badar J, Freire R, Grimson A, Weiss RS, Cohen PE, Smolka MB. A TOPBP1 allele causing male infertility uncouples XY silencing dynamics from sex body formation. Elife. 2024 Feb 23;12:RP90887. doi: 10.7554/eLife.90887. PMID: 38391183; PMCID: PMC10942628.
Horan TS, Ascenção CFR, Mellor C, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in double strand break repair processing, but not crossover formation during prophase I of meiosis in male mice. PLoS Genet. 2024 Feb 20;20(2):e1011175. doi: 10.1371/journal.pgen.1011175. PMID: 38377115; PMCID: PMC10906868.

2023

Ferreira GA, Thomé CH, Izumi C, Grassi ML, Lanfredi GP, Smolka M, Faça VM, Candido Dos Reis FJ. Proteomic analysis of exosomes secreted during the epithelial-mesenchymal transition and potential biomarkers of mesenchymal high-grade serous ovarian carcinoma. J Ovarian Res. 2023 Nov 29;16(1):232. doi: 10.1186/s13048-023-01304-0. PMID: 38031074; PMCID: PMC10685605.
Smolka MB, Lammerding J. ATR takes a crack at the nuclear envelope. Mol Cell. 2023 Oct 19;83(20):3588-3590. doi: 10.1016/j.molcel.2023.09.031. PMID: 37863026.
Ho B, Sanford EJ, Loll-Krippleber R, Torres NP, Smolka MB, Brown GW. Mec1-independent activation of the Rad53 checkpoint kinase revealed by quantitative analysis of protein localization dynamics. Elife. 2023 Jun 6;12:e82483. doi: 10.7554/eLife.82483. PMID: 37278514; PMCID: PMC10259420.

2022

Dibitetto D, Marshall S, Sanchi A, Liptay M, Badar J, Lopes M, Rottenberg S, Smolka MB. DNA-PKcs promotes fork reversal and chemoresistance. Mol Cell. 2022 Oct 20;82(20):3932-3942.e6. doi: 10.1016/j.molcel.2022.08.028. Epub 2022 Sep 20. PMID: 36130596; PMCID: PMC9588680.
Cao X, Shami Shah A, Sanford EJ, Smolka MB, Baskin JM. Proximity Labeling Reveals Spatial Regulation of the Anaphase-Promoting Complex/Cyclosome by a Microtubule Adaptor. ACS Chem Biol. 2022 Sep 16;17(9):2605-2618. doi: 10.1021/acschembio.2c00527. Epub 2022 Aug 11. PMID: 35952650; PMCID: PMC9933862.
Bell ES, Shah P, Zuela-Sopilniak N, Kim D, Varlet AA, Morival JLP, McGregor AL, Isermann P, Davidson PM, Elacqua JJ, Lakins JN, Vahdat L, Weaver VM, Smolka MB, Span PN, Lammerding J. Low lamin A levels enhance confined cell migration and metastatic capacity in breast cancer. Oncogene. 2022 Sep;41(36):4211-4230. doi: 10.1038/s41388-022-02420-9. Epub 2022 Jul 27. PMID: 35896617; PMCID: PMC9925375.
Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Hum Mol Genet. 2022 Aug 25;31(17):2899-2917. doi: 10.1093/hmg/ddac082. PMID: 35394024; PMCID: PMC9433724.
Sanford EJ, Smolka MB. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics. 2022 Aug;22(15-16):e2200064. doi: 10.1002/pmic.202200064. Epub 2022 Jun 26. PMID: 35695711; PMCID: PMC9950963.
Sims JR, Faça VM, Pereira C, Ascenção C, Comstock W, Badar J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. Phosphoproteomics of ATR signaling in mouse testes. Elife. 2022 Feb 8;11:e68648. doi: 10.7554/eLife.68648. PMID: 35133275; PMCID: PMC8824463.
Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. Elife. 2022 Feb 8;11:e68677. doi: 10.7554/eLife.68677. PMID: 35133274; PMCID: PMC8824475.

2021

Sanford EJ, Smolka MB. Fe-NTA Microcolumn Purification of Phosphopeptides from Immunoprecipitation (IP) Eluates for Mass Spectrometry Analysis. Bio Protoc. 2021 Aug 5;11(15):e4113. doi: 10.21769/BioProtoc.4113. PMID: 34458407; PMCID: PMC8376508.
Pellicanò G, Al Mamun M, Jurado-Santiago D, Villa-Hernández S, Yin X, Giannattasio M, Lanz MC, Smolka MB, Yeeles J, Shirahige K, García-Díaz M, Bermejo R. Checkpoint-mediated DNA polymerase ε exonuclease activity curbing counteracts resection-driven fork collapse. Mol Cell. 2021 Jul 1;81(13):2778-2792.e4. doi: 10.1016/j.molcel.2021.04.006. Epub 2021 Apr 30. PMID: 33932350; PMCID: PMC7612761.
Joiner AM, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J. 2021 Jun 15;40(12):e107607. doi: 10.15252/embj.2020107607. Epub 2021 May 21. PMID: 34018207; PMCID: PMC8204860.
Sanford EJ, Comstock WJ, Faça VM, Vega SC, Gnügge R, Symington LS, Smolka MB. Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper-resection. EMBO J. 2021 May 17;40(10):e104566. doi: 10.15252/embj.2020104566. Epub 2021 Mar 25. PMID: 33764556; PMCID: PMC8126923.
Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep. 2021 Feb 3;22(2):e51121. doi: 10.15252/embr.202051121. Epub 2021 Jan 25. PMID: 33491328; PMCID: PMC7857435.

Stuhlmann Lab

2024

Shahriar S, Biswas S, Zhao K, Akcan U, Tuohy MC, Glendinning MD, Kurt A, Wayne CR, Prochilo G, Price MZ, Stuhlmann H, Brekken RA, Menon V, Agalliu D. VEGF-A-mediated venous endothelial cell proliferation results in neoangiogenesis during neuroinflammation. Nat Neurosci. 2024 Oct;27(10):1904-1917. doi: 10.1038/s41593-024-01746-9. Epub 2024 Sep 10. PMID: 39256571.
Salvi S, Fruci S, Lacconi V, Totaro Aprile F, Rullo R, Stuhlmann H, Lanzone A, Campagnolo L, Massimiani M. Effect of Pravastatin on Placental Expression of Epidermal Growth Factor-like Domain 7 in Early-Onset Pre-Eclampsia: A New Potential Mechanism of Action. Biomedicines. 2024 Aug 22;12(8):1929. doi: 10.3390/biomedicines12081929. PMID: 39200393; PMCID: PMC11351877.
Chen RJ, Nabila A, Gal Toth J, Stuhlmann H, Toth M. The chemokine XCL1 functions as a pregnancy hormone to program offspring innate anxiety. Brain Behav Immun. 2024 May;118:178-189. doi: 10.1016/j.bbi.2024.02.032. Epub 2024 Feb 29. PMID: 38428650; PMCID: PMC11044916.

2023

Jin JC, Ananthanarayanan A, Brown JA, Rager SL, Bram Y, Sanidad KZ, Amir M, Baergen RN, Stuhlmann H, Schwartz RE, Perlman JM, Zeng MY. SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy. Pediatr Res. 2023 Apr;93(5):1375-1382. doi: 10.1038/s41390-022-02266-7. Epub 2022 Aug 19. PMID: 35986143; PMCID: PMC9388973.

2022

Chen RJ, Nabila A, Phalke S, Castro DF, Toth JG, Bergin P, Bastiaans J, Stuhlmann H, Pernis AB, Toth M. Serotonin-1A receptor, a psychiatric disease risk factor, influences offspring immunity via sex-dependent genetic nurture. iScience. 2022 Nov 15;25(12):105595. doi: 10.1016/j.isci.2022.105595. PMID: 36458257; PMCID: PMC9706704.
Argueta LB, Lacko LA, Bram Y, Tada T, Carrau L, Rendeiro AF, Zhang T, Uhl S, Lubor BC, Chandar V, Gil C, Zhang W, Dodson BJ, Bastiaans J, Prabhu M, Houghton S, Redmond D, Salvatore CM, Yang YJ, Elemento O, Baergen RN, tenOever BR, Landau NR, Chen S, Schwartz RE, Stuhlmann H. Inflammatory responses in the placenta upon SARS-CoV-2 infection late in pregnancy. iScience. 2022 May 20;25(5):104223. doi: 10.1016/j.isci.2022.104223. Epub 2022 Apr 11. PMID: 35434541; PMCID: PMC8996470.

2021

Massimiani M, Salvi S, Tiralongo GM, Moresi S, Stuhlmann H, Valensise H, Lanzone A, Campagnolo L. Circulating EGFL7 distinguishes between IUGR and PE: an observational case-control study. Sci Rep. 2021 Sep 9;11(1):17919. doi: 10.1038/s41598-021-97482-2. PMID: 34504270; PMCID: PMC8429426.
Coelho-Santos V, Berthiaume AA, Ornelas S, Stuhlmann H, Shih AY. Imaging the construction of capillary networks in the neonatal mouse brain. Proc Natl Acad Sci U S A. 2021 Jun 29;118(26):e2100866118. doi: 10.1073/pnas.2100866118. PMID: 34172585; PMCID: PMC8256089.
Massimiani M, Tiralongo GM, Salvi S, Fruci S, Lacconi V, La Civita F, Mancini M, Stuhlmann H, Valensise H, Campagnolo L. Treatment of pregnancies complicated by intrauterine growth restriction with nitric oxide donors increases placental expression of Epidermal Growth Factor-Like Domain 7 and improves fetal growth: A pilot study. Transl Res. 2021 Feb;228:28-41. doi: 10.1016/j.trsl.2020.08.002. Epub 2020 Aug 9. PMID: 32784003.

Travis Lab

2025

Dallal Bashi YH, Zhao X, McCoy CF, Kumar N, Teleshova N, Lamb DJ, Fernández Romero JA, Meyer A, Barnable P, Aravantinou M, Asowata OE, White MA, Travis AJ, Haddad LB, Shen X, Young VL, Boyd P, Malcolm RK. A prodrug strategy for sustained release of lactic acid from silicone elastomer vaginal rings. Int J Pharm. 2025 Nov 10;684:126120. doi: 10.1016/j.ijpharm.2025.126120. Epub 2025 Aug 26. PMID: 40876768.
Sosnicki DM, Travis AJ, Comizzoli P. In vitro exposure to epididymal extracellular vesicles from normospermic domestic cats improves developmental potential of sperm from teratospermic cats. Front Vet Sci. 2025 Jan 17;12:1547175. doi: 10.3389/fvets.2025.1547175. PMID: 39896847; PMCID: PMC11783848.
White MA, Cohen R, Travis AJ. Real-Time Imaging of Calcium Dynamics in Human Sperm After Precise Single-Cell Stimulation. Methods Mol Biol. 2025;2861:247-256. doi: 10.1007/978-1-0716-4164-4_18. PMID: 39395110.

2024

Sosnicki DM, Travis AJ, Comizzoli P. Extracellular vesicles are involved in the paracrine communication between epithelial cells in different regions of the domestic cat epididymis†. Biol Reprod. 2024 Nov 11;111(5):1056-1070. doi: 10.1093/biolre/ioae129. PMID: 39190878.
Meredith GR, Leong D, Frost C, Travis AJ. Facilitated Asynchronous Online Learning to Build Public Health Strategic Skills. J Public Health Manag Pract. 2024 Jan-Feb 01;30(1):56-65. doi: 10.1097/PHH.0000000000001813. Epub 2023 Aug 29. PMID: 37643075; PMCID: PMC10664790.

2023

Sosnicki DM, Cohen R, Asano A, Nelson JL, Mukai C, Comizzoli P, Travis AJ. Segmental differentiation of the murine epididymis: identification of segment-specific, GM1-enriched vesicles and regulation by luminal fluid factors†. Biol Reprod. 2023 Dec 11;109(6):864-877. doi: 10.1093/biolre/ioad120. PMID: 37694824; PMCID: PMC10724454.
Cohen R, Sosnicki DM, White MA, Nelson JL, Mukai C, Travis AJ. Real-Time Imaging of Acrosomal Calcium Dynamics and Exocytosis in Live Mouse Sperm. J Vis Exp. 2023 Oct 13;(200). doi: 10.3791/65962. PMID: 37902325.
Sharara FI, Ostermeier GC, Travis AJ. Defects in sperm capacitation/fertilizing ability are equally prevalent across ages in men seeking fertility assistance. Reprod Biomed Online. 2023 Jan;46(1):179-187. doi: 10.1016/j.rbmo.2022.09.020. Epub 2022 Sep 26. PMID: 36371338.

2022

Cummings KJ, Clarkberg M, Busche J, Travis AJ, Meredith GR, Weisfuse I, Cazer CL, Koretzky GA, Warnick LD. Case-control study to identify risk factors for SARS-CoV-2 infection among university students in the northeastern USA. Transbound Emerg Dis. 2022 Sep;69(5):e2688-e2693. doi: 10.1111/tbed.14619. Epub 2022 Jun 29. PMID: 35687478; PMCID: PMC9348057.
Meredith GR, Osman M, Cazer CL, Cummings KJ, Hecht J, Madsen CG, Santacrose LB, Dubovi AS, Clarkberg M, Johnson T, Fitzpatrick MD, Parrilla L, Li Y, Francis L, Weisfuse IB, Travis AJ, Jones AC, Warnick LD, Koretzky GA. Integrated Surveillance System for Controlling COVID-19 on a University Campus, 2020‒2021. Am J Public Health. 2022 Jul;112(7):980-984. doi: 10.2105/AJPH.2022.306838. PMID: 35728024; PMCID: PMC9222446.
Cohen R, Mukai C, Nelson JL, Zenilman SS, Sosnicki DM, Travis AJ. A genetically targeted sensor reveals spatial and temporal dynamics of acrosomal calcium and sperm acrosome exocytosis. J Biol Chem. 2022 May;298(5):101868. doi: 10.1016/j.jbc.2022.101868. Epub 2022 Mar 27. PMID: 35346690; PMCID: PMC9046242.

Vitousek Lab

2025

Taff CC, Wingfield JC, Vitousek MN. Corticosterone Reaction Norms to Temperature in Wild Birds: Implications for Understanding Endocrine Flexibility and Climate Vulnerability. Integr Comp Biol. 2025 Oct 16;65(4):1051-1060. doi: 10.1093/icb/icaf011. PMID: 40199741.
Real MVF, Vitousek MN, Sheehan MJ, Moeller AH. The mouse gut microbiota responds to predator odor and predicts host behavior. bioRxiv [Preprint]. 2025 Sep 25:2025.07.01.662568. doi: 10.1101/2025.07.01.662568. PMID: 40631147; PMCID: PMC12236647.
Vitousek MN, Taff CC, Williamson JL. Resilience and robustness: from sub-organismal responses to communities. Trends Ecol Evol. 2025 May;40(5):468-478. doi: 10.1016/j.tree.2025.03.001. Epub 2025 Mar 27. PMID: 40148158.
Wolf SE, Woodruff MJ, Chang van Oordt DA, Clotfelter ED, Cristol DA, Derryberry EP, Ferguson SM, Stanback MT, Taff CC, Vitousek MN, Westneat DF, Rosvall KA. Among-population variation in telomere regulatory proteins and their potential role as hidden drivers of intraspecific variation in life history. J Anim Ecol. 2025 Mar;94(3):303-315. doi: 10.1111/1365-2656.14071. Epub 2024 Mar 21. PMID: 38509838; PMCID: PMC11415550.
Rohwer VG, Houtz JL, Vitousek MN, Bailey RL, Miller ET. The Evolution of Using Shed Snake Skin in Bird Nests. Am Nat. 2025 Feb;205(2):170-183. doi: 10.1086/733208. Epub 2024 Dec 18. PMID: 39913940.

2024

Uehling JJ, Regnier E, Vitousek MN. Does Migration Constrain Glucocorticoid Phenotypes? Testing Corticosterone Levels during Breeding in Migratory Versus Resident Birds. Integr Comp Biol. 2024 Dec 20;64(6):1826-1835. doi: 10.1093/icb/icae110. PMID: 38992259.
McNew SM, Taff CC, Vitousek MN. Manipulation of a social signal affects DNA methylation of a stress-related gene in a free-living bird. J Exp Biol. 2024 Aug 1;227(15):jeb246819. doi: 10.1242/jeb.246819. Epub 2024 Jul 30. PMID: 39022893; PMCID: PMC11418189.
Schoenle LA, Zimmer C, Miller ET, Vitousek MN. Corrigendum to “Does variation in glucocorticoid concentrations predict fitness? A phylogenetic meta-analysis” [Gen. Comp. Endocrinol. 300 (2021) 113611]. Gen Comp Endocrinol. 2024 Aug 1;354:114518. doi: 10.1016/j.ygcen.2024.114518. Epub 2024 Apr 26. Erratum for: Gen Comp Endocrinol. 2021 Jan 1;300:113611. doi: 10.1016/j.ygcen.2020.113611. PMID: 38670848.
Taff CC, McNew SM, Campagna L, Vitousek MN. Corticosterone exposure is associated with long-term changes in DNA methylation, physiology and breeding decisions in a wild bird. Mol Ecol. 2024 Aug;33(15):e17456. doi: 10.1111/mec.17456. Epub 2024 Jul 2. PMID: 38953311.
Uehling JJ, Regnier E, Vitousek MN. Does migration constrain glucocorticoid phenotypes? Testing corticosterone levels during breeding in migratory versus resident birds. Integr Comp Biol. 2024 Jul 11:icae110. doi: 10.1093/icb/icae110. Epub ahead of print. PMID: 38992259.
McNew SM, Taff CC, Zimmer C, Uehling JJ, Ryan TA, Chang van Oordt D, Houtz JL, Injaian AS, Vitousek MN. Developmental stage-dependent effects of perceived predation risk on nestling tree swallows (Tachycineta bicolor). Ecology. 2024 Jun;105(6):e4307. doi: 10.1002/ecy.4307. Epub 2024 May 9. PMID: 38724013.
Chang van Oordt DA, Taff CC, Pipkin MA, Ryan TA, Vitousek MN. Experimentally elevated corticosterone does not affect bacteria killing ability of breeding female tree swallows (Tachycineta bicolor). Horm Behav. 2024 Apr;160:105500. doi: 10.1016/j.yhbeh.2024.105500. Epub 2024 Feb 4. PMID: 38316079.
Taff CC, Baldan D, Mentesana L, Ouyang JQ, Vitousek MN, Hau M. Endocrine flexibility can facilitate or constrain the ability to cope with global change. Philos Trans R Soc Lond B Biol Sci. 2024 Mar 25;379(1898):20220502. doi: 10.1098/rstb.2022.0502. Epub 2024 Feb 5. PMID: 38310929; PMCID: PMC10838644.
Wolf SE, Woodruff MJ, Chang van Oordt DA, Clotfelter ED, Cristol DA, Derryberry EP, Ferguson SM, Stanback MT, Taff CC, Vitousek MN, Westneat DF, Rosvall KA. Among-population variation in telomere regulatory proteins and their potential role as hidden drivers of intraspecific variation in life history. J Anim Ecol. 2024 Mar 21:10.1111/1365-2656.14071. doi: 10.1111/1365-2656.14071. Epub ahead of print. PMID: 38509838; PMCID: PMC11415550.

2023

Taff CC, McNew SM, Zimmer C, Uehling JJ, Houtz JL, Ryan TA, Chang van Oordt D, Injaian AS, Vitousek MN. Social signal manipulation and environmental challenges have independent effects on physiology, internal microbiome, and reproductive performance in tree swallows (Tachycineta bicolor). J Exp Zool A Ecol Integr Physiol. 2023 Oct;339(8):723-735. doi: 10.1002/jez.2722. Epub 2023 Jun 12. PMID: 37306329.
Vitousek MN, Dantzer B, Fuxjager MJ, Schlinger BA. Evolutionary behavioral endocrinology: Introduction to the special issue. Horm Behav. 2023 Jun;152:105356. doi: 10.1016/j.yhbeh.2023.105356. Epub 2023 Apr 7. PMID: 37031556.
Ryan TA, Taff CC, Zimmer C, Vitousek MN. Cold temperatures induce priming of the glucose stress response in tree swallows. Comp Biochem Physiol A Mol Integr Physiol. 2023 Jun;280:111419. doi: 10.1016/j.cbpa.2023.111419. Epub 2023 Mar 23. PMID: 36965830.
Zimmer C, Taff CC, Ardia DR, Rosvall KA, Kallenberg C, Bentz AB, Taylor AR, Johnson LS, Vitousek MN. Gene expression in the female tree swallow brain is associated with inter- and intra-population variation in glucocorticoid levels. Horm Behav. 2023 Jan;147:105280. doi: 10.1016/j.yhbeh.2022.105280. Epub 2022 Nov 17. PMID: 36403365.

2022

Chang van Oordt DA, Taff CC, Ryan TA, Vitousek MN. Timing of Breeding Reveals a Trade-Off between Immune Investment and Life History in Tree Swallows. Integr Comp Biol. 2022 Dec 30;62(6):1629-1639. doi: 10.1093/icb/icac033. PMID: 35561702.
Houtz JL, Taff CC, Vitousek MN. Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework. Integr Comp Biol. 2022 Aug 13;62(1):41-57. doi: 10.1093/icb/icac030. PMID: 35544275.
Taff CC, Wingfield JC, Vitousek MN. The relative speed of the glucocorticoid stress response varies independently of scope and is predicted by environmental variability and longevity across birds. Horm Behav. 2022 Aug;144:105226. doi: 10.1016/j.yhbeh.2022.105226. Epub 2022 Jul 18. PMID: 35863083.
Miller CR, Vitousek MN, Thaler JS. Light at night disrupts trophic interactions and population growth of lady beetles and pea aphids. Oecologia. 2022 Jul;199(3):527-535. doi: 10.1007/s00442-022-05146-3. Epub 2022 Mar 17. PMID: 35298703.
Taff CC, Zimmer C, Ryan TA, van Oordt DC, Aborn DA, Ardia DR, Johnson LS, Rose AP, Vitousek MN. Individual variation in natural or manipulated corticosterone does not covary with circulating glucose in a wild bird. J Exp Biol. 2022 Feb 15;225(4):jeb243262. doi: 10.1242/jeb.243262. Epub 2022 Feb 24. PMID: 35072205.

2021

Injaian AS, Uehling JJ, Taff CC, Vitousek MN. Effects of Artificial Light at Night on Avian Provisioning, Corticosterone, and Reproductive Success. Integr Comp Biol. 2021 Oct 4;61(3):1147-1159. doi: 10.1093/icb/icab055. PMID: 34021748.
Husak JF, Fuxjager MJ, Johnson MA, Vitousek MN, Donald JW, Francis CD, Goymann W, Hau M, Kircher BK, Knapp R, Martin LB, Miller ET, Schoenle LA, Williams TD. Life history and environment predict variation in testosterone across vertebrates. Evolution. 2021 May;75(5):1003-1010. doi: 10.1111/evo.14216. Epub 2021 Apr 2. PMID: 33755201.
Schoenle LA, Zimmer C, Miller ET, Vitousek MN. Does variation in glucocorticoid concentrations predict fitness? A phylogenetic meta-analysis. Gen Comp Endocrinol. 2021 Jan 1;300:113611. doi: 10.1016/j.ygcen.2020.113611. Epub 2020 Sep 18. Erratum in: Gen Comp Endocrinol. 2024 Aug 1;354:114518. doi: 10.1016/j.ygcen.2024.114518. PMID: 32950580.

Weiss Lab

2025

Tavares NT, Lourenço C, Constâncio V, Fernandes-Pontes F, Fonseca D, Silva-Santos R, Braga I, Maurício J, Henrique R, Liu M, Weiss RS, Bagrodia A, Jerónimo C, Lobo J. MicroRNA-371-373 cluster extracellular vesicle-based communication in testicular germ cell tumors. Cell Commun Signal. 2025 May 30;23(1):252. doi: 10.1186/s12964-025-02250-8. PMID: 40448114; PMCID: PMC12124061.
Loehr AR, Timmerman DM, Liu M, Gillis AJM, Matthews M, Bloom JC, Nicholls PK, Page DC, Miller AD, Looijenga LHJ, Weiss RS. Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection. Sci Rep. 2025 Feb 6;15(1):4452. doi: 10.1038/s41598-025-88554-8. PMID: 39910147; PMCID: PMC11799207.

2024

Zhang B, Mullmann J, Ludewig AH, Fernandez IR, Bales TR, Weiss RS, Schroeder FC. Acylspermidines are conserved mitochondrial sirtuin-dependent metabolites. Nat Chem Biol. 2024 Jul;20(7):812-822. doi: 10.1038/s41589-023-01511-2. Epub 2024 Jan 2. PMID: 38167917.
Ascenção C, Sims JR, Dziubek A, Comstock W, Fogarty EA, Badar J, Freire R, Grimson A, Weiss RS, Cohen PE, Smolka MB. A TOPBP1 allele causing male infertility uncouples XY silencing dynamics from sex body formation. Elife. 2024 Feb 23;12:RP90887. doi: 10.7554/eLife.90887. PMID: 38391183; PMCID: PMC10942628.
Erstling JA, Bag N, Gardinier TC, Kohle FFE, DomNwachukwu N, Butler SD, Kao T, Ma K, Turker MZ, Feuer GB, Lee R, Naguib N, Tallman JF, Malarkey HF, Tsaur L, Moore WL, Chapman DV, Aubert T, Mehta S, Cerione RA, Weiss RS, Baird BA, Wiesner UB. Overcoming Barriers Associated with Oral Delivery of Differently Sized Fluorescent Core-Shell Silica Nanoparticles. Adv Mater. 2024 Jan;36(1):e2305937. doi: 10.1002/adma.202305937. Epub 2023 Nov 23. PMID: 37689973.

2023

Shioda T, Weiss RS, Bagrodia A, Frazier AL. Comment on “Comment on ‘A Nested Case-Control Study of Serum Per- and Polyfluoroalkyl Substances and Testicular Germ Cell Tumors among U.S. Air Force Servicemen'”. Environ Health Perspect. 2023 Dec;131(12):128001. doi: 10.1289/EHP14247. Epub 2023 Dec 15. PMID: 38099920; PMCID: PMC10723136.
Roberts LC, Warnick LD, Weiss RS. Genomics at Cornell University College of Veterinary Medicine. Am J Vet Res. 2023 Jul 18;84(8):ajvr.23.06.0127. doi: 10.2460/ajvr.23.06.0127. PMID: 37442545.

2022

Latifkar A, Wang F, Mullmann JJ, Panizza E, Fernandez IR, Ling L, Miller AD, Fischbach C, Weiss RS, Lin H, Cerione RA, Antonyak MA. IGF2BP2 promotes cancer progression by degrading the RNA transcript encoding a v-ATPase subunit. Proc Natl Acad Sci U S A. 2022 Nov 8;119(45):e2200477119. doi: 10.1073/pnas.2200477119. Epub 2022 Nov 2. PMID: 36322753; PMCID: PMC9659396.
Fonseca A, Lobo J, Hazard FK, Gell J, Nicholls PK, Weiss RS, Klosterkemper L, Volchenboum SL, Nicholson JC, Frazier AL, Amatruda JF, Bagrodia A, Lockley M, Murray MJ. Advancing clinical and translational research in germ cell tumours (GCT): recommendations from the Malignant Germ Cell International Consortium. Br J Cancer. 2022 Nov;127(9):1577-1583. doi: 10.1038/s41416-022-02000-4. Epub 2022 Oct 13. PMID: 36229581; PMCID: PMC9596690.
Shah P, McGuigan CW, Cheng S, Vanpouille-Box C, Demaria S, Weiss RS, Lammerding J. ATM Modulates Nuclear Mechanics by Regulating Lamin A Levels. Front Cell Dev Biol. 2022 Jun 1;10:875132. doi: 10.3389/fcell.2022.875132. PMID: 35721517; PMCID: PMC9198445.
Zhang S, Nelson OD, Price IR, Zhu C, Lu X, Fernandez IR, Weiss RS, Lin H. Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2117013119. doi: 10.1073/pnas.2117013119. Epub 2022 Mar 8. PMID: 35259022; PMCID: PMC8931372.
Kobayashi M, Kobayashi M, Odajima J, Shioda K, Hwang YS, Sasaki K, Chatterjee P, Kramme C, Kohman RE, Church GM, Loehr AR, Weiss RS, Jüppner H, Gell JJ, Lau CC, Shioda T. Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers. Stem Cell Reports. 2022 Mar 8;17(3):507-521. doi: 10.1016/j.stemcr.2022.01.012. Epub 2022 Feb 10. PMID: 35148847; PMCID: PMC9039862.
Sims JR, Faça VM, Pereira C, Ascenção C, Comstock W, Badar J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. Phosphoproteomics of ATR signaling in mouse testes. Elife. 2022 Feb 8;11:e68648. doi: 10.7554/eLife.68648. PMID: 35133275; PMCID: PMC8824463.
Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. Elife. 2022 Feb 8;11:e68677. doi: 10.7554/eLife.68677. PMID: 35133274; PMCID: PMC8824475.

2021

Loehr AR, Pierpont TM, Gelsleichter E, Galang AMD, Fernandez IR, Moore ES, Guo MZ, Miller AD, Weiss RS. Targeting Cancer Stem Cells with Differentiation Agents as an Alternative to Genotoxic Chemotherapy for the Treatment of Malignant Testicular Germ Cell Tumors. Cancers (Basel). 2021 Apr 23;13(9):2045. doi: 10.3390/cancers13092045. PMID: 33922599; PMCID: PMC8122873.
Abril YLN, Fernandez IR, Hong JY, Chiang YL, Kutateladze DA, Zhao Q, Yang M, Hu J, Sadhukhan S, Li B, He B, Remick B, Bai JJ, Mullmann J, Wang F, Maymi V, Dhawan R, Auwerx J, Southard T, Cerione RA, Lin H, Weiss RS. Pharmacological and genetic perturbation establish SIRT5 as a promising target in breast cancer. Oncogene. 2021 Mar;40(9):1644-1658. doi: 10.1038/s41388-020-01637-w. Epub 2021 Jan 21. PMID: 33479498; PMCID: PMC7935767.
Lyndaker AM, Pierpont TM, Loehr AR, Weiss RS. A Genetically Engineered Mouse Model of Malignant Testicular Germ Cell Tumors. Methods Mol Biol. 2021;2195:147-165. doi: 10.1007/978-1-0716-0860-9_11. PMID: 32852763.

Wolf Lab

2025

Carrisoza-Gaytán R, Daily A, Wolf KJ, Lasaad S, Cantalupo A, Nair P, Van Gaal R, Uhlén P, Lewis JA, Satlin LM. Ca2+ signal dynamics in maturing ureteric bud (UB) and collecting duct (CD) derived organoid tubules. Am J Physiol Cell Physiol. 2025 Sep 30. doi: 10.1152/ajpcell.00578.2025. Epub ahead of print. PMID: 41026830.
Wolf KJ, van Gaal RC, Uzel SGM, Rubins JE, Klaus AN, Printz A, Nair P, Kroll KT, Stankey P, Satlin LM, Lewis JA. Perfusable 3D models of ureteric bud and collecting duct tubules. bioRxiv [Preprint]. 2025 Jun 24:2025.06.19.659798. doi: 10.1101/2025.06.19.659798. PMID: 40667187; PMCID: PMC12262377.

2024

Kroll KT, Homan KA, Uzel SGM, Mata MM, Wolf KJ, Rubins JE, Lewis JA. A perfusable, vascularized kidney organoid-on-chip model. Biofabrication. 2024 Jul 5;16(4). doi: 10.1088/1758-5090/ad5ac0. PMID: 38906132.

2023

Garcia JH, Akins EA, Jain S, Wolf KJ, Zhang J, Choudhary N, Lad M, Shukla P, Rios J, Seo K, Gill SA, Carson WH, Carette LR, Zheng AC, Raleigh DR, Kumar S, Aghi MK. Multiomic screening of invasive GBM cells reveals targetable transsulfuration pathway alterations. J Clin Invest. 2023 Nov 16;134(3):e170397. doi: 10.1172/JCI170397. PMID: 37971886; PMCID: PMC10849762.

2022

Wolf KJ, Weiss JD, Uzel SGM, Skylar-Scott MA, Lewis JA. Biomanufacturing human tissues via organ building blocks. Cell Stem Cell. 2022 May 5;29(5):667-677. doi: 10.1016/j.stem.2022.04.012. PMID: 35523137; PMCID: PMC9617289.

2021

Lei R, Akins EA, Wong KCY, Repina NA, Wolf KJ, Dempsey GE, Schaffer DV, Stahl A, Kumar S. Multiwell Combinatorial Hydrogel Array for High-Throughput Analysis of Cell-ECM Interactions. ACS Biomater Sci Eng. 2021 Jun 14;7(6):2453-2465. doi: 10.1021/acsbiomaterials.1c00065. Epub 2021 May 24. PMID: 34028263; PMCID: PMC8900525.

Wolfner Lab

2025

Gordon KE, Ray S, Marcin JM, Gonzales PM, Li ML, Liang C, Wolfner MF, Lazzaro BP. Trade-off between antibacterial immune defense and oogenesis progression in female Drosophila melanogaster. Genetics. 2025 Oct 8;231(2):iyaf151. doi: 10.1093/genetics/iyaf151. PMID: 40746174; PMCID: PMC12505294.
Yang M, White MA, Findlay GD, Vignogna RC, Apger-McGlaughon J, Clark NL, Choi JY, Fromme JC, Wolfner MF. Female membrane proteins regulate postmating ovulation in Drosophila melanogaster by ovulin-dependent and -independent pathways. Proc Natl Acad Sci U S A. 2025 Sep 16;122(37):e2508783122. doi: 10.1073/pnas.2508783122. Epub 2025 Sep 8. PMID: 40920921; PMCID: PMC12452909.
Chen DS, Marrero K, Sanchez-Lopez JA, Belenky M, Thomalla JM, Buehner NA, Apel I, Levi Y, Hafezi Y, Wang S, Clark AG, Heifetz Y, Siegal ML, Wolfner MF. Asymmetric development and function of paired sperm-storage organs in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2025 Aug 26;122(34):e2512096122. doi: 10.1073/pnas.2512096122. Epub 2025 Aug 19. PMID: 40828028; PMCID: PMC12403100.
Guay SY, Patel PH, Thomalla JM, McDermott KL, O’Toole JM, Arnold SE, Obrycki SJ, Wolfner MF, Findlay GD. An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster. Genetics. 2025 Mar 17;229(3):iyaf008. doi: 10.1093/genetics/iyaf008. PMID: 39903197; PMCID: PMC12168066.
Thomalla JM, Wolfner MF. No transcription, no problem: Protein phosphorylation changes and the transition from oocyte to embryo. Curr Top Dev Biol. 2025;162:165-205. doi: 10.1016/bs.ctdb.2025.01.001. Epub 2025 Feb 18. PMID: 40180509; PMCID: PMC12412753.

2024

Guay SY, Patel PH, Thomalla JM, McDermott KL, O’Toole JM, Arnold SE, Obrycki SJ, Wolfner MF, Findlay GD. An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster. bioRxiv [Preprint]. 2024 Dec 14:2024.08.08.607187. doi: 10.1101/2024.08.08.607187. Update in: Genetics. 2025 Mar 17;229(3):iyaf008. doi: 10.1093/genetics/iyaf008. PMID: 39149251; PMCID: PMC11326263.
Amaro IA, Wohl MP, Pitcher S, Alfonso-Parra C, Avila FW, Paige AS, Helinski MEH, Duvall LB, Harrington LC, Wolfner MF, McMeniman CJ. Sex peptide receptor is not required for refractoriness to remating or induction of egg laying in Aedes aegypti. Genetics. 2024 May 7;227(1):iyae034. doi: 10.1093/genetics/iyae034. PMID: 38551457; PMCID: PMC11075561.
Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. Commun Biol. 2024 Jan 12;7(1):90. doi: 10.1038/s42003-023-05717-x. PMID: 38216628; PMCID: PMC10786823.

2023

Brown NC, Gordon B, McDonough-Goldstein CE, Misra S, Findlay GD, Clark AG, Wolfner MF. The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster. Elife. 2023 Dec 21;12:e86409. doi: 10.7554/eLife.86409. PMID: 38126735; PMCID: PMC10834028.
Thomalla JM, Wolfner MF. Reproductive biology: A genetic recipe for parthenogenesis. Curr Biol. 2023 Sep 11;33(17):R904-R906. doi: 10.1016/j.cub.2023.07.055. PMID: 37699347; PMCID: PMC10753294.
Wolfner MF, Suarez SS, Dorus S. Suspension of hostility: Positive interactions between spermatozoa and female reproductive tracts. Andrology. 2023 Jul;11(5):943-947. doi: 10.1111/andr.13349. Epub 2022 Dec 22. PMID: 36448311; PMCID: PMC10227186.
Delbare SYN, Jain AM, Clark AG, Wolfner MF. Transcriptional programs are activated and microRNAs are repressed within minutes after mating in the Drosophila melanogaster female reproductive tract. BMC Genomics. 2023 Jun 27;24(1):356. doi: 10.1186/s12864-023-09397-z. PMID: 37370014; PMCID: PMC10294459.
Delbare SYN, Venkatraman S, Scuderi K, Wells MT, Wolfner MF, Basu S, Clark AG. Time series transcriptome analysis implicates the circadian clock in the Drosophila melanogaster female’s response to sex peptide. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2214883120. doi: 10.1073/pnas.2214883120. Epub 2023 Jan 27. Erratum in: Proc Natl Acad Sci U S A. 2023 May 2;120(18):e2305270120. doi: 10.1073/pnas.2305270120. PMID: 36706221; PMCID: PMC9945991.

2022

Misra S, Buehner NA, Singh A, Wolfner MF. Female factors modulate Sex Peptide’s association with sperm in Drosophila melanogaster. BMC Biol. 2022 Dec 14;20(1):279. doi: 10.1186/s12915-022-01465-2. PMID: 36514080; PMCID: PMC9749180.
McQueen EW, Afkhami M, Atallah J, Belote JM, Gompel N, Heifetz Y, Kamimura Y, Kornhauser SC, Masly JP, O’Grady P, Peláez J, Rebeiz M, Rice G, Sánchez-Herrero E, Santos Nunes MD, Santos Rampasso A, Schnakenberg SL, Siegal ML, Takahashi A, Tanaka KM, Turetzek N, Zelinger E, Courtier-Orgogozo V, Toda MJ, Wolfner MF, Yassin A. A standardized nomenclature and atlas of the female terminalia of Drosophila melanogaster. Fly (Austin). 2022 Dec;16(1):128-151. doi: 10.1080/19336934.2022.2058309. PMID: 35575031; PMCID: PMC9116418.
Wigby S, Brown NC, Sepil I, Wolfner MF. On how to identify a seminal fluid protein: A commentary on Hurtado et al. Insect Mol Biol. 2022 Oct;31(5):533-536. doi: 10.1111/imb.12783. Epub 2022 Aug 17. PMID: 35975871; PMCID: PMC9452446.
Chen DS, Clark AG, Wolfner MF. Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster. Genetics. 2022 Jul 30;221(4):iyac096. doi: 10.1093/genetics/iyac096. PMID: 35809068; PMCID: PMC9339280.
White MA, Wolfner MF. The Effects of Male Seminal Fluid Proteins on Gut/Gonad Interactions in Drosophila. Insects. 2022 Jul 13;13(7):623. doi: 10.3390/insects13070623. PMID: 35886799; PMCID: PMC9324770.
Gordon KE, Wolfner MF, Lazzaro BP. A single mating is sufficient to induce persistent reduction of immune defense in mated female Drosophila melanogaster. J Insect Physiol. 2022 Jul;140:104414. doi: 10.1016/j.jinsphys.2022.104414. Epub 2022 Jun 18. PMID: 35728669; PMCID: PMC10162487.
McCullough EL, Whittington E, Singh A, Pitnick S, Wolfner MF, Dorus S. The life history of Drosophila sperm involves molecular continuity between male and female reproductive tracts. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2119899119. doi: 10.1073/pnas.2119899119. Epub 2022 Mar 7. PMID: 35254899; PMCID: PMC8931355.
Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O’Brien LE, Dow JAT; FCA Consortium§; Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc’hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O’Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science. 2022 Mar 4;375(6584):eabk2432. doi: 10.1126/science.abk2432. Epub 2022 Mar 4. PMID: 35239393; PMCID: PMC8944923.

2021

Amaro IA, Ahmed-Braimah YH, League GP, Pitcher SA, Avila FW, Cruz PC, Harrington LC, Wolfner MF. Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract. BMC Genomics. 2021 Dec 15;22(1):896. doi: 10.1186/s12864-021-08201-0. PMID: 34906087; PMCID: PMC8672594.
League GP, Degner EC, Pitcher SA, Hafezi Y, Tennant E, Cruz PC, Krishnan RS, Garcia Castillo SS, Alfonso-Parra C, Avila FW, Wolfner MF, Harrington LC. The impact of mating and sugar feeding on blood-feeding physiology and behavior in the arbovirus vector mosquito Aedes aegypti. PLoS Negl Trop Dis. 2021 Sep 30;15(9):e0009815. doi: 10.1371/journal.pntd.0009815. PMID: 34591860; PMCID: PMC8509887.
White MA, Chen DS, Wolfner MF. She’s got nerve: roles of octopamine in insect female reproduction. J Neurogenet. 2021 Sep;35(3):132-153. doi: 10.1080/01677063.2020.1868457. Epub 2021 Apr 28. PMID: 33909537; PMCID: PMC8455407.
Suarez SS, Wolfner MF. Cilia take the egg on a magic carpet ride. Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):e2108887118. doi: 10.1073/pnas.2108887118. PMID: 34162738; PMCID: PMC8271566.
Meyer H, Buhr A, Callaerts P, Schiemann R, Wolfner MF, Marygold SJ. Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster. MicroPubl Biol. 2021 Jun 23;2021:10.17912/micropub.biology.000410. doi: 10.17912/micropub.biology.000410. PMID: 34189422; PMCID: PMC8223033.
Immarigeon C, Frei Y, Delbare SYN, Gligorov D, Machado Almeida P, Grey J, Fabbro L, Nagoshi E, Billeter JC, Wolfner MF, Karch F, Maeda RK. Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2001897118. doi: 10.1073/pnas.2001897118. PMID: 33876742; PMCID: PMC8053986.
Koreman GT, Xu Y, Hu Q, Zhang Z, Allen SE, Wolfner MF, Wang B, Han C. Upgraded CRISPR/Cas9 tools for tissue-specific mutagenesis in Drosophila. Proc Natl Acad Sci U S A. 2021 Apr 6;118(14):e2014255118. doi: 10.1073/pnas.2014255118. PMID: 33782117; PMCID: PMC8040800.
Ahmed-Braimah YH, Wolfner MF, Clark AG. Differences in Postmating Transcriptional Responses between Conspecific and Heterospecific Matings in Drosophila. Mol Biol Evol. 2021 Mar 9;38(3):986-999. doi: 10.1093/molbev/msaa264. PMID: 33035303; PMCID: PMC7947788.
Allen SE, Koreman GT, Sarkar A, Wang B, Wolfner MF, Han C. Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes. PLoS Biol. 2021 Jan 14;19(1):e3001061. doi: 10.1371/journal.pbio.3001061. PMID: 33444322; PMCID: PMC7837743.
White MA, Bonfini A, Wolfner MF, Buchon N. Drosophila melanogaster sex peptide regulates mated female midgut morphology and physiology. Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2018112118. doi: 10.1073/pnas.2018112118. PMID: 33443193; PMCID: PMC7817148.

Yu Lab

2025

Zhang J, Leung AK, Zhu Y, Yao L, Willis A, Pan X, Ozer A, Zhou Z, Siklenka K, Barrera A, Liang J, Tippens ND, Reddy TE, Lis JT, Yu H. Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide. Genome Biol. 2025 Nov 3;26(1):378. doi: 10.1186/s13059-025-03828-8. PMID: 41185025; PMCID: PMC12581240.
Ozer A, Kang JJ, Tang Y, Yugandhar K, Yu S, DeBerardine MD, Omar K, Lis JT, Yu H. Identification of human RNA Polymerase II interactors at early stages of transcription. bioRxiv [Preprint]. 2025 Oct 8:2025.10.08.681243. doi: 10.1101/2025.10.08.681243. PMID: 41279442; PMCID: PMC12632396.
Shah SR, Chen Y, Leung AK, Navarro PVC, Paramo MI, Gupta J, Gurumurthy A, Fite RF, Weimer AK, Du Q, Mohyeldin AM, Egli D, Creusot RJ, Ryan RJH, Snyder MP, Clark AG, Lis JT, Yu H. The regulatory landscape of nascent transcription in human health and disease. bioRxiv [Preprint]. 2025 Sep 26:2025.09.24.676871. doi: 10.1101/2025.09.24.676871. PMID: 41040139; PMCID: PMC12485982.
Liu Y, Cooper DN, Yu H. Disease-specific variant pathogenicity prediction using multimodal biomedical language models. bioRxiv [Preprint]. 2025 Sep 15:2025.09.09.675184. doi: 10.1101/2025.09.09.675184. PMID: 41000707; PMCID: PMC12458274.
Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations. Nat Biotechnol. 2025 Sep;43(9):1510-1524. doi: 10.1038/s41587-024-02428-4. Epub 2024 Oct 24. PMID: 39448882.
Odell J, Tang Y, Ambekar YS, Kidiyoor GR, Saadi H, Woodworth GF, Holt LJ, Scarcelli G, Yu H, Lammerding J. The Deformability of the Mammalian Cell Nucleus is Determined by the Identity of the Lamin Rod Domain. bioRxiv [Preprint]. 2025 Jul 22:2025.07.22.666133. doi: 10.1101/2025.07.22.666133. PMID: 40777269; PMCID: PMC12330664.
Zhou Z, Li A, Zhang J, Yu H, Ozer A, Lis JT. Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context. bioRxiv [Preprint]. 2025 Jul 9:2025.07.07.663560. doi: 10.1101/2025.07.07.663560. PMID: 40672313; PMCID: PMC12265581.
Xiong D, Torres M, Murray D, Li L, Naravane AC, Fragoza R, Honig B, Yu H. Integrating structural homology with deep learning to achieve highly accurate protein-protein interface prediction for the human interactome. bioRxiv [Preprint]. 2025 Jun 12:2025.06.09.658393. doi: 10.1101/2025.06.09.658393. PMID: 40661495; PMCID: PMC12259034.
Yao L, Shah SR, Ozer A, Zhang J, Pan X, Xia T, Fangal VD, Leung AK, Wei M, Lis JT, Yu H. High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples. bioRxiv [Preprint]. 2025 Apr 8:2025.04.02.646189. doi: 10.1101/2025.04.02.646189. PMID: 40291712; PMCID: PMC12026507.
Li L, Roy PG, Liu Y, Zhang Z, Xiong D, Savan R, Gokhale NS, Schang LM, Das J, Yu H. Comprehensive Atomic-Scale 3D Viral-Host Protein Interactomes Enable Dissection of Key Mechanisms and Evolutionary Processes Underlying Viral Pathogenesis. bioRxiv [Preprint]. 2025 Apr 2:2025.03.28.645946. doi: 10.1101/2025.03.28.645946. PMID: 40236211; PMCID: PMC11996397.
Paramo MI, Leung AK, Shah SR, Zhang J, Tippens ND, Liang J, Yao L, Jin Y, Pan X, Ozer A, Lis JT, Yu H. Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity. bioRxiv [Preprint]. 2025 Mar 14:2025.03.14.643265. doi: 10.1101/2025.03.14.643265. PMID: 40161809; PMCID: PMC11952525.
Zhang Y, Leung AK, Kang JJ, Sun Y, Wu G, Li L, Sun J, Cheng L, Qiu T, Zhang J, Wierbowski SD, Gupta S, Booth JG, Yu H. A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology. Nat Commun. 2025 Jan 24;16(1):975. doi: 10.1038/s41467-024-54176-3. PMID: 39856048; PMCID: PMC11760531.
Wang N, Pachai MR, Li D, Lee CJ, Warda S, Khudoynazarova MN, Cho WH, Xie G, Shah SR, Yao L, Qian C, Wong EWP, Yan J, Tomas FV, Hu W, Kuo F, Gao SP, Luo J, Smith AE, Han M, Gao D, Ge K, Yu H, Chandarlapaty S, Iyer GV, Rosenberg JE, Solit DB, Al-Ahmadie HA, Chi P, Chen Y. Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A-menin to bivalent promoters. Nat Genet. 2025 Jan;57(1):165-179. doi: 10.1038/s41588-024-02015-y. Epub 2025 Jan 13. PMID: 39806204; PMCID: PMC11735410.

2024

You Chen, Sagar R. Shah, Alden K. Leung, Mauricio I. Paramo, Kelly Cochran, Anshul Kundaje, Andrew G. Clark, John T. Lis, Haiyuan Yu. Directionality of transcriptional regulatory elements. bioRxiv. 2024 Dec 01; 621925; doi: https://doi.org/10.1101/2024.12.01.621925
Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A. Dissecting the cis-regulatory syntax of transcription initiation with deep learning. bioRxiv [Preprint]. 2024 Nov 21:2024.05.28.596138. doi: 10.1101/2024.05.28.596138. PMID: 38853896; PMCID: PMC11160661.
Wan M, Minelli ME, Zhao Q, Marshall S, Yu H, Smolka M, Mao Y. Phosphoribosyl modification of poly-ubiquitin chains at the Legionella-containing vacuole prohibiting autophagy adaptor recognition. Nat Commun. 2024 Aug 30;15(1):7481. doi: 10.1038/s41467-024-51273-1. PMID: 39214972; PMCID: PMC11364841.
Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nat Biotechnol. 2023 Jan;41(1):128-139. doi: 10.1038/s41587-022-01474-0. Epub 2022 Oct 10. PMID: 36217030; PMCID: PMC9851973.

2023

Chen Y, Paramo MI, Zhang Y, Yao L, Shah SR, Jin Y, Zhang J, Pan X, Yu H. Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annu Rev Genet. 2023 Nov 27;57:201-222. doi: 10.1146/annurev-genet-030723-120717. Epub 2023 Aug 10. PMID: 37562413.
Ding X, Singh P, Schimenti K, Tran TN, Fragoza R, Hardy J, Orwig KE, Olszewska M, Kurpisz MK, Yatsenko AN, Conrad DF, Yu H, Schimenti JC. In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes. Proc Natl Acad Sci U S A. 2023 Jul 25;120(30):e2219925120. doi: 10.1073/pnas.2219925120. Epub 2023 Jul 17. PMID: 37459509; PMCID: PMC10372637.

2022

Leung AK, Yao L, Yu H. Functional genomic assays to annotate enhancer-promoter interactions genome wide. Hum Mol Genet. 2022 Oct 20;31(R1):R97-R104. doi: 10.1093/hmg/ddac204. PMID: 36018818; PMCID: PMC9585677.
Santos MN, Paushter DH, Zhang T, Wu X, Feng T, Lou J, Du H, Becker SM, Fragoza R, Yu H, Hu F. Progranulin-derived granulin E and lysosome membrane protein CD68 interact to reciprocally regulate their protein homeostasis. J Biol Chem. 2022 Sep;298(9):102348. doi: 10.1016/j.jbc.2022.102348. Epub 2022 Aug 4. PMID: 35933009; PMCID: PMC9450144.
Yao L, Liang J, Ozer A, Leung AK, Lis JT, Yu H. A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. Nat Biotechnol. 2022 Jul;40(7):1056-1065. doi: 10.1038/s41587-022-01211-7. Epub 2022 Feb 17. PMID: 35177836; PMCID: PMC9288987.
Lee D, Xiong D, Wierbowski S, Li L, Liang S, Yu H. Deep learning methods for 3D structural proteome and interactome modeling. Curr Opin Struct Biol. 2022 Apr;73:102329. doi: 10.1016/j.sbi.2022.102329. Epub 2022 Feb 6. PMID: 35139457; PMCID: PMC8957610.
Chen Y, Clark AG, Yu H. Advancing discovery of risk-altering variants for complex diseases by functionally informed fine-mapping. Neuron. 2022 Mar 16;110(6):905-907. doi: 10.1016/j.neuron.2022.02.018. PMID: 35298913.
Hou Y, Zhou Y, Jehi L, Luo Y, Gack MU, Chan TA, Yu H, Eng C, Pieper AA, Cheng F. Aging-related cell type-specific pathophysiologic immune responses that exacerbate disease severity in aged COVID-19 patients. Aging Cell. 2022 Feb;21(2):e13544. doi: 10.1111/acel.13544. Epub 2022 Jan 12. PMID: 35023286; PMCID: PMC8844132.
Xiong D, Lee D, Li L, Zhao Q, Yu H. Implications of disease-related mutations at protein-protein interfaces. Curr Opin Struct Biol. 2022 Feb;72:219-225. doi: 10.1016/j.sbi.2021.11.012. Epub 2021 Dec 24. PMID: 34959033; PMCID: PMC8863207.
Chen S, Liu Y, Zhang Y, Wierbowski SD, Lipkin SM, Wei X, Yu H. A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. Genome Res. 2022 Jan;32(1):135-149. doi: 10.1101/gr.275437.121. Epub 2021 Dec 28. PMID: 34963661; PMCID: PMC8744679.

2021

Wierbowski SD, Liang S, Liu Y, Chen Y, Gupta S, Andre NM, Lipkin SM, Whittaker GR, Yu H. A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. Nat Methods. 2021 Dec;18(12):1477-1488. doi: 10.1038/s41592-021-01318-w. Epub 2021 Nov 29. PMID: 34845387; PMCID: PMC8665054.
Yugandhar K, Zhao Q, Gupta S, Xiong D, Yu H. Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics. 2021 Dec;21(23-24):e2100145. doi: 10.1002/pmic.202100145. Epub 2021 Oct 28. PMID: 34647422.
Furman CM, Wang TY, Zhao Q, Yugandhar K, Yu H, Alani E. Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair. Nucleic Acids Res. 2021 Sep 20;49(16):9327-9341. doi: 10.1093/nar/gkab694. PMID: 34390347; PMCID: PMC8450099.
Singh P, Fragoza R, Blengini CS, Tran TN, Pannafino G, Al-Sweel N, Schimenti KJ, Schindler K, Alani EA, Yu H, Schimenti JC. Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging. Nat Commun. 2021 Aug 18;12(1):5005. doi: 10.1038/s41467-021-25028-1. PMID: 34408140; PMCID: PMC8373927.
Joiner AM, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J. 2021 Jun 15;40(12):e107607. doi: 10.15252/embj.2020107607. Epub 2021 May 21. PMID: 34018207; PMCID: PMC8204860.
Zhou Y, Xu J, Hou Y, Leverenz JB, Kallianpur A, Mehra R, Liu Y, Yu H, Pieper AA, Jehi L, Cheng F. Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. Alzheimers Res Ther. 2021 Jun 9;13(1):110. doi: 10.1186/s13195-021-00850-3. PMID: 34108016; PMCID: PMC8189279.
Du H, Wong MY, Zhang T, Santos MN, Hsu C, Zhang J, Yu H, Luo W, Hu F. A multifaceted role of progranulin in regulating amyloid-beta dynamics and responses. Life Sci Alliance. 2021 Jun 8;4(7):e202000874. doi: 10.26508/lsa.202000874. PMID: 34103390; PMCID: PMC8200295.
Li G, Pahari S, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. Bioinformatics. 2021 May 17;37(7):992-999. doi: 10.1093/bioinformatics/btaa761. PMID: 32866236; PMCID: PMC8128451.
Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep. 2021 Feb 3;22(2):e51121. doi: 10.15252/embr.202051121. Epub 2021 Jan 25. PMID: 33491328; PMCID: PMC7857435.
Zhang, Y., Wierbowski, S.D. & Yu, H. Combining views for newly sequenced organisms. Nat Mach Intell 3, 1011–1012 (2021). https://doi.org/10.1038/s42256-021-00426-8

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