| Year |
Citation |
Score |
| 2024 |
Birkemeier M, Swindle A, Bowman J, Lynch VJ. Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows (). Biorxiv : the Preprint Server For Biology. PMID 38617256 DOI: 10.1101/2024.04.04.588129 |
0.409 |
|
| 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 |
0.592 |
|
| 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 |
0.612 |
|
| 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 |
0.328 |
|
| 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 |
0.499 |
|
| 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 |
0.339 |
|
| 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 |
0.602 |
|
| 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 |
0.64 |
|
| 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 |
0.379 |
|
| 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 |
0.763 |
|
| 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 |
0.574 |
|
| 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 |
0.466 |
|
| 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 |
0.569 |
|
| 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 |
0.455 |
|
| 2010 |
Wagner GP, Lynch VJ. Evolutionary novelties. Current Biology : Cb. 20: R48-52. PMID 20129035 DOI: 10.1016/j.cub.2009.11.010 |
0.443 |
|
| 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 |
0.487 |
|
| 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 |
0.463 |
|
| 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 |
0.572 |
|
| 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 |
0.445 |
|
| 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 |
0.616 |
|
| 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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