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Vincent J. Lynch, Ph.D. - Publications

Affiliations: 
2008 Yale University, New Haven, CT 
Area:
evolution of complex characters
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. Biorxiv : the Preprint Server For Biology. PMID 38463968 DOI: 10.1101/2024.02.27.582135  0.363
2022 Vazquez JM, Pena MT, Muhammad B, Kraft M, Adams LB, Lynch VJ. Parallel evolution of reduced cancer risk and tumor suppressor duplications in . Elife. 11. PMID 36480266 DOI: 10.7554/eLife.82558  0.595
2022 Mika K, Lynch VJ. Transposable Elements Continuously Remodel the Regulatory Landscape, Transcriptome, and Function of Decidual Stromal Cells. Genome Biology and Evolution. 14. PMID 36423206 DOI: 10.1093/gbe/evac164  0.434
2022 Mika K, Whittington CM, McAllan BM, Lynch VJ. Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy. Elife. 11. PMID 35770963 DOI: 10.7554/eLife.74297  0.325
2021 Glaberman S, Bulls SE, Vazquez JM, Chiari Y, Lynch VJ. Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles. Genome Biology and Evolution. PMID 34792580 DOI: 10.1093/gbe/evab244  0.615
2021 Mika K, Marinić M, Singh M, Muter J, Brosens JJ, Lynch VJ. Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes. Elife. 10. PMID 34623259 DOI: 10.7554/eLife.69584  0.327
2021 Lynch VJ, Wagner GP. Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. PMID 34125492 DOI: 10.1002/jez.b.23063  0.5
2021 Marinić M, Mika K, Chigurupati S, Lynch VJ. Evolutionary transcriptomics implicates in the origins of implantation and regulation of gestation length. Elife. 10. PMID 33522483 DOI: 10.7554/eLife.61257  0.338
2021 Vazquez JM, Lynch VJ. Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. Elife. 10. PMID 33513090 DOI: 10.7554/eLife.65041  0.605
2020 Marinić M, Rana S, Lynch VJ. Derivation of endometrial gland organoids from term placenta. Placenta. 101: 75-79. PMID 32937244 DOI: 10.1016/J.Placenta.2020.08.017  0.303
2020 Marinić M, Lynch VJ. Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage. Plos Genetics. 16: e1008666. PMID 32302297 DOI: 10.1371/Journal.Pgen.1008666  0.384
2020 Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional architecture of deleterious genetic variants in the genome of a Wrangel Island mammoth. Genome Biology and Evolution. PMID 32031213 DOI: 10.1093/Gbe/Evz279  0.34
2018 Vazquez JM, Sulak M, Chigurupati S, Lynch VJ. A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage. Cell Reports. 24: 1765-1776. PMID 30110634 DOI: 10.1016/J.Celrep.2018.07.042  0.643
2017 Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, Perry GH, Lynch VJ, Brown CD. Transposable elements are the primary source of novelty in primate gene regulation. Genome Research. PMID 28855262 DOI: 10.1101/Gr.218149.116  0.54
2016 Mika KM, Lynch VJ. An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression. American Journal of Human Genetics. PMID 27745831 DOI: 10.1016/J.Ajhg.2016.09.002  0.323
2016 Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ. TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. Elife. 5. PMID 27642012 DOI: 10.7554/Elife.11994  0.38
2016 Burrows CK, Kosova G, Herman C, Patterson K, Hartmann KE, Velez Edwards DR, Stephenson MD, Lynch VJ, Ober C. Expression Quantitative Trait Locus Mapping Studies in Mid-secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes. Plos Genetics. 12: e1005858. PMID 27447835 DOI: 10.1371/Journal.Pgen.1005858  0.44
2016 Kin K, Maziarz J, Chavan AR, Kamat M, Vasudevan S, Birt A, Emera D, Lynch VJ, Ott TL, Pavlicev M, Wagner GP. The transcriptomic evolution of mammalian pregnancy: gene expression innovations in endometrial stromal fibroblasts. Genome Biology and Evolution. PMID 27401177 DOI: 10.1093/Gbe/Evw168  0.768
2016 Nnamani MC, Ganguly S, Erkenbrack EM, Lynch VJ, Mizoue LS, Tong Y, Darling HL, Fuxreiter M, Meiler J, Wagner GP. A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1. Cell Reports. PMID 27239043 DOI: 10.1016/J.Celrep.2016.04.088  0.764
2016 Lynch VJ. GENETICS. A copy-and-paste gene regulatory network. Science (New York, N.Y.). 351: 1029-30. PMID 26941305 DOI: 10.1126/Science.Aaf2977  0.458
2015 Lynch VJ, Bedoya-Reina OC, Ratan A, Sulak M, Drautz-Moses DI, Perry GH, Miller W, Schuster SC. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Reports. 12: 217-28. PMID 26146078 DOI: 10.1016/J.Celrep.2015.06.027  0.378
2015 Kin K, Nnamani MC, Lynch VJ, Michaelides E, Wagner GP. Cell-type phylogenetics and the origin of endometrial stromal cells. Cell Reports. 10: 1398-409. PMID 25732829 DOI: 10.1016/J.Celrep.2015.01.062  0.606
2015 Lynch VJ, Nnamani MC, Kapusta A, Brayer K, Plaza SL, Mazur EC, Emera D, Sheikh SZ, Grützner F, Bauersachs S, Graf A, Young SL, Lieb JD, DeMayo FJ, Feschotte C, et al. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Reports. 10: 551-61. PMID 25640180 DOI: 10.1016/J.Celrep.2014.12.052  0.804
2015 Kosova G, Stephenson MD, Lynch VJ, Ober C. Evolutionary forward genomics reveals novel insights into the genes and pathways dysregulated in recurrent early pregnancy loss. Human Reproduction (Oxford, England). 30: 519-29. PMID 25586782 DOI: 10.1093/Humrep/Deu355  0.454
2014 Gallagher C, Clarke C, Aherne ST, Katikireddy KR, Doolan P, Lynch V, Shaw S, Bobart-Hone A, Murphy C, Clynes M, Power W, O'Sullivan F. Comparative transcriptomic analysis of cultivated limbal epithelium and donor corneal tissue reveals altered wound healing gene expression. Investigative Ophthalmology & Visual Science. 55: 5795-805. PMID 25125605 DOI: 10.1167/Iovs.14-14664  0.309
2014 Lynch VJ, May G, Wagner GP. Correction: Corrigendum: Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB Nature. 508: 420-420. DOI: 10.1038/Nature13201  0.55
2013 Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. Plos Genetics. 9: e1003470. PMID 23637635 DOI: 10.1371/Journal.Pgen.1003470  0.459
2013 Wagner GP, Kin K, Lynch VJ. A model based criterion for gene expression calls using RNA-seq data. Theory in Biosciences = Theorie in Den Biowissenschaften. 132: 159-64. PMID 23615947 DOI: 10.1007/S12064-013-0178-3  0.575
2012 Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences = Theorie in Den Biowissenschaften. 131: 281-5. PMID 22872506 DOI: 10.1007/S12064-012-0162-3  0.467
2012 Padua MB, Lynch VJ, Alvarez NV, Garthwaite MA, Golos TG, Bazer FW, Kalkunte S, Sharma S, Wagner GP, Hansen PJ. ACP5 (Uteroferrin): phylogeny of an ancient and conserved gene expressed in the endometrium of mammals. Biology of Reproduction. 86: 123. PMID 22278982 DOI: 10.1095/Biolreprod.111.097964  0.592
2012 Emera D, Casola C, Lynch VJ, Wildman DE, Agnew D, Wagner GP. Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements. Molecular Biology and Evolution. 29: 239-47. PMID 21813467 DOI: 10.1093/Molbev/Msr189  0.805
2012 Wagner GP, Lynch VJ, Nnamani M. Origin of the Endometrial Gene Regulatory Network of Placental Mammals. Biology of Reproduction. 87: 33-33. DOI: 10.1093/Biolreprod/87.S1.33  0.57
2011 Lynch VJ, May G, Wagner GP. Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature. 480: 383-6. PMID 22080951 DOI: 10.1038/Nature10595  0.603
2011 Lynch VJ, Leclerc RD, May G, Wagner GP. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nature Genetics. 43: 1154-9. PMID 21946353 DOI: 10.1038/Ng.917  0.759
2011 Brayer KJ, Lynch VJ, Wagner GP. Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation. Proceedings of the National Academy of Sciences of the United States of America. 108: E414-20. PMID 21788518 DOI: 10.1073/Pnas.1100990108  0.55
2011 Lynch VJ, Wagner GP. Revisiting a classic example of transcription factor functional equivalence: are Eyeless and Pax6 functionally equivalent or divergent? Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 316: 93-8. PMID 20853421 DOI: 10.1002/Jez.B.21373  0.62
2011 Padua MB, Alvarez NV, Lynch VJ, Garthwaite MA, Golos TG, Kalkunte S, Sharma S, Bazer FW, Hansen PJ. Uteroferrin (ACP5): Expression of an Ancient Gene During Pregnancy in Mammals. Biology of Reproduction. 85: 381-381. DOI: 10.1093/Biolreprod/85.S1.381  0.454
2010 Wagner GP, Lynch VJ. Evolutionary novelties. Current Biology : Cb. 20: R48-52. PMID 20129035 DOI: 10.1016/j.cub.2009.11.010  0.444
2010 Lynch VJ, Wagner GP. Did egg-laying boas break Dollo's law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae). Evolution; International Journal of Organic Evolution. 64: 207-16. PMID 19659599 DOI: 10.1111/J.1558-5646.2009.00790.X  0.488
2010 Kohlsdorf T, Lynch VJ, Rodrigues MT, Brandley MC, Wagner GP. Data and data interpretation in the study of limb evolution: A reply to Galis et al. On the reevolution of digits in the lizard genus bachia Evolution. 64: 2477-2485. DOI: 10.1111/J.1558-5646.2010.01042.X  0.464
2009 Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biology and Evolution. 1: 85-98. PMID 20333180 DOI: 10.1093/Gbe/Evp010  0.573
2009 Lynch VJ, Brayer K, Gellersen B, Wagner GP. HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genes. Plos One. 4: e6845. PMID 19727442 DOI: 10.1371/Journal.Pone.0006845  0.64
2009 Lynch VJ. Live-birth in vipers (Viperidae) is a key innovation and adaptation to global cooling during the Cenozoic. Evolution; International Journal of Organic Evolution. 63: 2457-65. PMID 19563326 DOI: 10.1111/J.1558-5646.2009.00733.X  0.347
2009 Lynch VJ. Use with caution: developmental systems divergence and potential pitfalls of animal models. The Yale Journal of Biology and Medicine. 82: 53-66. PMID 19562005  0.348
2009 Lynch VJ, Wagner GP. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes. Plos Genetics. 5: e1000349. PMID 19165336 DOI: 10.1371/Journal.Pgen.1000349  0.564
2008 Kohlsdorf T, Cummings MP, Lynch VJ, Stopper GF, Takahashi K, Wagner GP. A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13. Journal of Molecular Evolution. 67: 581-93. PMID 18855040 DOI: 10.1007/S00239-008-9156-7  0.756
2008 Lynch VJ, Tanzer A, Wang Y, Leung FC, Gellersen B, Emera D, Wagner GP. Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proceedings of the National Academy of Sciences of the United States of America. 105: 14928-33. PMID 18809929 DOI: 10.1073/Pnas.0802355105  0.823
2008 Lynch VJ, Wagner GP. Resurrecting the role of transcription factor change in developmental evolution. Evolution; International Journal of Organic Evolution. 62: 2131-54. PMID 18564379 DOI: 10.1111/J.1558-5646.2008.00440.X  0.599
2008 Wagner GP, Lynch VJ. The gene regulatory logic of transcription factor evolution. Trends in Ecology & Evolution. 23: 377-85. PMID 18501470 DOI: 10.1016/J.Tree.2008.03.006  0.601
2007 Wagner GP, Otto W, Lynch V, Stadler PF. A stochastic model for the evolution of transcription factor binding site abundance. Journal of Theoretical Biology. 247: 544-53. PMID 17475285 DOI: 10.1016/J.Jtbi.2007.03.001  0.489
2007 Lynch VJ. Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes. Bmc Evolutionary Biology. 7: 2. PMID 17233905 DOI: 10.1186/1471-2148-7-2  0.444
2006 Lynch VJ, Roth JJ, Wagner GP. Adaptive evolution of Hox-gene homeodomains after cluster duplications. Bmc Evolutionary Biology. 6: 86. PMID 17078881 DOI: 10.1186/1471-2148-6-86  0.617
2006 Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Molecular Biology and Evolution. 23: 121-36. PMID 16162861 DOI: 10.1093/Molbev/Msj020  0.541
2005 Wagner GP, Lynch VJ. Molecular evolution of evolutionary novelties: the vagina and uterus of therian mammals. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 304: 580-92. PMID 16252266 DOI: 10.1002/Jez.B.21074  0.64
2005 Wagner GP, Takahashi K, Lynch V, Prohaska SJ, Fried C, Stadler PF, Amemiya C. Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. Journal of Molecular Evolution. 60: 665-76. PMID 15983874 DOI: 10.1007/S00239-004-0252-Z  0.57
2004 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP. Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings. Biological Sciences / the Royal Society. 271: 2201-7. PMID 15539344 DOI: 10.1098/Rspb.2004.2848  0.78
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