Vincent J Lynch

Vincent J Lynch

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Vincent J Lynch

Vincent J Lynch

Publications by authors named "Vincent J Lynch"

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An Ancient Fecundability-Associated Polymorphism Creates a GATA2 Binding Site in a Distal Enhancer of HLA-F.

Am J Hum Genet 2018 10 20;103(4):509-521. Epub 2018 Sep 20.

Department of Human Genetics, The University of Chicago, 920 East 58(th) Street, CLSC 319C, Chicago, IL 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2018.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174278PMC
October 2018

Insights on cancer resistance in vertebrates: reptiles as a parallel system to mammals.

Nat Rev Cancer 2018 08;18(8):525

University of Chicago, Department of Human Genetics & Department of Organismal Biology & Anatomy, Chicago, IL, USA.

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http://dx.doi.org/10.1038/s41568-018-0033-4DOI Listing
August 2018

A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage.

Cell Rep 2018 08;24(7):1765-1776

Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.07.042DOI Listing
August 2018

Transposable elements are the primary source of novelty in primate gene regulation.

Genome Res 2017 10 30;27(10):1623-1633. Epub 2017 Aug 30.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1101/gr.218149.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630026PMC
October 2017

An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression.

Am J Hum Genet 2016 Nov 13;99(5):1059-1071. Epub 2016 Oct 13.

Department of Human Genetics, University of Chicago, 920 East 58(th) Street, CLSC 319C, Chicago, IL 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097936PMC
November 2016

The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts.

Genome Biol Evol 2016 08 25;8(8):2459-73. Epub 2016 Aug 25.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut Yale Systems Biology Institute, Yale University, West Haven, Connecticut Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan

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http://dx.doi.org/10.1093/gbe/evw168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010902PMC
August 2016

A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1.

Cell Rep 2016 06 26;15(10):2097-2108. Epub 2016 May 26.

Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale University Medical School, New Haven, CT 06510, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.04.088DOI Listing
June 2016

GENETICS. A copy-and-paste gene regulatory network.

Authors:
Vincent J Lynch

Science 2016 Mar;351(6277):1029-30

Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 319C, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.aaf2977DOI Listing
March 2016

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.

Cell Rep 2015 Jul 2;12(2):217-28. Epub 2015 Jul 2.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506B Wartik Lab, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.celrep.2015.06.027DOI Listing
July 2015

Evolutionary forward genomics reveals novel insights into the genes and pathways dysregulated in recurrent early pregnancy loss.

Hum Reprod 2015 Mar 12;30(3):519-29. Epub 2015 Jan 12.

Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL 60637, USA

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http://dx.doi.org/10.1093/humrep/deu355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325674PMC
March 2015

Cell-type phylogenetics and the origin of endometrial stromal cells.

Cell Rep 2015 Mar 26;10(8):1398-409. Epub 2015 Feb 26.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, New Haven, CT 06516, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.01.062DOI Listing
March 2015

A model based criterion for gene expression calls using RNA-seq data.

Theory Biosci 2013 Sep 25;132(3):159-64. Epub 2013 Apr 25.

Yale Systems Biology Institute, 300 Heffernan Drive, West Haven, CT 06516, USA.

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http://dx.doi.org/10.1007/s12064-013-0178-3DOI Listing
September 2013

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

PLoS Genet 2013 Apr 25;9(4):e1003470. Epub 2013 Apr 25.

Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636048PMC
April 2013

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.

Theory Biosci 2012 Dec 8;131(4):281-5. Epub 2012 Aug 8.

Department of Ecology and Evolutionary Biology, Yale Systems Biology Institute, Yale University, 300 Heffernan Drive, West Haven, CT 06516, USA.

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http://link.springer.com/10.1007/s12064-012-0162-3
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http://dx.doi.org/10.1007/s12064-012-0162-3DOI Listing
December 2012

ACP5 (Uteroferrin): phylogeny of an ancient and conserved gene expressed in the endometrium of mammals.

Biol Reprod 2012 Apr 27;86(4):123. Epub 2012 Apr 27.

Department of Animal Sciences and DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, Florida 32611-0910, USA.

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https://academic.oup.com/biolreprod/article/2530740/ACP5-Ute
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http://dx.doi.org/10.1095/biolreprod.111.097964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338662PMC
April 2012

Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.

Mol Biol Evol 2012 Jan 2;29(1):239-47. Epub 2011 Aug 2.

Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, USA.

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http://dx.doi.org/10.1093/molbev/msr189DOI Listing
January 2012

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB.

Nature 2011 Nov 13;480(7377):383-6. Epub 2011 Nov 13.

Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1038/nature10595DOI Listing
November 2011

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.

Nat Genet 2011 Sep 25;43(11):1154-9. Epub 2011 Sep 25.

Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA.

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http://www.nature.com/articles/ng.917
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http://dx.doi.org/10.1038/ng.917DOI Listing
September 2011

Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation.

Proc Natl Acad Sci U S A 2011 Aug 25;108(32):E414-20. Epub 2011 Jul 25.

Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1073/pnas.1100990108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156161PMC
August 2011

Revisiting a classic example of transcription factor functional equivalence: are Eyeless and Pax6 functionally equivalent or divergent?

J Exp Zool B Mol Dev Evol 2011 Mar 17;316B(2):93-8. Epub 2010 Sep 17.

Department of Ecology and Evolutionary Biology and Yale Institute for Systems Biology, Yale University, New Haven, Connecticut 06511, USA.

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http://doi.wiley.com/10.1002/jez.b.21373
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http://dx.doi.org/10.1002/jez.b.21373DOI Listing
March 2011

Did egg-laying boas break Dollo's law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae).

Evolution 2010 Jan 30;64(1):207-16. Epub 2009 Jul 30.

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551.

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http://dx.doi.org/10.1111/j.1558-5646.2009.00790.xDOI Listing
January 2010

Evolutionary novelties.

Curr Biol 2010 Jan;20(2):R48-52

Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1016/j.cub.2009.11.010DOI Listing
January 2010

Live-birth in vipers (Viperidae) is a key innovation and adaptation to global cooling during the Cenozoic.

Authors:
Vincent J Lynch

Evolution 2009 Sep 26;63(9):2457-65. Epub 2009 Jun 26.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2009.00733.xDOI Listing
September 2009

HoxA-11 and FOXO1A cooperate to regulate decidual prolactin expression: towards inferring the core transcriptional regulators of decidual genes.

PLoS One 2009 Sep 3;4(9):e6845. Epub 2009 Sep 3.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006845PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731163PMC
September 2009

Use with caution: developmental systems divergence and potential pitfalls of animal models.

Authors:
Vincent J Lynch

Yale J Biol Med 2009 Jun;82(2):53-66

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701150PMC
June 2009

Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies.

Genome Biol Evol 2009 May 25;1:85-98. Epub 2009 May 25.

Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/gbe/evp010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817405PMC
May 2009

Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes.

PLoS Genet 2009 Jan 23;5(1):e1000349. Epub 2009 Jan 23.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2622764PMC
January 2009

A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13.

J Mol Evol 2008 Dec;67(6):581-93

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.

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http://link.springer.com/10.1007/s00239-008-9156-7
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http://dx.doi.org/10.1007/s00239-008-9156-7DOI Listing
December 2008

Resurrecting the role of transcription factor change in developmental evolution.

Evolution 2008 Sep 28;62(9):2131-54. Epub 2008 Jun 28.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2008.00440.xDOI Listing
September 2008

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals.

Proc Natl Acad Sci U S A 2008 Sep 22;105(39):14928-33. Epub 2008 Sep 22.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0802355105
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http://dx.doi.org/10.1073/pnas.0802355105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567470PMC
September 2008

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals.

Proc Natl Acad Sci U S A 2008 Sep 22;105(39):14928-33. Epub 2008 Sep 22.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0802355105
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http://dx.doi.org/10.1073/pnas.0802355105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567470PMC
September 2008

The gene regulatory logic of transcription factor evolution.

Trends Ecol Evol 2008 Jul 22;23(7):377-85. Epub 2008 May 22.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA.

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http://dx.doi.org/10.1016/j.tree.2008.03.006DOI Listing
July 2008

Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes.

Authors:
Vincent J Lynch

BMC Evol Biol 2007 Jan 18;7. Epub 2007 Jan 18.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1186/1471-2148-7-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1783844PMC
January 2007

Adaptive evolution of Hox-gene homeodomains after cluster duplications.

BMC Evol Biol 2006 Nov 1;6:86. Epub 2006 Nov 1.

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06551, USA.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-6-86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636070PMC
November 2006

The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts.

Mol Biol Evol 2006 Jan 14;23(1):121-36. Epub 2005 Sep 14.

Department of Ecology and Evolutionary Biology, Yale University, USA.

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http://dx.doi.org/10.1093/molbev/msj020DOI Listing
January 2006

Molecular evolution of evolutionary novelties: the vagina and uterus of therian mammals.

J Exp Zool B Mol Dev Evol 2005 Nov;304(6):580-92

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106, USA.

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http://doi.wiley.com/10.1002/jez.b.21074
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http://dx.doi.org/10.1002/jez.b.21074DOI Listing
November 2005

Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals.

Proc Biol Sci 2004 Nov;271(1554):2201-7

Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06551, USA.

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http://dx.doi.org/10.1098/rspb.2004.2848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691855PMC
November 2004