Wes Warren, Ph.D.,  McDonnell Genome Institute

Dr. Wesley Warren joined the McDonnell Genome Institute in 2001 where he currently serves as Assistant Director of Comparative Genomics. Dr. Warren is an internationally recognized expert in animal comparative genomics. He has received the honor of being published multiple times on the cover of NATURE featuring the chicken, platypus, orangutan, elephant shark, Y chromosomes and, most recently, the small ape gibbon. Dr. Warren's NATURE publication on the zebra finch genome focused on the genetic drivers of vocal learning and was featured as the lead news story for both NPR and ABC Nightly News. The application of genomics to the identification of biological markers for environmental and physiological drivers within multiple phylums remains a key research focus for Dr. Warren.

Dr. Warren's research interests focus on the use of whole genome analysis methods to dissect the underlying molecular signatures linked to biological observations in various species of vertebrates. Dr. Warren's research group uses various whole genome comparative methods to examine changes in gene evolution, including loss and gain events and unknown natural or artificial selection marks, as a means to better understand human biology. The identification of these gene aberrations in evolutionary time promises to engender new thoughts on the molecular workings of observed traits. Dr. Warren has played a lead role in the analysis of many vertebrate genomes, including chicken, platypus, zebra finch, orangutan, vervet, platyfish, elephant shark, cat, house fly and tarsier genomes and is an integral team member in the analysis of many others. He also co-leads a consortium tasked with the sequencing and characterization of the Y chromosomes of several mammals and the bird Z and W chromosomes. In addition to whole genome analysis research, Dr. Warren leads a de novo genome assembly group that is seeking better ways to construct assemblies from next-generation sequencing platforms.

Dr. Warren received his B.S. degree from Oklahoma State University (animal sciences, 1984), M.S. degree from Clemson University (reproductive physiology, 1987) and Ph.D. from the University of Missouri (molecular endocrinology, 1990). He completed a post-doctoral fellowship at G.D. Searle Pharmaceutical before joining Monsanto Company, where he held several leadership roles including group manager of genome initiatives. Prior to joining Washington University, he was Senior Director of Operations at Incyte Genomics.

De Novo Collaborations

Contact Dr. Warren if you are interested in collaborating on a genome sequencing and analysis project in the following categories:

  • Mammals
  • Birds
  • Fish

Publications

title citation publication date
Divergence and Functional Degradation of a Sex Chromosome-like Supergene. Curr Biol. 2016 Jan 20. pii: S0960-9822(15)01562-6. doi: 10.1016/j.cub.2015.11.069. [Epub ahead of print] 2016-01-20
Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun. 2016 Jan 25;7:10474. doi: 10.1038/ncomms10474. 2016-01-25
X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics. 2016 Jan 7;17(1):37. doi: 10.1186/s12864-015-2361-z. 2016-01-07
Whole Body Melanoma Transcriptome Response in Medaka. PLoS One. 2015 Dec 29;10(12):e0143057. doi: 10.1371/journal.pone.0143057. eCollection 2015. 2015-12-29
INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2015 Nov 10. [Epub ahead of print] 2015-11-10
The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-component and Metazoan-type Tyrosine Kinase Signaling. Genome Biol Evol. 2015 Nov 27. pii: evv237. [Epub ahead of print] 2015-11-27
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14936-14941. Epub 2015 Nov 16. 2015-12-01
The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res. 2015 Sep 16. pii: gr.192922.115. [Epub ahead of print] 2015-09-16
Joint MiRNA/mRNA Expression Profiling Reveals Changes Consistent with Development of Dysfunctional Corpus Luteum after Weight Gain. PLoS One. 2015 Aug 10;10(8):e0135163. doi: 10.1371/journal.pone.0135163. eCollection 2015. 2015-08-10
Response to Hron et al. Genome Biol. 2015 Aug 18;16:165. doi: 10.1186/s13059-015-0725-y. 2015-08-18
Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. 2015-07-14
Corrigendum: Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids. Sci Rep. 2015 Jul 28;5:12590. doi: 10.1038/srep12590. 2015-07-28
Physical mapping and refinement of the painted turtle genome (Chrysemys picta) inform amniote genome evolution and challenges turtle-bird chromosomal conservation. Genome Biol Evol. 2015 Jun 24. pii: evv119. [Epub ahead of print] 2015-06-24
Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits. BMC Biol. 2015 Jun 20;13(1):41. [Epub ahead of print] 2015-06-20
Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica. Fish Shellfish Immunol. 2015 May 14. pii: S1050-4648(15)00221-1. doi: 10.1016/j.fsi.2015.05.004. [Epub ahead of print] 2015-05-14
Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. 2014-12-12
Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 2014 Dec 18;15(12):565. [Epub ahead of print] 2014-12-18
Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11. 2014-12-12
Extensive error in the number of genes inferred from draft genome assemblies PLoS Comput Biol. 2014 Dec 4;10(12):e1003998. doi: 10.1371/journal.pcbi.1003998. eCollection 2014. 2014-12-04
Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell. 2014 Nov 6;159(4):800-13. doi: 10.1016/j.cell.2014.09.052. Epub 2014 Oct 30. 2014-11-06
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17230-17235. Epub 2014 Nov 10. 2014-12-02
Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res. 2014 Dec;24(12):2066-76. doi: 10.1101/gr.180893.114. Epub 2014 Nov 4. 2014-12-01
The cavefish genome reveals candidate genes for eye loss. Nat Commun. 2014 Oct 20;5:5307. doi: 10.1038/ncomms6307. 2014-10-20
Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment Genome Biology 2014, doi:10.1186/s13059-014-0466-3 2014-10-14
Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679. 2014-09-11
High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 2014 Jul 8;3:11. doi: 10.1186/2047-217X-3-11. eCollection 2014. 2014-07-08
A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish. Genetics. 2014 Apr 2;197(2):625-641. [Epub ahead of print] 2014-04-02
The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014 Jul 20. doi: 10.1038/ng.3042. [Epub ahead of print] 2014-07-20
Venkatesh et al. reply. Nature. 2014 Jul 10;511(7508):E9-10. doi: 10.1038/nature13447. 2014-07-10
On the origin of SCPP genes. Evol Dev. 2014 May;16(3):125-6. doi: 10.1111/ede.12072. Epub 2014 May 5. 2014-05-01
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014 Apr 24;508(7497):494-9. doi: 10.1038/nature13206. 2014-04-24
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science. 2014 Apr 25;344(6182):380-6. doi: 10.1126/science.1249656. 2014-04-25
Genome of the human hookworm Necator americanus. Nat Genet. 2014 Jan 19. doi: 10.1038/ng.2875. [Epub ahead of print] 2014-01-19
Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826. 2014-01-09
Echidna venom gland transcriptome provides insights into the evolution of monotreme venom. PLoS One. 2013 Nov 12;8(11):e79092. doi: 10.1371/journal.pone.0079092. 2013-11-12
Systems biology of the vervet monkey. ILAR J. 2013 Jan;54(2):122-43. doi: 10.1093/ilar/ilt049. 2013-11-01
The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 2013 Dec 2. [Epub ahead of print] 2013-12-03
No bull: Upholding community standards in public sharing of biological datasets. Proc Natl Acad Sci U S A. 2013 Oct 30. [Epub ahead of print] 2013-10-30
Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus. Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16933-8. doi: 10.1073/pnas.1317192110. Epub 2013 Oct 1. 2013-10-15
The development and characterization of a 60K SNP chip for chicken. BMC Genomics. 2011 May 31;12(1):274. doi: 10.1186/1471-2164-12-274. 2011-05-31
Characterizing the chromosomes of the platypus (Ornithorhynchus anatinus). Chromosome Res. 2007;15(8):961-74. doi: 10.1007/s10577-007-1186-2. Epub 2008 Jan 9. 2007-01-01
Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome. 2008 Apr;51(4):294-302. doi: 10.1139/G08-010. 2008-04-01
Resources for genetic and genomic studies of Xenopus. Methods Mol Biol. 2006;322:1-16. 2006-01-01
A limited role for gene duplications in the evolution of platypus venom. Mol Biol Evol. 2012 Jan;29(1):167-77. doi: 10.1093/molbev/msr180. Epub 2011 Aug 3. 2012-01-01
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov-Dec;100(6):659-74. doi: 10.1093/jhered/esp086. Epub 2009 Nov 5. 2009-11-01
Digital gene expression for non-model organisms. Genome Res. 2011 Nov;21(11):1905-15. doi: 10.1101/gr.122135.111. Epub 2011 Aug 15. 2012-10-01
Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biol. 2011 Jul 28;12(7):406. doi: 10.1186/gb-2011-12-7-406. 2011-07-28
A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci. 2011 Apr 29;4(2):257-70. doi: 10.4056/sigs.1664145. 2011-04-29
Higher-order genome organization in platypus and chicken sperm and repositioning of sex chromosomes during mammalian evolution. Chromosoma. 2009 Feb;118(1):53-69. doi: 10.1007/s00412-008-0177-1. Epub 2008 Aug 26. 2009-02-01
Independent specialization of the human and mouse X chromosomes for the male germ line. Nat Genet. 2013 Jul 21. doi: 10.1038/ng.2705. [Epub ahead of print] 2013-07-21
To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed. PLoS One. 2013 Jun 27;8(6):e67105. Print 2013. 2013-06-27
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet. 2013 Jun 9. doi: 10.1038/ng.2657. [Epub ahead of print] 2013-06-09
Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Sci Rep. 2013 Apr 30;3:1756. doi: 10.1038/srep01756. 2013-04-30
Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)]. Aquat Toxicol. 2013 Mar 20;134-135C:74-81. doi: 10.1016/j.aquatox.2013.03.003. [Epub ahead of print] 2013-03-20
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet. 2013 Mar 31. doi: 10.1038/ng.2604. [Epub ahead of print] 2013-03-31
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013 Mar 28;14(3):R28. [Epub ahead of print] 2013-03-18
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet. 2013 Feb 24. doi: 10.1038/ng.2568. [Epub ahead of print] 2013-02-24
Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources. Comp Biochem Physiol Part D Genomics Proteomics. 2013 Mar;8(1):11-6. doi: 10.1016/j.cbd.2012.10.006. Epub 2012 Nov 9. 2012-11-09
The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics. 2012 Feb;190(2):389-401. doi: 10.1534/genetics.111.132639. 2012-02-01
The Evolutionary Origins of Monotreme Crural Glands Toxicon. 2012. 60:122-123. 2012-08-01
Specifying and Sustaining Pigmentation Patterns in Domestic and Wild Cats Science. 2012 Sep 21;337(6101):1536-41. 2012-09-23
Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216. Mol Biol Evol. 2012 Aug 30. [Epub ahead of print] 2012-08-30
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles. Mol Cell Proteomics. 2012 Aug 16. [Epub ahead of print] 2012-08-16
A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. 2012-06-13
Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. 2012-06-13
A non-human primate system for large-scale genetic studies of complex traits. Hum Mol Genet. 2012 May 3. [Epub ahead of print] 2012-05-03
Insights into hominid evolution from the gorilla genome sequence. Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842. 2012-03-07
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature. 2012 Feb 22. doi: 10.1038/nature10843. [Epub ahead of print] 2012-02-22
Graph accordance of next-generation sequence assemblies. Bioinformatics. 2011 Oct 23. [Epub ahead of print] 2011-10-23
A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. 2011-10-12
Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F(1) interspecies hybrids. Comp Biochem Physiol C Toxicol Pharmacol. 2011 Apr 3. [Epub ahead of print] 2011-04-03
Transcriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A. PLoS One. 2011 Apr 5;6(4):e18379. 2011-04-05
A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 2011 Mar 31;12(3):R31. [Epub ahead of print] 2011-03-31
The draft genome of the parasitic nematode Trichinella spiralis Nat Genet. 2011 Mar;43(3):228-35. Epub 2011 Feb 20. 2011-02-20
The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle PLoS Genet. 2011 Feb 10;7(2):e1002007. 2011-02-10
Comparative and demographic analysis of orang-utan genomes Nature. 2011 Jan 27;469(7331):529-33. 2011-01-27
Novel venom gene discovery in the platypus. Genome Biol. 2010;11(9):R95. Epub 2010 Sep 29. 2010-09-29
Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature. 2010 Jul 11. [Epub ahead of print] 2010-07-11
The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30;328(5978):633-6. 2010-04-30
Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals. BMC Genomics. 2010 Apr 1;11:220. 2010-04-01
Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biol. 2010 Apr 1;8:29. 2010-04-01
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 2010 Mar;19 Suppl 1:266-76. 2010-03-19
Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species. PLoS One. 2010 Mar 8;5(3):e9556. 2010-03-08
A Catalog of Reference Genomes from the Human Microbiome. Science. 2010 May 21;328(5981):994-999. 2010-05-21
The genome of a songbird. Nature. 2010 Apr 1;464(7289):757-62. 2010-04-01
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature. 2010 Jan 28;463(7280):536-9. Epub 2010 Jan 13. 2010-01-13
Understanding and utilising mammalian venom via a platypus venom transcriptome. J Proteomics. 2009 Mar 6;72(2):155-64. Epub 2008 Dec 25. 2009-03-06
Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet. 2008 Aug 10. [Epub ahead of print] 2008-08-10
Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics. 2008 Aug 26. [Epub ahead of print] 2008-08-26
Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals. BMC Biol. 2008 Jul 25;6:34. 2008-07-25
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. 2008 Jun;18(6):965-73. Epub 2008 May 7. 2008-05-31
Defensins and the convergent evolution of platypus and reptile venom genes. Genome Res. 2008 Jun;18(6):986-94. Epub 2008 May 7. 2008-06-12
Loss of genes implicated in gastric function during platypus evolution. Genome Biol. 2008;9(5):R81. Epub 2008 May 15. 2008-05-15
Origin of INSL3-mediated testicular descent in therian mammals. Genome Res. 2008 Jun;18(6):974-85. Epub 2008 May 7. 2008-06-15
Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. 2008-05-08
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods. 2008 Mar;5(3):247-52. Epub 2008 Feb 24. 2008-03-08
Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34. 2007-04-13
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature. 2004 Dec 9;432(7018):717-22. 2004-12-09
Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 2006 Jun;16(6):768-75. 2006-06-01
Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Mol Biochem Parasitol. 2005 Sep;143(1):49-57. 2005-08-31
A physical map of the chicken genome. Nature. 2004 Dec 9;432(7018):679-80. 2004-12-09
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005 Apr 7;434(7034):724-31. 2005-04-07
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature. 2004 Dec 9;432(7018):695-716. 2004-12-10
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid Nat Genet. 2004 Dec;36(12):1268-74. Epub 2004 Dec. 2004-11-07
Fosmid-based physical mapping of the Histoplasma capsulatum genome. Genome Res. 2004 Aug;14(8):1603-9. 2004-08-15
Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 2004 Apr;14(4):766-79. 2004-04-01