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Items: 1 to 50 of 108

1.

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.

Bryois J, Garrett ME, Song L, Safi A, Giusti-Rodriguez P, Johnson GD, Shieh AW, Buil A, Fullard JF, Roussos P, Sklar P, Akbarian S, Haroutunian V, Stockmeier CA, Wray GA, White KP, Liu C, Reddy TE, Ashley-Koch A, Sullivan PF, Crawford GE.

Nat Commun. 2018 Aug 7;9(1):3121. doi: 10.1038/s41467-018-05379-y.

2.

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee.

Pizzollo J, Nielsen WJ, Shibata Y, Safi A, Crawford GE, Wray GA, Babbitt CC.

Genome Biol Evol. 2018 Mar 1;10(3):826-839. doi: 10.1093/gbe/evy041.

3.

Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures.

Byrne M, Koop D, Morris VB, Chui J, Wray GA, Cisternas P.

Dev Dyn. 2018 Jan;247(1):239-249. doi: 10.1002/dvdy.24584. Epub 2017 Nov 9.

4.

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.

Linchangco GV Jr, Foltz DW, Reid R, Williams J, Nodzak C, Kerr AM, Miller AK, Hunter R, Wilson NG, Nielsen WJ, Mah CL, Rouse GW, Wray GA, Janies DA.

Mol Phylogenet Evol. 2017 Oct;115:161-170. doi: 10.1016/j.ympev.2017.07.022. Epub 2017 Jul 27.

PMID:
28757447
5.

Gene expression and adaptive noncoding changes during human evolution.

Babbitt CC, Haygood R, Nielsen WJ, Wray GA.

BMC Genomics. 2017 Jun 5;18(1):435. doi: 10.1186/s12864-017-3831-2.

6.

Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan.

Koop D, Cisternas P, Morris VB, Strbenac D, Yang JY, Wray GA, Byrne M.

BMC Dev Biol. 2017 Feb 13;17(1):4. doi: 10.1186/s12861-017-0145-1.

7.

Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification.

Runcie DE, Dorey N, Garfield DA, Stumpp M, Dupont S, Wray GA.

Genome Biol Evol. 2016 Dec 1;8(12):3672-3684. doi: 10.1093/gbe/evw272.

8.

Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains.

Dutta V, Altermann E, Olson J, Wray GA, Siletzky RM, Kathariou S.

Genome Announc. 2016 Aug 18;4(4). pii: e00833-16. doi: 10.1128/genomeA.00833-16.

9.

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.

Israel JW, Martik ML, Byrne M, Raff EC, Raff RA, McClay DR, Wray GA.

PLoS Biol. 2016 Mar 4;14(3):e1002391. doi: 10.1371/journal.pbio.1002391. eCollection 2016 Mar. Erratum in: PLoS Biol. 2016 Jun;14(6):e1002489.

10.

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.

Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA.

BMC Bioinformatics. 2016 Jan 22;17:48. doi: 10.1186/s12859-016-0883-2.

11.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

12.

Molecular clocks and the early evolution of metazoan nervous systems.

Wray GA.

Philos Trans R Soc Lond B Biol Sci. 2015 Dec 19;370(1684). pii: 20150046. doi: 10.1098/rstb.2015.0046. Review.

13.

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.

Bauernfeind AL, Soderblom EJ, Turner ME, Moseley MA, Ely JJ, Hof PR, Sherwood CC, Wray GA, Babbitt CC.

Genome Biol Evol. 2015 Jul 10;7(8):2276-88. doi: 10.1093/gbe/evv132.

14.

Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma.

Byrne M, Koop D, Cisternas P, Strbenac D, Yang JY, Wray GA.

Mar Genomics. 2015 Dec;24 Pt 1:41-5. doi: 10.1016/j.margen.2015.05.019. Epub 2015 Jun 9.

PMID:
26066611
15.

High spatial resolution proteomic comparison of the brain in humans and chimpanzees.

Bauernfeind AL, Reyzer ML, Caprioli RM, Ely JJ, Babbitt CC, Wray GA, Hof PR, Sherwood CC.

J Comp Neurol. 2015 Oct 1;523(14):2043-61. doi: 10.1002/cne.23777. Epub 2015 Jul 14.

16.

Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.

Boyd JL, Skove SL, Rouanet JP, Pilaz LJ, Bepler T, Gordân R, Wray GA, Silver DL.

Curr Biol. 2015 Mar 16;25(6):772-779. doi: 10.1016/j.cub.2015.01.041. Epub 2015 Feb 19.

17.

Does evolutionary theory need a rethink?

Laland K, Uller T, Feldman M, Sterelny K, Müller GB, Moczek A, Jablonka E, Odling-Smee J, Wray GA, Hoekstra HE, Futuyma DJ, Lenski RE, Mackay TF, Schluter D, Strassmann JE.

Nature. 2014 Oct 9;514(7521):161-4. doi: 10.1038/514161a. No abstract available.

PMID:
25297418
18.

Genetic comparisons yield insight into the evolution of enamel thickness during human evolution.

Horvath JE, Ramachandran GL, Fedrigo O, Nielsen WJ, Babbitt CC, St Clair EM, Pfefferle LW, Jernvall J, Wray GA, Wall CE.

J Hum Evol. 2014 Aug;73:75-87. doi: 10.1016/j.jhevol.2014.01.005. Epub 2014 May 5.

PMID:
24810709
19.

Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

Wygoda JA, Yang Y, Byrne M, Wray GA.

Genome Biol Evol. 2014 Apr;6(4):964-73. doi: 10.1093/gbe/evu070.

20.

Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission.

Muntané G, Horvath JE, Hof PR, Ely JJ, Hopkins WD, Raghanti MA, Lewandowski AH, Wray GA, Sherwood CC.

Cereb Cortex. 2015 Jun;25(6):1596-607. doi: 10.1093/cercor/bht354. Epub 2014 Jan 9.

21.

The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network.

Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA.

PLoS Biol. 2013 Oct;11(10):e1001696. doi: 10.1371/journal.pbio.1001696. Epub 2013 Oct 29.

22.
23.

Social environment influences the relationship between genotype and gene expression in wild baboons.

Runcie DE, Wiedmann RT, Archie EA, Altmann J, Wray GA, Alberts SC, Tung J.

Philos Trans R Soc Lond B Biol Sci. 2013 Apr 8;368(1618):20120345. doi: 10.1098/rstb.2012.0345. Print 2013 May 19.

24.

Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus.

Garfield D, Haygood R, Nielsen WJ, Wray GA.

Evol Dev. 2012 Mar-Apr;14(2):152-67. doi: 10.1111/j.1525-142X.2012.00532.x.

PMID:
23017024
25.

Genetics of gene expression responses to temperature stress in a sea urchin gene network.

Runcie DE, Garfield DA, Babbitt CC, Wygoda JA, Mukherjee S, Wray GA.

Mol Ecol. 2012 Sep;21(18):4547-62. doi: 10.1111/j.1365-294X.2012.05717.x. Epub 2012 Aug 1.

26.

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE.

PLoS Genet. 2012 Jun;8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28.

27.

Changes in gene expression associated with reproductive maturation in wild female baboons.

Babbitt CC, Tung J, Wray GA, Alberts SC.

Genome Biol Evol. 2012;4(2):102-9. doi: 10.1093/gbe/evr134. Epub 2011 Dec 8.

28.

A potential role for glucose transporters in the evolution of human brain size.

Fedrigo O, Pfefferle AD, Babbitt CC, Haygood R, Wall CE, Wray GA.

Brain Behav Evol. 2011;78(4):315-26. doi: 10.1159/000329852. Epub 2011 Oct 7.

29.

Evolution. CNCing is believing.

Wray GA.

Science. 2011 Aug 19;333(6045):946-7. doi: 10.1126/science.1210771. No abstract available.

PMID:
21852480
30.

Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases.

Bilbo SD, Wray GA, Perkins SE, Parker W.

Med Hypotheses. 2011 Oct;77(4):494-504. doi: 10.1016/j.mehy.2011.06.019. Epub 2011 Jul 7.

PMID:
21741180
31.

Allele-specific gene expression in a wild nonhuman primate population.

Tung J, Akinyi MY, Mutura S, Altmann J, Wray GA, Alberts SC.

Mol Ecol. 2011 Feb;20(4):725-39. doi: 10.1111/j.1365-294X.2010.04970.x. Epub 2011 Jan 13.

32.

Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution.

Pfefferle AD, Warner LR, Wang CW, Nielsen WJ, Babbitt CC, Fedrigo O, Wray GA.

J Hum Evol. 2011 Feb;60(2):205-212. doi: 10.1016/j.jhevol.2010.10.004. Epub 2010 Dec 28.

33.

Genomic signatures of diet-related shifts during human origins.

Babbitt CC, Warner LR, Fedrigo O, Wall CE, Wray GA.

Proc Biol Sci. 2011 Apr 7;278(1708):961-9. doi: 10.1098/rspb.2010.2433. Epub 2010 Dec 22. Review.

34.

Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.

Yokoyama KD, Thorne JL, Wray GA.

Genome Biol Evol. 2011;3:66-74. doi: 10.1093/gbe/evq078. Epub 2010 Nov 30.

35.

Extensive changes in the expression of the opioid genes between humans and chimpanzees.

Cruz-Gordillo P, Fedrigo O, Wray GA, Babbitt CC.

Brain Behav Evol. 2010;76(2):154-62. doi: 10.1159/000320968. Epub 2010 Nov 15.

PMID:
21079395
36.

Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.

Oliver TA, Garfield DA, Manier MK, Haygood R, Wray GA, Palumbi SR.

Genome Biol Evol. 2010;2:800-14. doi: 10.1093/gbe/evq063. Epub 2010 Oct 8.

37.

Generation-biased gene expression in a bryophyte model system.

Szövényi P, Rensing SA, Lang D, Wray GA, Shaw AJ.

Mol Biol Evol. 2011 Jan;28(1):803-12. doi: 10.1093/molbev/msq254. Epub 2010 Sep 20.

PMID:
20855429
38.

A pipeline to determine RT-QPCR control genes for evolutionary studies: application to primate gene expression across multiple tissues.

Fedrigo O, Warner LR, Pfefferle AD, Babbitt CC, Cruz-Gordillo P, Wray GA.

PLoS One. 2010 Sep 2;5(9). pii: e12545. doi: 10.1371/journal.pone.0012545.

39.

Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations.

Tung J, Alberts SC, Wray GA.

Trends Genet. 2010 Aug;26(8):353-62. doi: 10.1016/j.tig.2010.05.005. Epub 2010 Jun 25. Review.

40.

Contrasts between adaptive coding and noncoding changes during human evolution.

Haygood R, Babbitt CC, Fedrigo O, Wray GA.

Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7853-7. doi: 10.1073/pnas.0911249107. Epub 2010 Apr 12.

41.

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA.

Genome Biol Evol. 2010 Jan 18;2:67-79. doi: 10.1093/gbe/evq002.

42.

Developmental evolution: how beetles evolved their shields.

Fédrigo O, Wray GA.

Curr Biol. 2010 Jan 26;20(2):R64-6. doi: 10.1016/j.cub.2009.12.012.

43.

Multiple Functional Variants in cis Modulate PDYN Expression.

Babbitt CC, Silverman JS, Haygood R, Reininga JM, Rockman MV, Wray GA.

Mol Biol Evol. 2010 Feb;27(2):465-79. doi: 10.1093/molbev/msp276. Epub 2009 Nov 12.

PMID:
19910384
44.

Comparative embryology without a microscope: using genomic approaches to understand the evolution of development.

Garfield DA, Wray GA.

J Biol. 2009;8(7):65. doi: 10.1186/jbiol161. Epub 2009 Jul 21. Review.

45.

Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitro.

Warner LR, Babbitt CC, Primus AE, Severson TF, Haygood R, Wray GA.

Brain Res. 2009 Sep 8;1288:1-8. doi: 10.1016/j.brainres.2009.06.086. Epub 2009 Jul 8.

PMID:
19591812
46.

Evolution of a malaria resistance gene in wild primates.

Tung J, Primus A, Bouley AJ, Severson TF, Alberts SC, Wray GA.

Nature. 2009 Jul 16;460(7253):388-91. doi: 10.1038/nature08149. Epub 2009 Jun 24.

PMID:
19553936
47.

Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation.

Tung J, Fédrigo O, Haygood R, Mukherjee S, Wray GA.

Mol Biol Evol. 2009 Sep;26(9):2047-59. doi: 10.1093/molbev/msp113. Epub 2009 Jun 8.

48.

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.

Yokoyama KD, Ohler U, Wray GA.

Nucleic Acids Res. 2009 Jul;37(13):e92. doi: 10.1093/nar/gkp423. Epub 2009 May 29.

49.

Genetics. Enhancing gene regulation.

Wray GA, Babbitt CC.

Science. 2008 Sep 5;321(5894):1300-1. doi: 10.1126/science.1163568. No abstract available.

PMID:
18772422
50.

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs.

Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD.

Genome Res. 2008 Mar;18(3):489-99. doi: 10.1101/gr.7265208. Epub 2008 Feb 1.

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