People
Wes Warren
Wesley Warren is a professor of comparative genomics in Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics.Dr. Warren is a recognized leader in the field of comparative genomics with a theme of looking at biology with a molecular lens.
His scientific journey started with basic animal physiology and has progressed to single cell transcriptome analysis of a broad spectrum of species. Dr. Warren’s research involves the use of whole genome comparative methods to examine genetic adaptation events within existing or newly discovered model organisms as a means to better understand human biology. His research has contributed broadly to a conceptual framework in the field of evolutionary medicine as illustrated by his labs sequencing, assembling and characterizing genomes throughout a broad span of Darwins tree of life. Many of his studies have resulted in highly impactful outcomes benefiting scientific understanding of these species. Today the availability of large volumes of genome sequence data has fundamentally changed our approach to trait discovery, whether it be in the form of genome assemblies, population sequencing, or gene expression variation in bulk or at single cell resolution.
Dr. Warren’s lab is now carrying out single nuclei transcriptome experiments to identify a cell types specific molecular profile that contributes to our understanding of a species many phenotypes, that could substantially enlighten the ambiguous path that connects genes to their traits.
News about Wes Warren
Nov 07, 2023
How the tiger’s nose knows
Mar 02, 2021
Genetic link in primate points to source of adaption and longevity in capuchins
2023
The immune cell landscape and response of Marek’s disease resistant and susceptible chickens infected with Marek’s disease virus. Warren, Wesley C.; Rice, Edward S. a; Meyer, Ashley a; Hearn, Cari J. b; Steep, Alec c; Hunt, Henry D. b; Monson, Melissa S. d, e; Lamont, Susan J. d; Cheng, Hans H.. Scientific Reports ; Volume 13, Issue 1.
Date published: December 1, 2023Featured in this article: Wes Warren.
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A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Puritz, Jonathan B.; Guo, Ximing b; Hare, Matthew c; He, Yan b; Hillier, LaDeana W. d; Jin, Shubo b; Liu, Ming b; Lotterhos, Katie E. e; Minx, Pat f; Modak, Tejashree g; Proestou, Dina h; Rice, Edward S. i. Molecular Ecology Resources; Open Access.
Date published: July 12, 2023Featured in this article: Wes Warren.
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Genomic landscape and gene expression profiles of feline oral squamous cell carcinoma. Rodney, Alana R. a; Skidmore, Zachary L. b; Grenier, Jennifer K. c; Griffith, Obi L. b; Miller, Andrew D. c; Chu, Shirley d; Ahmed, Faraz c; Bryan, Jeffrey N. d; Peralta, Santiago; Warren, Wesley C.. Frontiers in Veterinary Science ; Volume 10.
Date published: July 12, 2023Featured in this article: Wes Warren.
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A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos). Judkins, Megan E. a; Roemer, Gary W. c, o; Millsap, Brian A. d; Barnes, Joseph G. e; Bedrosian, Bryan E. f; Clarke, Stephen L. g; Domenech, Robert h; Herring, Garth i; Lamont, Myles j; Smith, Brian W. k; Stahlecker, Dale W. l; Stuber, Matthew J. m. Conservation Genetics; Volume 24, Issue 3, Pages 391 - 404.
Date published: June 1, 2023Featured in this article: Wes Warren.
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Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. Labbé, Frédéric a; Abdeladhim, Maha b; Abrudan, Jenica c; Araki, Alejandra Saori d; Araujo, Ricardo N. e; Arensburger, Peter f; Benoit, Joshua B. g; Brazil, Reginaldo Pecanha h; Bruno, Rafaela V. d; Rivas, Gustavo Bueno da Silva d, i; de Abreu, Vinicius Carvalho j; Charamis, Jason k. PLoS Neglected Tropical Diseases; Volume 17, Issue 4.
Date published: April 1, 2023Featured in this article: Wes Warren.
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High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Lu, Yuan; Rice, Edward b; Du, Kang a; Kneitz, Susanne c; Naville, Magali d; Dechaud, Corentin d; Volff, Jean-Nicolas d; Boswell, Mikki a; Boswell, William a; Hillier, LaDeana e; Tomlinson, Chad f; Milin, Kremitzki f. Genome Research; Volume 33, Issue 4, Pages 557 - 571.
Date published: April 1, 2023Featured in this article: Wes Warren.
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Single-nuclei RNA sequencing (snRNA-seq) uncovers trophoblast cell types and lineages in the mature bovine placenta. Davenport, Kimberly M. a; Ortega, M. Sofia a; Liu, Hongyu a; O’Neil, Eleanore V. a; Kelleher, Andrew M. b; Warren, Wesley C. a, c; Spencer, Thomas E.. Proceedings of the National Academy of Sciences of the United States of America; Volume 120, Issue 12.
Date published: March 21, 2023Featured in this article: Wes Warren.
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2022
Epigenetic Regulation of Cancer Immune Cells. Avella D M, Radhakrishnana V, Kanve S N, Manjunath Y, Li G, Kimchi E T, Staveley-O’Carroll K F, Warren W C, Kaifi J T, Mitchem J B. Seminars in Cancer Biology; Volume 83, Pages 377 - 383.
Date published: August 1, 2022Featured in this article: Wes Warren.
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Tumorigenic circulating tumor cells from xenograft mouse models of non-metastatic NSCLC patients reveal distinct single cell heterogeneity and drug responses. Suvilesh K, Nussbaum Y, Radhakrishnan V, Manjunath Y, Avella D, Staveley-O’Carroll K, Kimchi E, Chaudhuri A, Shyu C, Li G, Pantel K, Warren, W. Molecular Cancer; Volume 21, Issue 1.
Date published: March 12, 2022Featured in this article: Wes Warren.
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Discordant Genome Assemblies Drastically Alter the Interpretation of Single-Cell RNA Sequencing Data Which Can Be Mitigated by a Novel Integration Method. Potts H, Lemieux M, Rice E, Warren W, Choudhury R, Mommersteeg M. Cells; Volume 11, Issue 4.
Date published: February 2, 2022Featured in this article: Wes Warren.
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2021
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Gonçalves AT, Escobar-Sepulveda H, Liachko I, Nelson B, Roberts S, Warren W. Scientific Data; 8(1):60.
Date published: December 1, 2021Featured in this article: Wes Warren.
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A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Warren WC, Boggs TE, Borowsky R, Carlson BM, Ferrufino E, Gross JB, Hillier LD, Hu Z, Keene AC, Kenzior A, Kowalko JE, Tomlinson C, Kremitzki M, Lemieux ME, Graves-Lindsay T, McGaugh SE, Miller JT, Mommersteeg MTM, Moran RL, Peuß R, Rice ES, Riddle MR, Sifuentes-Romero I, Stanhope BA, Tabin CJ, Thakur S, Yamamoto Y, Rohner N. Nature Communications; 12(1):1447.
Date published: December 1, 2021Featured in this article: Wes Warren.
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The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze S-H, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. BMC Biology; 19(1):41.
Date published: December 1, 2021Featured in this article: Wes Warren.
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Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control (BMC Biology, (2021), 19, 1, (41), 10.1186/s12915-021-00975-9). Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze S-H, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. BMC Biology; 19(1):150.
Date published: December 1, 2021Featured in this article: Wes Warren.
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Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. BMC Genomics; 22(1):188.
Date published: December 1, 2021Featured in this article: Wes Warren.
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A domestic cat whole exome sequencing resource for trait discovery. Rodney AR, Buckley RM, Fulton RS, Fronick C, Richmond T, Helps CR, Pantke P, Trent DJ, Vernau KM, Munday JS, Lewin AC, Middleton R, Lyons LA, Warren WC. Scientific Reports; 11(1):7159.
Date published: December 1, 2021Featured in this article: Wes Warren.
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Multi-omic analyses in Abyssinian cats with primary renal amyloid deposits. Genova F, Nonnis S, Maffioli E, Tedeschi G, Strillacci MG, Carisetti M, Sironi G, Cupaioli FA, Di Nanni N, Mezzelani A, Mosca E, Helps CR, Leegwater PAJ, Dorso L, Buckley RM, Aberdein D, Alves PC, Andersson AO, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Haase B, Häggström J, Harvey RJ, Hasegawa D, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RHL, Lohi H, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Peterson-Jones SM, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y, Lyons LA, Longeri M. Scientific Reports; 11(1):8339.
Date published: December 1, 2021Featured in this article: Wes Warren.
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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, Jarvis ED, Kirschel ANG, Digby A, Veale A, Bronikowski A, Murphy B, Robertson B, Baker C, Mazzoni C, Balakrishnan C, Lee C, Mead D, Teeling E, Aiden EL, Todd E, Eichler E, Naylor GJP, Zhang G, Smith J, Wolf J, Touchon J, Delmore K, Jakobsen K, Komoroske L, Wilkinson M, Genner M, Pšenička M, Fuxjager M, Stratton M, Liedvogel M, Gemmell N, Minias P, Dunn PO, Sudmant P, Morin P, Ayub Q, Kraus R, Vernes S, Smith S, Lama T, Edwards T, Smith T, Gilbert T, Marques-Bonet T, Einfeldt T, Venkatesh B, Johnson W, Warren W, Bukhman Y. Genome Biology; 22(1):120.
Date published: December 1, 2021Featured in this article: Wes Warren.
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Genome assemblies across the diverse evolutionary spectrum of leishmania protozoan parasites. Warren WC, Akopyants NS, Dobson DE, Hertz-Fowler C, Lye L-F, Myler PJ, Ramasamy G, Shanmugasundram A, Silva-Franco F, Steinbiss S, Tomlinson C, Wilson RK, Beverley SM. Microbiology Resource Announcements; 10(35):e00545-21.
Date published: September 1, 2021Featured in this article: Wes Warren.
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Erratum: The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS (Proc. Natl. Acad. Sci. U.S.A. (2021) 118 (e2010632118) DOI: 10.1073/pnas.2010632118). Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, del Campo J, Hernandez SC, Fiore AD, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E. Proceedings of the National Academy of Sciences of the United States of America; 118(34):e2112613118.
Date published: August 24, 2021Featured in this article: Wes Warren.
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Mining the 99 Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus). Lyons LA, Buckley RM, Harvey RJ, Abitbol M, Aberdein D, Alves PC, Ohlsson Andersson A, Bellone RR, Bergström TF, Bilgen N, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Davis BW, Davison L, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Hasegawa D, Haase B, Jagannathan V, Lait P, Hernandez I, Hytönen MK, Kaukonen M, Kosho T, Leclerc E, Lear TL, Leeb T, Li RHL, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Middleton R, Munday JS, Murphy WJ, Myers AN, Pedersen NC, Peterson-Jones SM, Rothschild MF, Rusbridge C, Schoenebeck JJ, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y. Animal Genetics; 52(3):321-332.
Date published: June 1, 2021Featured in this article: Wes Warren.
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Explainable artificial intelligence in high-throughput drug repositioning for subgroup stratifications with interventionable potential. Al-Taie Z, Liu D, Mitchem JB, Papageorgiou C, Kaifi JT, Warren WC, Shyu C-R. Journal of Biomedical Informatics; 118:103792.
Date published: June 1, 2021Featured in this article: Wes Warren.
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3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Cacciatore ÁS, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire GB, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei P-J, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Palma FD, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Aiden EL, Rowland BD. Science; 372(6545):abe2218.
Date published: May 28, 2021Featured in this article: Wes Warren.
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Current and prospective methods for assessing anti-tumor immunity in colorectal cancer. Nussbaum YI, Manjunath Y, Suvilesh KN, Warren WC, Shyu C-R, Kaifi JT, Ciorba MA, Mitchem JB. International Journal of Molecular Sciences; 22(9):4802.
Date published: May 1, 2021Featured in this article: Wes Warren.
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Towards complete and error-free genome assemblies of all vertebrate species. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW III, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hanningan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli K-P, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Nature; 592(7856):737-746.
Date published: April 29, 2021Featured in this article: Wes Warren.
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The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. Schartl M, Kneitz S, Ormanns J, Schmidt C, Anderson JL, Amores A, Catchen J, Wilson C, Geiger D, Winkler C, Hedrich R, Warren WC, Walter R, Meyer A, Postlethwait JH. Current Biology; 31(5):911-922.e4.
Date published: March 8, 2021Featured in this article: Wes Warren.
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Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis). Bredemeyer KR, Harris AJ, Li G, Zhao L, Foley NM, Roelke-Parker M, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Journal of Heredity; 112(2):165-173.
Date published: March 1, 2021Featured in this article: Wes Warren.
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The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, del Campo J, Hernandez SC, Fiore AD, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E. Proceedings of the National Academy of Sciences of the United States of America; 118(7):e2010632118.
Date published: February 16, 2021Featured in this article: Wes Warren.
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Transcriptomic changes of murine visceral fat exposed to intermittent hypoxia at single cell resolution. Khalyfa A, Warren W, Andrade J, Bottoms CA, Rice ES, Cortese R, Kheirandish-Gozal L, Gozal D. International Journal of Molecular Sciences; 22(1):1-24.
Date published: January 1, 2021Featured in this article: Wes Warren.
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Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly. Lu Y, Bierbach D, Ormanns J, Warren WC, Walter RB, Schartl M. Genome Research; 31(3):372-379.
Date published: January 1, 2021Featured in this article: Wes Warren.
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Epigenetic Regulation of Cancer Immune Cells. Avella Patino DM, Radhakrishnan V, Suvilesh KN, Manjunath Y, Li G, Kimchi ET, Staveley-O'Carroll KF, Warren WC, Kaifi JT, Mitchem JB. Seminars in Cancer Biology; 1-7.
Date published: January 1, 2021Featured in this article: Wes Warren.
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2020
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, Devogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Science; 370(6523):eabc6617.
Date published: December 18, 2020Featured in this article: Wes Warren.
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Author Correction: Elephant shark genome provides unique insights into gnathostome evolution (Nature, (2014), 505, 7482, (174-179), 10.1038/nature12826). Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay B-H, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Nature; 588(7837):E15.
Date published: December 10, 2020Featured in this article: Wes Warren.
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Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns. Lu Y, Boswell M, Boswell W, Salinas R, Savage M, Reyes J, Walter S, Marks R, Gonzalez T, Medrano G, Warren WC, Schartl M, Walter RB. BMC Genomics; 21(1):787.
Date published: December 1, 2020Featured in this article: Wes Warren.
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Oncogenic allelic interaction in Xiphophorus highlights hybrid incompatibility. Lu Y, Sandoval A, Voss S, Lai Z, Kneitz S, Boswell W, Boswell M, Savage M, Walter C, Warren W, Schartl M, Walter R. Proceedings of the National Academy of Sciences of the United States of America; 117(47):29786-29794.
Date published: November 24, 2020Featured in this article: Wes Warren.
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Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages. Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho T-J, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Genome Research; 31(12):1716-1726.
Date published: November 18, 2020Featured in this article: Wes Warren.
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A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. Buckley RM, Davis BW, Brashear WA, Farias FHG, Kuroki K, Graves T, Hillier LW, Kremitzki M, Li G, Middleton RP, Minx P, Tomlinson C, Lyons LA, Murphy WJ, Warren WC. PLoS Genetics; 16(10):e1008926.
Date published: October 22, 2020Featured in this article: Wes Warren.
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Intra-Strain Genetic Variation of Platyfish (Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory. Lu Y, Olivas T, Boswell M, Boswell W, Warren WC, Schartl M, Walter RB. Frontiers in Genetics; 11:562594.
Date published: October 6, 2020Featured in this article: Wes Warren.
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A novel swine sex-linked marker and its application across different mammalian species. Lucas CG, Spate AM, Samuel MS, Spate LA, Warren WC, Prather RS, Wells KD. Transgenic Research; 29(4):395-407.
Date published: August 1, 2020Featured in this article: Wes Warren.
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Neuronal ceroid lipofuscinosis in a domestic cat associated with a DNA sequence variant that creates a premature stop codon in CLN6. Katz ML, Buckley RM, Biegen V, O'Brien DP, Johnson GC, Warren WC, Lyons LA. G3: Genes, Genomes, Genetics; 10(8):2741-2751.
Date published: August 1, 2020Featured in this article: Wes Warren.
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Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy. Cogné B, Latypova X, Senaratne LDS, Martin L, Koboldt DC, Kellaris G, Fievet L, Le Meur G, Caldari D, Debray D, Nizon M, Frengen E, Bowne SJ, Buckley RM, Aberdein D, Alves PC, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RHL, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y, Cadena EL, Daiger SP, Bujakowska KM, Pierce EA, Gorin M, Katsanis N, Bézieau S, Petersen-Jones SM, Occelli LM, Lyons LA, Legeai-Mallet L, Sullivan LS, Davis EE, Isidor B. American Journal of Human Genetics; 106(6):893-904.
Date published: June 4, 2020Featured in this article: Wes Warren.
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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Du K, Stöck M, Kneitz S, Klopp C, Woltering JM, Adolfi MC, Feron R, Prokopov D, Makunin A, Kichigin I, Schmidt C, Fischer P, Kuhl H, Wuertz S, Gessner J, Kloas W, Cabau C, Iampietro C, Parrinello H, Tomlinson C, Journot L, Postlethwait JH, Braasch I, Trifonov V, Warren WC, Meyer A, Guiguen Y, Schartl M. Nature Ecology and Evolution; 4(6):841-852.
Date published: June 1, 2020Featured in this article: Wes Warren.
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Werewolf, there wolf: Variants in hairless associated with hypotrichia and roaning in the lykoi cat breed. Buckley RM, Gandolfi B, Creighton EK, Pyne CA, Bouhan DM, Leroy ML, Senter DA, Gobble JR, Abitbol M, Lyons LA, Lyons LA, Buckley RM, Aberdein D, Garrick DJ, Munday JS, Alves PC, Barsh GS, Kaelin CB, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Todhunter RJ, Wilcox EA, Distl O, Dodman NH, Ellinwood NM, Rothschild MF, Fogle JE, Forman OP, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Yu Y, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Lohi H, Kosho T, Leclerc E, Lear TL, Leeb T, Li RHL, Longeri M, Magnuson MA, Malik R, Mane SP, Murphy WJ, Pedersen NC, Stern JA, Peterson-Jones SM, Rusbridge C, Shapiro B, Swanson WF, Terio KA, Warren WC, Wildschutte JH. Genes; 11(6):1-15.
Date published: June 1, 2020Featured in this article: Wes Warren.
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A deletion in GDF7 is associated with a heritable forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts in cats. Yu Y, Creighton EK, Buckley RM, Lyons LA, Buckley RM, Aberdein D, Alves PC, Barsh GS, Bellone RR, Bergström TF, Boyko AR, Brockman JA, Casal ML, Castelhano MG, Distl O, Dodman NH, Ellinwood NM, Fogle JE, Forman OP, Garrick DJ, Ginns EI, Häggström J, Harvey RJ, Hasegawa D, Haase B, Helps CR, Hernandez I, Hytönen MK, Kaukonen M, Kaelin CB, Kosho T, Leclerc E, Lear TL, Leeb T, Li RHL, Lohi H, Longeri M, Magnuson MA, Malik R, Mane SP, Munday JS, Murphy WJ, Pedersen NC, Peterson-Jones SM, Rothschild MF, Rusbridge C, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Warren WC, Wilcox EA, Wildschutte JH, Yu Y, Lyons LA. Genes; 11(6):1-15.
Date published: June 1, 2020Featured in this article: Wes Warren.
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The quail genome: Insights into social behaviour, seasonal biology and infectious disease response. Morris KM, Hindle MM, Boitard S, Burt DW, Danner AF, Eory L, Forrest HL, Gourichon D, Gros J, Hillier LW, Jaffredo T, Khoury H, Lansford R, Leterrier C, Loudon A, Mason AS, Meddle SL, Minvielle F, Minx P, Pitel F, Seiler JP, Shimmura T, Tomlinson C, Vignal A, Webster RG, Yoshimura T, Warren WC, Smith J. BMC Biology; 18(1):14.
Date published: February 12, 2020Featured in this article: Wes Warren.
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A 50K SNP array reveals genetic structure for bald eagles (Haliaeetus leucocephalus). Judkins ME, Couger BM, Warren WC, Van Den Bussche RA. Conservation Genetics; 21(1):65-76.
Date published: February 1, 2020Featured in this article: Wes Warren.
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2019
Application of the Transcriptional Disease Signature (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish Model. Lu Y, Boswell W, Boswell M, Klotz B, Kneitz S, Regneri J, Savage M, Mendoza C, Postlethwait J, Warren WC, Schartl M, Walter RB. Scientific Reports; 9(1):530.
Date published: December 1, 2019Featured in this article: Wes Warren.
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Author Correction: Applications and efficiencies of the first cat 63K DNA array (Scientific Reports, (2018), 8, 1, (7024), 10.1038/s41598-018-25438-0). Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton DG, Warren WC, Wasim M, Lyons LA. Scientific Reports; 9(1):4664.
Date published: December 1, 2019Featured in this article: Wes Warren.
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Human-specific tandem repeat expansion and differential gene expression during primate evolution. Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Warren WC, Pollen AA, Chaisson MJP, Eichler EE. Proceedings of the National Academy of Sciences of the United States of America; 116(46):23243-23253.
Date published: November 12, 2019Featured in this article: Wes Warren.
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Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Genome Biology; 20(1):187.
Date published: September 2, 2019Featured in this article: Wes Warren.
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The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior. Schartl M, Kneitz S, Volkoff H, Adolfi M, Schmidt C, Fischer P, Minx P, Tomlinson C, Meyer A, Warren WC. Genome Biology and Evolution; 11(8):2099-2106.
Date published: July 8, 2019Featured in this article: Wes Warren.
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A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Vignal A, Boitard S, Thébault N, Dayo G-K, Yapi-Gnaore V, Youssao Abdou Karim I, Berthouly-Salazar C, Pálinkás-Bodzsár N, Guémené D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X. Molecular Ecology Resources; 19(4):997-1014.
Date published: July 1, 2019Featured in this article: Wes Warren.
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Expression signatures of cisplatin- And trametinib-treated early-stage medaka melanomas. Klotz B, Kneitz S, Lu Y, Boswell W, Postlethwait J, Warren W, Walter RB, Schartl M. G3: Genes, Genomes, Genetics; 9(7):2267-2276.
Date published: July 1, 2019Featured in this article: Wes Warren.
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Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites. Filosa JN, Berry CT, Ruthel G, Beverley SM, Warren WC, Tomlinson C, Myler PJ, Dudkin EA, Povelones ML, Povelones M. PLoS Neglected Tropical Diseases; 13(7):e0007570.
Date published: July 1, 2019Featured in this article: Wes Warren.
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Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM. Genome Research; 29(4):576-589.
Date published: April 1, 2019Featured in this article: Wes Warren.
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Antarctic blackfin icefish genome reveals adaptations to extreme environments. Kim B-M, Amores A, Kang S, Ahn D-H, Kim J-H, Kim I-C, Lee JH, Lee SG, Lee H, Lee J, Kim H-W, Desvignes T, Batzel P, Sydes J, Titus T, Wilson CA, Catchen JM, Warren WC, Schartl M, Detrich HW III, Postlethwait JH, Park H. Nature Ecology and Evolution; 3(3):469-478.
Date published: March 1, 2019Featured in this article: Wes Warren.
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Characterizing the Major Structural Variant Alleles of the Human Genome. Audano PA, Sulovari A, Graves-Lindsay TA, Cansilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE. Cell; 176(3):663-675.e19.
Date published: January 24, 2019Featured in this article: Wes Warren.
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2018
First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. Genova F, Longeri M, Lyons LA, Bagnato A, Gandolfi B, Aberdein D, Alves PC, Barsh GS, Beale HC, Bergström TF, Boyko AR, Brockman JA, Castelhano MG, Chan PP, Davis BW, Distl O, Dodman NH, Matthew Ellinwood N, Fogle JE, Forman OP, Garrick DJ, Häggström J, Helps CR, Hytönen MK, Ibrahim DM, Kaukonen M, Kaelin CB, Leclerc E, Lear TL, Leeb T, Lohi H, Lupiáñez DG, Magnuson MA, Malik R, Montague MJ, Munday JS, Murphy WJ, Ostrander EA, Pedersen NC, Petersen-Jones SM, Rothschild MF, Shapiro B, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Ueda Y, Warren WC, Wilcox EA, Wildschutte JH, Ginns EI, Strillacci MG. BMC Genomics; 19(1):895.
Date published: December 10, 2018Featured in this article: Wes Warren.
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Author Correction: Applications and efficiencies of the first cat 63K DNA array (Scientific Reports DOI: 10.1038/s41598-018-25438-0). Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton DG, Warren WC, Wasim M, Lyons LA. Scientific Reports; 8(1):8746.
Date published: December 1, 2018Featured in this article: Wes Warren.
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Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Nature Communications; 9(1):5136.
Date published: December 1, 2018Featured in this article: Wes Warren.
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Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model. Lu Y, Boswell M, Boswell W, Kneitz S, Klotz B, Savage M, Salinas R, Marks R, Regneri J, Postlethwait J, Warren WC, Schartl M, Walter R. PLoS Genetics; 14(12):e1007875.
Date published: December 1, 2018Featured in this article: Wes Warren.
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The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. Molecular Ecology; 27(22):4397-4416.
Date published: November 1, 2018Featured in this article: Wes Warren.
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Erratum to: Ancient hybridization and strong adaptation to viruses across African vervet monkey populations (Nature Genetics, (2017), 49, 12, (1705-1713), 10.1038/ng.3980). Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, Nordborg M. Nature Genetics; 50(11):1617.
Date published: November 1, 2018Featured in this article: Wes Warren.
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Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Perry BW, Card DC, Mcglothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Horrmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo C-H, Mcgaugh SE, Bronikowski AM, De Koning APJ, Edwards SV, Pfrender ME, Minx P, Brodie ED, Brodie ED, Warren WC, Castoe TA. Genome Biology and Evolution; 10(8):2110-2129.
Date published: August 1, 2018Featured in this article: Wes Warren.
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Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions. Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Pigment Cell and Melanoma Research; 31(4):496-508.
Date published: July 1, 2018Featured in this article: Wes Warren.
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High-resolution comparative analysis of great ape genomes. Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. Science; 360(6393):eaar6343.
Date published: June 8, 2018Featured in this article: Wes Warren.
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Expression signatures of early-stage and advanced medaka melanomas. Klotz B, Kneitz S, Regensburger M, Hahn L, Dannemann M, Kelso J, Nickel B, Lu Y, Boswell W, Postlethwait J, Warren W, Kunz M, Walter RB, Schartl M. Comparative Biochemistry and Physiology Part - C: Toxicology and Pharmacology; 208:20-28.
Date published: June 1, 2018Featured in this article: Wes Warren.
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Diversity of immunoglobulin light chain genes in non-teleost ray-finned fish uncovers IgL subdivision into five ancient isotypes. Guselnikov SV, Baranov KO, Najaskshin AM, Mechetina LV, Chikaev NA, Makunin AI, Kulemzin SV, Andreyushkova DA, Stöck M, Wuertz S, Gessner J, Warren WC, Schartl M, Trifonov VA, Taranin AV. Frontiers in Immunology; 9(MAY):1079.
Date published: May 28, 2018Featured in this article: Wes Warren.
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Improved genome assembly and annotation for the Rock Pigeon (Columba livia). Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, Domyan ET, Suh A, Warren WC, Yandell M, Thomas P Gilbert M, Shapiro MD. G3: Genes, Genomes, Genetics; 8(5):1391-1398.
Date published: May 1, 2018Featured in this article: Wes Warren.
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Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Warren WC, García-Pérez R, Xu S, Lampert KP, Chalopin D, Stöck M, Loewe L, Lu Y, Kuderna L, Minx P, Montague MJ, Tomlinson C, Hillier LW, Murphy DN, Wang J, Wang Z, Garcia CM, Thomas GCW, Volff J-N, Farias F, Aken B, Walter RB, Pruitt KD, Marques-Bonet T, Hahn MW, Kneitz S, Lynch M, Schartl M. Nature Ecology and Evolution; 2(4):669-679.
Date published: April 1, 2018Featured in this article: Wes Warren.
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The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development. Wagner JT, Singh PP, Romney AL, Riggs CL, Minx P, Woll SC, Roush J, Warren WC, Brunet A, Podrabsky JE. BMC Genomics; 19(1):155.
Date published: February 20, 2018Featured in this article: Wes Warren.
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Applications and efficiencies of the first cat 63K DNA array. Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton DG, Warren WC, Wasim M, Lyons LA. Scientific Reports; 8(1):7024.
Date published: January 1, 2018Featured in this article: Wes Warren.
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2017
Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge. Bateta R, Wang J, Wu Y, Weiss BL, Warren WC, Murilla GA, Aksoy S, Mireji PO. Parasites and Vectors; 10(1):614.
Date published: December 19, 2017Featured in this article: Wes Warren.
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Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi O-W, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Scmitt CA, Svardal H, Jorgensen MJ, Kaplan JR, Villar D, Aken BL, Flicek P, Nag R, Wong ES, Blangero J, Dyer TD, Bogomolov M, Benjamini Y, Weinstock GM, Dewar K, Sabatti C, Wilson RK, Jentsch DJ, Warren W, Coppola G, Woods RP, Freimer NB. Nature Genetics; 49(12):1714-1721.
Date published: December 1, 2017Featured in this article: Wes Warren.
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Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, Nordborg M. Nature Genetics; 49(12):1705-1713.
Date published: December 1, 2017Featured in this article: Wes Warren.
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The Novel Evolution of the Sperm Whale Genome. Warren WC, Kuderna L, Alexander A, Catchen J, Pérez-Silva JG, López-Otín C, Quesada V, Minx P, Tomlinson C, Montague MJ, Farias FHG, Walter RB, Marques-Bonet T, Glenn T, Kieran TJ, Wise SS, Wise JP, Waterhouse RM. Genome Biology and Evolution; 9(12):3260-3264.
Date published: December 1, 2017Featured in this article: Wes Warren.
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The genome and adult somatic transcriptome of the mormyrid electric fish paramormyrops kingsleyae. Gallant JR, Losilla M, Tomlinson C, Warren WC. Genome Biology and Evolution; 9(12):3525-3530.
Date published: December 1, 2017Featured in this article: Wes Warren.
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The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular Ecology; 26(22):6384-6399.
Date published: November 1, 2017Featured in this article: Wes Warren.
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A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan tro 3.0). Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. GigaScience; 6(11):gix098.
Date published: November 1, 2017Featured in this article: Wes Warren.
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A Resource of Genome-Wide Single Nucleotide Polymorphisms (Snps) for the Conservation and Management of Golden Eagles. Van Den Bussche RA, Judkins ME, Montague MJ, Warren WC. Journal of Raptor Research; 51(3):368-377.
Date published: September 1, 2017Featured in this article: Wes Warren.
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Gene expression in Leishmania is regulated predominantly by gene dosage. Iantorno SA, Durrant C, Khan A, Sanders MJ, Beverley SM, Warren WC, Berriman M, Sacks DL, Cotton JA, Grigg ME. mBio; 8(5):e01393-17.
Date published: September 1, 2017Featured in this article: Wes Warren.
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Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, Do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, DI Stephano L, DInguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, Fitzgerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, De Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, De Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ, Rast JP, Rollinson D, Rosse IC, Rotgans B, Routledge EJ, Ryan KM, Scholte LLS, Storey KB, Swain M, Tennessen JA, Tomlinson C, Trujillo DL, Volpi EV, Walker AJ, Wang T, Wannaporn I, Warren WC, Wu X-J, Yoshino TP, Yusuf M, Zhang S-M, Zhao M, Wilson RK. Nature Communications; 8:16153.
Date published: August 23, 2017Featured in this article: Wes Warren.
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Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Molecular Carcinogenesis; 56(8):1935-1944.
Date published: August 1, 2017Featured in this article: Wes Warren.
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Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Passow CN, Brown AP, Arias-Rodriguez L, Yee M-C, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Molecular Ecology; 26(16):4211-4225.
Date published: August 1, 2017Featured in this article: Wes Warren.
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The practical use of genome sequencing data in the management of a feline colony pedigree. Farias FHG, Tomlinson C, Labuda J, Perez-Camargo G, Middleton R, Warren WC. BMC Veterinary Research; 13(1):225.
Date published: July 27, 2017Featured in this article: Wes Warren.
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Corrigendum: A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine. Schauer KL, Lemoine CMR, Pelin A, Corradi N, Warren WC, Grosell M. Scientific Reports; 7:46844.
Date published: June 19, 2017Featured in this article: Wes Warren.
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The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species. Lencer ES, Warren WC, Harrison R, McCune AR. BMC Genomics; 18(1):424.
Date published: May 30, 2017Featured in this article: Wes Warren.
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Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, Do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, DI Stephano L, DInguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, Fitzgerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, De Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, De Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ, Rast JP, Rollinson D, Rosse IC, Rotgans B, Routledge EJ, Ryan KM, Scholte LLS, Storey KB, Swain M, Tennessen JA, Tomlinson C, Trujillo DL, Volpi EV, Walker AJ, Wang T, Wannaporn I, Warren WC, Wu X-J, Yoshino TP, Yusuf M, Zhang S-M, Zhao M, Wilson RK. Nature Communications; 8:15451.
Date published: May 16, 2017Featured in this article: Wes Warren.
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Discovery and genotyping of structural variation from long-read haploid genome sequence data. Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin C-S, Korlach J, Wilson RK, Eichler EE. Genome Research; 27(5):677-685.
Date published: May 1, 2017Featured in this article: Wes Warren.
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Early-Onset Progressive Retinal Atrophy Associated with an IQCB1 Variant in African Black-Footed Cats (Felis nigripes). Oh A, Pearce JW, Gandolfi B, Creighton EK, Suedmeyer WK, Selig M, Bosiack AP, Castaner LJ, Whiting REH, Belknap EB, Lyons LA, Aderdein D, Alves PC, Barsh GS, Beale HC, Boyko AR, Castelhano MG, Chan P, Ellinwood NM, Garrick DJ, Helps CR, Kaelin CB, Leeb T, Lohi H, Longeri M, Malik R, Montague MJ, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Swanson WF, Terio KA, Todhunter RJ, Warren WC. Scientific Reports; 7:43918.
Date published: March 21, 2017Featured in this article: Wes Warren.
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Avian W and mammalian y chromosomes convergently retained dosage-sensitive regulators. Bellott DW, Skaletsky H, Cho T-J, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC. Nature Genetics; 49(3):387-394.
Date published: March 1, 2017Featured in this article: Wes Warren.
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Building and Improving Reference Genome Assemblies: This paper reviews the problems and algorithms of assembling a complete genome from millions of short DNA sequencing reads. Meltz Steinberg K, Schneider VA, Alkan C, Montague MJ, Warren WC, Church DM, Wilson RK. Proceedings of the IEEE; 105(3):422-435.
Date published: March 1, 2017Featured in this article: Wes Warren.
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Precision Medicine in Cats: Novel Niemann-Pick Type C1 Diagnosed by Whole-Genome Sequencing. Mauler DA, Gandolfi B, Reinero CR, O'Brien DP, Spooner JL, Lyons LA, Aberdein D, Alves PC, Barsh GS, Beale HC, Boyko AR, Brockman JA, Castelhano MG, Chan PP, Matthew Ellinwood N, Fogle JE, Garrick DJ, Helps CR, Hytönen MK, Kaukonen M, Kaelin CB, Leclerc E, Leeb T, Lohi H, Longeri M, Malik R, Montague MJ, Munday JS, Murphy WJ, Pedersen NC, Rothschild MF, Stern JA, Swanson WF, Terio KA, Todhunter RJ, Ueda Y, Warren WC, Wilcox EA, Wildschutte JH. Journal of Veterinary Internal Medicine; 31(2):539-544.
Date published: March 1, 2017Featured in this article: Wes Warren.
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The landscape of extreme genomic variation in the highly adaptable Atlantic killifish. Reid NM, Jackson CE, Gilbert D, Minx P, Montague MJ, Hampton TH, Helfrich LW, King BL, Nacci DE, Aluru N, Karchner SI, Colbourne JK, Hahn ME, Shaw JR, Oleksiak MF, Crawford DL, Warren WC, Whitehead A. Genome Biology and Evolution; 9(3):659-676.
Date published: March 1, 2017Featured in this article: Wes Warren.
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A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats. Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, Lyons LA, 99 Lives Consortium, Alves PC, Barsh GS, Beale HC, Boyko AR, Castelhano MG, Chan P, Ellinwood NM, Helps CR, Kaelin CB, Leeb T, Lohi H, Longeri M, Montague MJ, Murphy WJ, Pedersen NC, Rothschild MF, Swanson WF, Terio KA, Todhunter RJ, Warren WC. Mammalian Genome; 28(1-2):47-55.
Date published: February 1, 2017Featured in this article: Wes Warren.
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A new chicken genome assembly provides insight into avian genome structure. Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. G3: Genes, Genomes, Genetics; 7(1):109-117.
Date published: January 1, 2017Featured in this article: Wes Warren.
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2016
The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Reid NM, Proestou DA, Clark BW, Warren WC, Colbourne JK, Shaw JR, Karchner SI, Hahn ME, Nacci D, Oleksiak MF, Crawford DL, Whitehead A. Science; 354(6317):1305-1308.
Date published: December 9, 2016Featured in this article: Wes Warren.
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Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Schmitz J, Noll A, Raabe CA, Churakov G, Voss R, Kiefmann M, Rozhdestvensky T, Brosius J, Baertsch R, Clawson H, Roos C, Zimin A, Minx P, Montague MJ, Wilson RK, Warren WC. Nature Communications; 7:12997.
Date published: October 6, 2016Featured in this article: Wes Warren.
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A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine. Schauer KL, Lemoine CMR, Pelin A, Corradi N, Warren WC, Grosell M. Scientific Reports; 6:34494.
Date published: October 3, 2016Featured in this article: Wes Warren.
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Pangolin genomes and the evolution of mammalian scales and immunity. Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli K-P, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo S-J, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ. Genome Research; 26(10):1312-1322.
Date published: October 1, 2016Featured in this article: Wes Warren.
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De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. Mohamed Yusoff A, Tan TK, Hari R, Koepfli K-P, Wee WY, Antunes A, Sitam FT, Rovie-Ryan JJ, Karuppannan KV, Wong GJ, Lipovich L, Warren WC, O'Brien SJ, Choo SW. Scientific Reports; 6:28199.
Date published: September 13, 2016Featured in this article: Wes Warren.
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Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates. Mason VC, Li G, Minx P, Schmitz J, Churakov G, Doronina L, Melin AD, Dominy NJ, Lim NT-L, Springer MS, Wilson RK, Warren WC, Helgen KM, Murphy WJ. Science Advances; 2(8):e1600633.
Date published: August 1, 2016Featured in this article: Wes Warren.
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Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models. Kneitz S, Mishra RR, Chalopin D, Postlethwait J, Warren WC, Walter RB, Schartl M. BMC Genomics; 17(1):357.
Date published: May 17, 2016Featured in this article: Wes Warren.
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Opsin repertoire and expression patterns in horseshoe crabs: Evidence from the genome of limulus polyphemus (arthropoda: Chelicerata). Battelle B-A, Ryan JF, Kempler KE, Saraf SR, Marten CE, Warren WC, Minx PJ, Montague MJ, Green PJ, Schmidt SA, Fulton L, Patel NH, Protas ME, Wilson RK, Porter ML. Genome Biology and Evolution; 8(5):1571-1589.
Date published: May 1, 2016Featured in this article: Wes Warren.
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Erratum: Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection (Proceedings of the National Academy of Sciences of the United States of America (2015) 112 (14936-14941) DOI 10.1073/pnas.1506226112). Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JMC, Sorgine MHF, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GRC, Calderón-Fernández G, A Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CRO, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, Da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DST, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Latorre-Estivalis JM, Lavore A, Lazoski C, Lazzari CR, Lorenzo MG, Majerowicz D, Mariotti M, Masuda H, Megy K, Melo ACA, Missirlis F, Mota T, Noriega FG, Nunes RD, Oliveira RLL, Oliverira-Silva GO, Pascual A, Pavan MG, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MAC, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JMC, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL. Proceedings of the National Academy of Sciences of the United States of America; 113(10):E1415-E1416.
Date published: March 8, 2016Featured in this article: Wes Warren.
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Divergence and functional degradation of a sex chromosome-like supergene. Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ, Minx P, Stager M, Betuel A, Cheviron ZA, Warren WC, Gonser RA, Balakrishnan CN. Current Biology; 26(3):344-350.
Date published: February 8, 2016Featured in this article: Wes Warren.
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Evolutionary signals of selection on cognition from the great tit genome and methylome. Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, De Jager V, Megens H-J, Warren WC, Minx P, Crooijmans RPMA, Corcoran P, Adriaensen F, Belda E, Bushuev A, Cichon M, Charmantier A, Dingemanse N, Doligez B, Eeva T, Erikstad KE, Fedorov S, Hau M, Hille S, Hinde C, Kempenaers B, Kerimov A, Krist M, Mand R, Matthysen E, Nager R, Norte C, Orell M, Richner H, Slagsvold T, Tilgar V, Tinbergen J, Torok J, Tschirren B, Yuta T, Sheldon BC, Slate J, Zeng K, Van Oers K, Visser ME, Groenen MAM. Nature Communications; 7:10474.
Date published: January 25, 2016Featured in this article: Wes Warren.
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X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff J-N, Postlethwait JH, Schartl M, Minx P, Warren WC, Walter RB. BMC Genomics; 17(1):37.
Date published: January 7, 2016Featured in this article: Wes Warren.
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INTEGRATE: Gene fusion discovery using whole genome and transcriptome data. Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. Genome Research; 26(1):108-118.
Date published: January 1, 2016Featured in this article: Wes Warren.
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Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda. Gloria-Soria A, Dunn WA, Telleria EL, Evans BR, Okedi L, Echodu R, Warren WC, Montague MJ, Aksoy S, Caccone A. G3: Genes, Genomes, Genetics; 6(6):1573-1584.
Date published: January 1, 2016Featured in this article: Wes Warren.
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A high-resolution SNP array-based linkage map anchors a new domestic cat draft genome assembly and provides detailed patterns of recombination. Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ. G3: Genes, Genomes, Genetics; 6(6):1607-1616.
Date published: January 1, 2016Featured in this article: Wes Warren.
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The physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling. Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, Landerweber LF, Maric C, Miller D, Noegel AA, Peace R, Pierron G, Sasaki T, Schallenberg-Rüdinger M, Schleicher M, Singh R, Spaller T, Storey KB, Suzuki T, Tomlinson C, Tyson JJ, Warren WC, Werner ER, Werner-Felmayer G, Wilson RK, Winckler T, Gott JM, Glöckner G, Marwan W. Genome Biology and Evolution; 8(1):109-125.
Date published: January 1, 2016Featured in this article: Wes Warren.
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PGD: a pangolin genome hub for the research community. Tan TK, Tan KY, Hari R, Mohamed Yusoff A, Wong GJ, Siow CC, Mutha NV, Rayko M, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Paterson IC, Warren WC, Johnson WE, O'Brien SJ, Choo SW. Database : the journal of biological databases and curation; 2016.
Date published: January 1, 2016Featured in this article: Wes Warren.
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2015
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JMC, Sorgine MHF, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GRC, Calderón-Fernández G, A Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CRO, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, Da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DST, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Latorre-Estivalis JM, Lavore A, Lazoski C, Lazzari CR, Lorenzo MG, Majerowicz D, Mariotti M, Masuda H, Megy K, Melo ACA, Missirlis F, Mota T, Noriega FG, Nunes RD, Oliveira RLL, Oliverira-Silva GO, Pascual A, Pavan MG, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MAC, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JMC, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL. Proceedings of the National Academy of Sciences of the United States of America; 112(48):14936-14941.
Date published: December 1, 2015Featured in this article: Wes Warren.
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The genome of the vervet (Chlorocebus æthiops sabæus). Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi O-W, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GWC, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. Genome Research; 25(12):1921-1933.
Date published: December 1, 2015Featured in this article: Wes Warren.
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Whole Body Melanoma Transcriptome Response in Medaka. Schartl M, Shen Y, Maurus K, Walter R, Tomlinson C, Wilson RK, Postlethwait J, Warren WC. PLoS ONE; 10(12):0143057.
Date published: December 1, 2015Featured in this article: Wes Warren.
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Identification and analysis of divergent immune gene families within the Tasmanian devil genome. Morris KM, Cheng Y, Warren W, Papenfuss AT, Belov K. BMC Genomics; 16(1):1017.
Date published: November 26, 2015Featured in this article: Wes Warren.
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Developing tools for the study of molluscan immunity: Thesequencing of the genome of the eastern oyster, Crassostrea virginica. Gómez-Chiarri M, Warren WC, Guo X, Proestou D. Fish and Shellfish Immunology; 46(1):2-4.
Date published: September 1, 2015Featured in this article: Wes Warren.
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Third Report on Chicken Genes and Chromosomes 2015. Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, De Koning D-J, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux P-F, Schmidt CJ, Schneider A-S, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Cytogenetic and Genome Research; 145(2):78-179.
Date published: August 20, 2015Featured in this article: Wes Warren.
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Response to Hron et al. Lovell PV, Wirthlin M, Carbone L, Warren WC, Mello CV. Genome Biology; 16(1):165.
Date published: August 18, 2015Featured in this article: Wes Warren.
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Joint MiRNA/mRNA expression profiling reveals changes consistent with development of dysfunctional corpus luteum after weight gain. Bradford AP, Jones K, Kechris K, Chosich J, Montague M, Warren WC, May MC, Al-Safi Z, Kuokkanen S, Appt SE, Polotsky AJ. PLoS ONE; 10(8):e0135163.
Date published: August 10, 2015Featured in this article: Wes Warren.
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Erratum: Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids (Scientific Reports (2015) 3:(1756) 10.1038/srep01756). Hartig G, Churakov G, Warren WC, Brosius J, Makałowski W, Schmitz J. Scientific Reports; 5:12590.
Date published: July 28, 2015Featured in this article: Wes Warren.
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Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation. Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, Valenzuela N. Genome Biology and Evolution; 7(7):2038-2050.
Date published: July 1, 2015Featured in this article: Wes Warren.
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Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits. Huang YS, Ramensky V, Service SK, Jasinska AJ, Jung Y, Choi O-W, Cantor RM, Juretic N, Wasserscheid J, Kaplan JR, Jorgensen MJ, Dyer TD, Dewer K, Blangero J, Wilson RK, Warren W, Weinstock GM, Freimer NB. BMC Biology; 13(1):41.
Date published: June 20, 2015Featured in this article: Wes Warren.
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2014
Comparative genomics reveals insights into avian genome evolution and adaptation. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, Da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim K-W, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MTP, Wang J, Ye C, Liang S, Yan Z, Zepeda ML, Campos PF, Velazquez AMV, Samaniego JA, Avila-Arcos M, Martin MD, Barnett R, Ribeiro AM, Mello CV, Lovell PV, Almeida D, Maldonado E, Pereira J, Sunagar K, Philip S, Dominguez-Bello MG, Bunce M, Lambert D, Brumfield RT, Sheldon FH, Holmes EC, Gardner PP, Steeves TE, Stadler PF, Burge SW, Lyons E, Smith J, McCarthy F, Pitel F, Rhoads D, Froman DP. Science; 346(6215):1311-1320.
Date published: December 12, 2014Featured in this article: Wes Warren.
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Whole-genome analyses resolve early branches in the tree of life of modern birds. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracaft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Science; 346(6215):1320-1331.
Date published: December 12, 2014Featured in this article: Wes Warren.
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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Montague MJ, Li G, Golfi B, Khan R, Aken BL, Searle SMJ, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GWC, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC. Proceedings of the National Academy of Sciences of the United States of America; 111(48):17230-17235.
Date published: December 2, 2014Featured in this article: Wes Warren.
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Single haplotype assembly of the human genome from a hydatidiform mole. Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK. Genome Research; 24(12):2066-2076.
Date published: December 1, 2014Featured in this article: Wes Warren.
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Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW. PLoS Computational Biology; 10(12).
Date published: December 1, 2014Featured in this article: Wes Warren.
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Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Soh YQS, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, De Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC. Cell; 159(4):800-813.
Date published: November 6, 2014Featured in this article: Wes Warren.
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The cavefish genome reveals candidate genes for eye loss. McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L, Minx P, Murphy D, O'Quin KE, Rétaux S, Rohner N, Searle SMJ. Stahl BA, Tabin C, Volff J-N, Yoshizawa M, Warren WC. Nature Communications; 5:5307.
Date published: October 20, 2014Featured in this article: Wes Warren.
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Corrigendum: Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Nature; 514(7520):126.
Date published: October 2, 2014Featured in this article: Wes Warren.
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Corrigendum: Elephant shark genome provides unique insights into gnathostome evolution. Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay B-H, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Nature; 513(7519):574.
Date published: September 24, 2014Featured in this article: Wes Warren.
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Gibbon genome and the fast karyotype evolution of small apes. Carbone L, Alan Harris R, Gnerre S, Verramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, De Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, Ten Hallers B, Terhune E, Thomas GWC, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Nature; 513(7517):195-201.
Date published: September 11, 2014Featured in this article: Wes Warren.
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The common marmoset genome provides insight into primate biology and evolution. Worley KC, Warren WC, Rogers J, Locke D, Muzny DM, Mardis ER, Weinstock GM, Tardif SD, Aagaard KM, Archidiacono N, Arul Rayan N, Batzer MA, Beal K, Brejova B, Capozzi O, Capuano SB, Casola C, Chandrabose MM, Cree A, Diep Dao M, De Jong PJ, Cruz-Herrera del Rosario R, Delehaunty KD, Dinh HH, Eichler EE, Fitzgerald S, Flicek P, Fontenot CC, Fowler RG, Ronick C, Fulton LA, Fulton RS, Gabisi RA, Gerlach D, Graves TA, Gunaratne PH, Hahn MW, Haig D, Han Y, Harris RA, Herrero J, Hillier LW, Hubley R, Hughes JF, Hume J, Jhangiani SN, Jorde LB, Joshi V, Karakor E, Konkel MK, Kosiol C, LKovar C, Kriventseva EV, Lee SL, Lewis LR, Liu Y-S, Lopez J, Lopez-Otin C, Lorente-Galdos B, Mansfield KG, Marques-Bonet T, Minx P, Misceo D, Moncrieff JS, Morgan MB, Nazareth LV, Newsham I, Nguyen NB, Okwuonu GO, Prabhakar S, Perales L, Pu L-L, Puente XS, Quesada V, Ranck MC, Raney BJ, Raveendran M, Deiros DR, Rocchi M, Rodriguez D, Ross C, Ruffier M, Ruiz SJ, Sajjadian S, Santibanez J, Schrider DR, Searle S, Skaletsky H, Soibam B, Smit AFA, Tennakoon JB, Tomaska L, Ullmer B, Vejnar CE, Ventura M, Vilella AJ, Vinar T, Vogel J-H, Walker JA, Wang Q, Warner CM, Wildman DE, Witherspoon DJ, Wright RA, Wu Y, Xiao W, Xing J, Zdobnov EM, Zhu B, Gibbs RA, Wilson RK. Nature Genetics; 46(8):850-857.
Date published: August 1, 2014Featured in this article: Wes Warren.
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High-coverage sequencing and annotated assemblies of the budgerigar genome. Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Philippy AM, Jarvis ED. GigaScience; 3(1):11.
Date published: July 8, 2014Featured in this article: Wes Warren.
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A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. Genetics; 197(2):625-641.
Date published: June 1, 2014Featured in this article: Wes Warren.
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On the origin of SCPP genes. Venkatesh B, Lee AP, Ravi V, Maurya AK, Korzh V, Lim ZM, Ingham PW, Boehm T, Brenner S, Warren WC. Evolution and Development; 16(3):125-126.
Date published: May 1, 2014Featured in this article: Wes Warren.
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Genome of the human hookworm Necator americanus. Tang YT, Gao X, Rosa BA, Abubucker S, Hallsworth-Pepin K, Martin J, Tyagi R, Heizer E, Zhang X, Bhonagiri-Palsikar V, Minx P, Warren WC, Wang Q, Zhan B, Hotez PJ, Sternberg PW, Dougall A, Gaze ST, Mulvenna J, Sotillo J, Ranganathan S, Rabelo EM, Wilson RK, Felgner PL, Bethony J, Hawdon JM, Gasser RB, Loukas A, Mitreva M. Nature Genetics; 46(3):261-269.
Date published: March 1, 2014Featured in this article: Wes Warren.
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Erratum: The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (Proceedings of the National Academy of Sciences of the United States of America (2013) 110, 51, (20645-20650) DOI: 10.1073/pnas. 1314475110). Castoe TA, De Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BSW, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowsi AM, Yandell M, Warren WC, Secor SM, Pollock DD. Proceedings of the National Academy of Sciences of the United States of America; 111(8):3194.
Date published: February 25, 2014Featured in this article: Wes Warren.
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Elephant shark genome provides unique insights into gnathostome evolution. Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay B-H, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC. Nature; 505(7482):174-179.
Date published: January 1, 2014Featured in this article: Wes Warren.
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Mammalian y chromosomes retain widely expressed dosage-sensitive regulators. Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Nature; 508(7497):494-499.
Date published: January 1, 2014Featured in this article: Wes Warren.
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Genome sequence of the tsetse fly (Glossina morsitans ): Vector of African trypanosomiasis. Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Touré Y, Attardo GM, Darby AC, Toyoda A, Hertz-Fowler C, Larkin DM, Cotton JA, Sanders MJ, Swain MT, Quail MA, Inoue N, Ravel S, Taylor TD, Srivastava TP, Sharma V, Warren W, Wilson RK, Suzuki Y, Lawson D, Hughes DST, Megy K, Masiga DK, Mireji PO, Hansen IA, Van Den Abbeele J, Benoit JB, Bourtzis K, Obiero GFO, Robertson HM, Jones JW, Zhou J-J, Field LM, Friedrich M, Nyanjom SRG, Telleria EL, Caljon G, Ribeiro JMC, Acosta-Serrano A, Ooi C-P, Rose C, Price DP, Haines LR, Christoffels A, Sim C, Pham DQD, Denlinger DL, Geiser DL, Omedo IA, Winzerling JJ, Peyton JT, Marucha KK, Jonas M, Meuti ME, Rawlings ND, Zhang Q, Macharia RW, Michalkova V, Dashti ZJS, Baumann AA, Gäde G, Marco HG, Caers J, Schoofs L, Riehle MA, Hu W, Tu Z, Tarone AM, Malacrida AR, Kibet CK, Scolari F, Koekemoer JJO, Willis J, Gomulski LM, Falchetto M, Scott MJ, Fu S, Sze S-H, Luiz T, Weiss B, Walshe DP, Wang J, Wamalwa M, Mwangi S, Ramphul UN, Snyder AK, Brelsfoard CL, Thomas GH, Tsiamis G, Arensburger P, Rio RVM, Macdonald SJ, Panji S, Kruger A, Benkahla A, Balyeidhusa ASP, Msangi A, Okoro CK, Stephens D, Stanley EJ, Mpondo F, Wamwiri F, Mramba F, Siwo G, Withinji G, Harkins G, Murilla G, Lehväslaiho H, Malele I, Auma JE, Kinyua JK, Ouma J, Okedi L, Manga L, Aslett M, Koffi M, Gaunt MW, Makgamathe M, Mulder N, Manangwa O, Abila PP, Wincker P, Gregory R, Bateta R, Sakate R, Ommeh S, Lehane S, Imanishi T, Osamor VC, Kawahara Y. Science; 344(6182):380-386.
Date published: January 1, 2014Featured in this article: Wes Warren.
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Venkatesh et al. reply. Venkatesh B, Lee AP, Swann JB, Ohta Y, Flajnik MF, Kasahara M, Boehm T, Warren WC. Nature; 511(7508):E9-E10.
Date published: January 1, 2014Featured in this article: Wes Warren.
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Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment. Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S, Leichter CA, Li M, Meisel RP, Minx P, Murphy TD, Nelson DR, Reid WR, Rinkevich FD, Robertson HM, Sackton TB, Sattelle DB, Thibaud-Nissen F, Tomlinson C, van de Zande L, Walden KK, Wilson RK, Liu N. Genome Biology; 15(10):466.
Date published: January 1, 2014Featured in this article: Wes Warren.
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Conserved syntenic clusters of protein coding genes are missing in birds. Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV. Genome Biology; 15(12):565.
Date published: January 1, 2014Featured in this article: Wes Warren.
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2013
The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Castoe TA, De Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BSW, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowsi AM, Yandell M, Warren WC, Secor SM, Pollock DD. Proceedings of the National Academy of Sciences of the United States of America; 110(51):20645-20650.
Date published: December 17, 2013Featured in this article: Wes Warren.
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No bull: Upholding community standards in public sharing of biological datasets. Hughes JF, Skaletsky H, Bellott DW, Chowdhary BP, Warren WC, Worley KC, Wilson RK, Gibbs RA, Page DC. Proceedings of the National Academy of Sciences of the United States of America; 110(46):E4277.
Date published: November 12, 2013Featured in this article: Wes Warren.
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Echidna venom gland transcriptome provides insights into the evolution of monotreme venom. Wong ESW, Nicol S, Warren WC, Belov K. PLoS ONE; 8(11):e79092.
Date published: November 12, 2013Featured in this article: Wes Warren.
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Systems biology of the vervet monkey. Jasinska AJ, Schmitt CA, Service SK, Cantor RM, Dewar K, Jentsch JD, Kaplan JR, Turner TR, Warren WC, Weinstock GM, Woods RP, Freimer NB. ILAR Journal; 54(2):122-143.
Date published: November 1, 2013Featured in this article: Wes Warren.
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Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus. Kowalko JE, Rohner N, Linden TA, Rompani SB, Warren WC, Borowsky R, Tabin CJ, Jeffery WR, Yoshizawa M. Proceedings of the National Academy of Sciences of the United States of America; 110(42):16933-16938.
Date published: October 15, 2013Featured in this article: Wes Warren.
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Independent specialization of the human and mouse X chromosomes for the male germ line. Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK, Page DC. Nature Genetics; 45(9):1083-1087.
Date published: September 1, 2013Featured in this article: Wes Warren.
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The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim K-W, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N. Nature Genetics; 45(7):776-783.
Date published: July 1, 2013Featured in this article: Wes Warren.
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To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed. Gandolfi B, Alhaddad H, Affolter VK, Brockman J, Haggstrom J, Joslin SEK, Koehne AL, Millikin JC, Outerbridge CA, Warren WC, Lyons LA. PLoS ONE; 8(6):e67105.
Date published: June 27, 2013Featured in this article: Wes Warren.
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Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)]. Pabuwal V, Boswell M, Pasquali A, Wise SS, Kumar S, Shen Y, Garcia T, LaCerte C, Wise JP, Warren W, Walter RB. Aquatic Toxicology; 134-135:74-81.
Date published: June 5, 2013Featured in this article: Wes Warren.
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The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff J-N, Lesch K-P, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, Boore J, Searle S, Postlethwait JH, Warren WC. Nature Genetics; 45(5):567-572.
Date published: May 1, 2013Featured in this article: Wes Warren.
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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson Y-W, Nanlohy KG, Libants SV, Yeh C-Y, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, De Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Nature Genetics; 45(4):415-421.
Date published: April 1, 2013Featured in this article: Wes Warren.
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The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Bradley Shaffer H, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe T, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. Genome Biology; 14(3):R28.
Date published: March 28, 2013Featured in this article: Wes Warren.
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Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216. Venkatesh B, Ravi V, Lee AP, Warren WC, Brenner S. Molecular Biology and Evolution; 30(1):62-65.
Date published: January 1, 2013Featured in this article: Wes Warren.
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Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources. Shen Y, Garcia T, Pabuwal V, Boswell M, Pasquali A, Beldorth I, Warren W, Schartl M, Cresko WA, Walter RB. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics; 8(1):11-16.
Date published: January 1, 2013Featured in this article: Wes Warren.
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Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Hartig G, Churakov G, Warren WC, Brosius J, Makałowski W, Schmitz J. Scientific Reports; 3:1756.
Date published: January 1, 2013Featured in this article: Wes Warren.
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2012
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles. Wong ESW, Morgenstern D, Mofiz E, Gomert S, Morris KM, Temple-Smith P, Renfree MB, Whittington CM, King GF, Warren WC, Papenfuss AT, Belov K. Molecular and Cellular Proteomics; 11(11):1354-1364.
Date published: November 1, 2012Featured in this article: Wes Warren.
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Digital gene expression for non-model organisms (Genome Research (2011) 21, (1905-1915)). Hong LZ, Li J, Schmidt-Küntzel A, Warren WC, Barsh GS. Genome Research; 22(10):2088.
Date published: October 1, 2012Featured in this article: Wes Warren.
Specifying and sustaining pigmentation patterns in domestic and wild cats. Kaelin CB, Xu X, Hong LZ, David VA, McGowan KA, Schmidt-Küntzel A, Roelke ME, Pino J, Pontius J, Cooper GM, Manuel H, Swanson WF, Marker L, Harper CK, Van Dyk A, Yue B, Mullikin JC, Warren WC, Eizirik E, Kos L, O'Brien SJ, Barsh GS, Menotti-Raymond M. Science; 337(6101):1536-1541.
Date published: September 21, 2012Featured in this article: Wes Warren.
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A non-human primate system for large-scale genetic studies of complex traits. Jasinska AJ, Lin MK, Service S, Choi O-W, DeYoung J, Grujic O, Kong S-Y, Jung Y, Jorgensen MJ, Fairbanks LA, Turner T, Cantor RM, Wasserscheid J, Dewar K, Warren W, Wilson RK, Weinstock G, Jentsch JD, Freimer NB. Human Molecular Genetics; 21(15):3307-3316.
Date published: August 1, 2012Featured in this article: Wes Warren.
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Structure, function and diversity of the healthy human microbiome. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, Sodergren EJ, Versalovic J, Wollam AM, Worley KC, Wortman JR, Young SK, Zeng Q, Aagaard KM, Abolude OO, Allen-Vercoe E, Alm EJ, Alvarado L, Andersen GL, Anderson S, Appelbaum E, Arachchi HM, Armitage G, Arze CA, Ayvaz T, Baker CC, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser MJ, Bloom T, Bonazzi V, Paul Brooks J, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PSG, Chen I-MA, Chen L, Chhibba S, Chu K, Ciulla DM, Clemente JC, Clifton SW, Conlan S, Crabtree J, Cutting MA, Davidovics NJ, Davis CC, Desantis TZ, Deal C, Delehaunty KD, Dewhirst FE, Deych E, Ding Y, Dooling DJ, Dugan SP, Michael Dunne W, Scott Durkin A, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney LJ, Foster L, Di Francesco V, Friedman J, Friedrich DC, Fronick CC, Fulton LL, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni MY, Goldberg JM, Goll J, Gonzalez A, Griggs A, Gujja S, Kinder Haake S, Haas BJ, Hamilton HA, Harris EL, Hepburn TA, Herter B, Hoffmann DE, Holder ME, Howarth C, Huang KH, Huse SM, Izard J, Jansson JK, Jiang H, Jordan C, Joshi V, Katancik JA, Keitel WA, Kelley ST, Kells C, King NB, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, La Rosa PS, Lee SL, Lemon KP, Lennon N, Lewis CM, Lewis L, Ley RE, Li K, Liolios K, Liu B, Liu Y, Lo C-C, Lozupone CA, Dwayne Lunsford R, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavromatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, Oglaunghlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Pop M, Priest ME, Proctor LM, Qin X, Raes J, Ravel J, Reid JG, Rho M, Rhodes R, Riehle KP, Rivera MC, Rodriguez-Mueller B, Rogers Y-H, Ross MC, Russ C, Sanka RK, Sankar P, Fah Sathirapongsasuti J, Schloss JA, Schloss PD, Schmidt TM, Scholz M, Schriml L, Schubert AM, Segata N, Segre JA, Shannon WD, Sharp RR, Sharpton TJ, Shenoy N, Sheth NU, Simone GA, Singh I, Smillie CS, Sobel JD, Sommer DD, Spicer P, Sutton GG, Sykes SM, Tabbaa DG, Thiagarajan M, Tomlinson CM, Torralba M, Treangen TJ, Truty RM, Vishnivetskaya TA, Walker J, Wang L, Wang Z, Ward DV, Warren W, Watson MA, Wellington C, Wetterstrand KA, White JR, Wilczek-Boney K, Wu Y, Wylie KM, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans BP, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker JD, Birren BW, Gibbs RA, Highlander SK, Methé BA, Nelson KE, Petrosino JF, Weinstock GM, Wilson RK, White O. Nature; 486(7402):207-214.
Date published: June 14, 2012Featured in this article: Wes Warren.
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A framework for human microbiome research. Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, Sodergren EJ, Versalovic J, Wollam AM, Worley KC, Wortman JR, Young SK, Zeng Q, Aagaard KM, Abolude OO, Allen-Vercoe E, Alm EJ, Alvarado L, Andersen GL, Anderson S, Appelbaum E, Arachchi HM, Armitage G, Arze CA, Ayvaz T, Baker CC, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser MJ, Bloom T, Bonazzi VR, Brooks P, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PS, Chen I-MA, Chen L, Chhibba S, Chu K, Ciulla DM, Clemente JC, Clifton SW, Conlan S, Crabtree J, Cutting MA, Davidovics NJ, Davis CC, Desantis TZ, Deal C, Delehaunty KD, Dewhirst FE, Deych E, Ding Y, Dooling DJ, Dugan SP, Michael Dunne W, Scott Durkin A, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney L, Foster L, Di Francesco V, Friedman J, Friedrich DC, Fronick CC, Fulton LL, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni MY, Goldberg JM, Goll J, Gonzalez A, Griggs, A, Gujja S, Haas BJ, Hamilton HA, Harris EL, Hepburn TA, Herter B, Hoffmann DE, Holder ME, Howarth C, Huang KH, Huse SM, Izard J, Jansson JK, Jiang H, Jordan C, Joshi V, Katancik JA, Keitel WA, Kelley ST, Kells C, Kinder-Haake S, King NB, Knight R, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, La Rosa PS, Lee SL, Lemon KP, Lennon N, Lewis CW, Lewis L, Ley RE, Li K, Liolios K, Liu B, Liu Y, Lo C-C, Lozipone CA, Dwayne Lunsford R, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavrommatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, O'Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Priest ME, Proctor LM, Qin X, Raes J, Ravel J, Reid JG, Rho M, Rhodes R, Riehle KP, Rivera MC, Rodriguez-Mueller B, Rogers Y-H, Ross MC, Russ C, Sanka RK, Sankar P, Fah Sathirapongsasuti J, Schloss JA, Schloss PD, Scmidt TM, Scholz M, Schriml L, Schubert AM, Segata N, Segre JA, Shannon WD, Sharp RR, Sharpton TJ, Shenoy N, Sheth NU, Simone GA, Singh I, Smillie CS, Sobel JD, Sommer DD, Spicer P, Sutton GG, Sykes SM, Tabbaa DG, Thiagarajan M, Tomlinson CM, Torralba M, Treangen TJ, Truty RM, Vishnivetskaya TA, Walker J, Wang L, Wang Z, Ward DV, Warren W, Watson MA, Wellington C, Wetterstrand KA, White JR, Wilczek-Boney K, Qing Wu Y, Wylie KM, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans BP, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker JD, Birren BW, Gibbs RA, Highlander SK, Weinstock GM, Wilson RK, White O. Nature; 486(7402):215-221.
Date published: June 14, 2012Featured in this article: Wes Warren.
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Insights into hominid evolution from the gorilla genome sequence. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, De Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Nature; 483(7388):169-175.
Date published: March 8, 2012Featured in this article: Wes Warren.
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Strict evolutionary conservation followed rapid gene loss on human and rhesus y chromosomes. Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho T-J, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Nature; 483(7387):82-87.
Date published: March 1, 2012Featured in this article: Wes Warren.
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The genome architecture of the collaborative cross mouse genetic reference population. Iraqi FA, Mahajne M, Salaymah Y, Sandovski H, Tayem H, Vered K, Balmer L, Hall M, Manship G, Morahan G, Pettit K, Scholten J, Tweedie K, Wallace A, Weerasekera L, Cleak J, Durrant C, Goodstadt L, Mott R, Yalcin B, Aylor DL, Baric RS, Bell TA, Bendt KM, Brennan J, Brooks JD, Buus RJ, Crowley JJ, Calaway JD, Calaway ME, Cholka A, Darr DB, Didion JP, Dorman A, Everett ET, Ferris MT, Mathes WF, Fu C-P, Gooch TJ, Goodson SG, Gralinski LE, Hansen SD, Heise MT, Hoel J, Hua K, Kapita MC, Lee S, Lenarcic AB, Liu EY, Liu H, McMillan L, Magnuson TR, Manly KF, Miller DR, O'Brien DA, Odet F, Pakatci IK, Pan W, de Villena FP, Perou CM, Pomp D, Quackenbush CR, Robinson NN, Sharpless NE, Shaw GD, Spence JS, Sullivan PF, Sun W, Tarantino LM, Valdar W, Wang J, Wang W, Welsh CE, Whitmore A, Wiltshire T, Wright FA, Xie Y, Yun Z, Zhabotynsky V, Zhang Z, Zou F, Powell C, Steigerwalt J, Threadgill DW, Chesler EJ, Churchill GA, Gatti DM, Korstanje R, Svenson KL, Collins FS, Crawford N, Hunter K, Samir N, Kelada P, Peck BCE, Reilly K, Tavarez U, Bottomly D, Hitzeman R, Mcweeney SK, Frelinger J, Krovi H, Phillippi J, Spritz RA, Aicher L, Katze M, Rosenzweig E, Shusterman A, Nashef A, Weiss EI, Houri-Haddad Y, Soller M, Williams RW, Schughart K, Yang H, French JE, Benson AK, Kim J, Legge R, Low SJ, Ma F, Martinez I, Walter J, Broman KW, Hallgrimsson B, Klein O, Weinstock G, Warren WC, Yang YV, Schwartz D. Genetics; 190(2):389-401.
Date published: February 1, 2012Featured in this article: Wes Warren.
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Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids. Shen Y, Catchen J, Garcia T, Amores A, Beldorth I, Wagner J, Zhang Z, Postlethwait J, Warren W, Schartl M, Walter RB. Comparative Biochemistry and Physiology - C Toxicology and Pharmacology; 155(1):102-108.
Date published: January 1, 2012Featured in this article: Wes Warren.
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Graph accordance of next-generation sequence assemblies. Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM. Bioinformatics; 28(1):13-16.
Date published: January 1, 2012Featured in this article: Wes Warren.
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A limited role for gene duplications in the evolution of platypus venom. Wong ESW, Papenfuss AT, Whittington CM, Warren WC, Belov K. Molecular Biology and Evolution; 29(1):167-177.
Date published: January 1, 2012Featured in this article: Wes Warren.
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2011
Digital gene expression for non-model organisms. Hong LZ, Li J, Schmidt-Küntzel A, Warren WC, Barsh GS. Genome Research; 21(11):1905-1915.
Date published: November 1, 2011Featured in this article: Wes Warren.
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A high-resolution map of human evolutionary constraint using 29 mammals. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Viella AJ, Wen J, Xie X, Zody MC, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E. Nature; 478(7370):476-482.
Date published: October 27, 2011Featured in this article: Wes Warren.
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Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Castoe TA, de Koning AJ, Hall KT, Yokoama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, Pollock DD. Genome Biology; 12(7):406.
Date published: July 28, 2011Featured in this article: Wes Warren.
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Comparative genomics based on massive paralle transcriptome sequencing reveals patterns of substitution and selection across 10 bird species (Molecular Ecology (2010) 19:SUPPL.1 (266-276)). Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H. Molecular Ecology; 20(13):2871.
Date published: July 1, 2011Featured in this article: Wes Warren.
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The development and characterization of a 60K SNP chip for chicken. Groenen MAM, Megens H-J, Zare Y, Warren WC, Hillier LW, Crooijmans RPMA, Vereijken A, Okimoto R, Muir WM, Cheng HH. BMC Genomics; 12:274.
Date published: May 31, 2011Featured in this article: Wes Warren.
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A vertebrate case study of the quality of assemblies derived from next-generation sequences. Ye L, Hillier LW, Minx P, Thane N, Locke DP, Martin JC, Chen L, Mitreva M, Miller JR, Haub KV, Dooling DJ, Mardis ER, Wilson RK, Weinstock GM, Warren WC. Genome Biology; 12(3):R31.
Date published: March 31, 2011Featured in this article: Wes Warren.
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The draft genome of the parasitic nematode Trichinella spiralis. Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L, Minx P, Yang S-P, Warren WC, Fulton RS, Bhonagiri V, Zhang X, Hallsworth-Pepin K, Clifton SW, McCarter JP, Appleton J, Mardis ER, Wilson RK. Nature Genetics; 43(3):228-235.
Date published: March 1, 2011Featured in this article: Wes Warren.
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé M-J, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-TorresMó MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR. PLoS Genetics; 7(2):e1002007.
Date published: February 1, 2011Featured in this article: Wes Warren.
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Comparative and demographic analysis of orang-utan genomes. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang S-P, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet t, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Valle GD, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordõez GR, Ĺpez-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, De Jong PJ, Weinstock GM, Roger J, Mardis ER, Gibbs RA, Wilson RK. Nature; 469(7331):529-533.
Date published: January 27, 2011Featured in this article: Wes Warren.
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Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A. Zhang Z, Wang Y, Wang S, Liu J, Warren W, Mitreva M, Walter RB. PLoS ONE; 6(4):e18379.
Date published: January 1, 2011Featured in this article: Wes Warren.
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A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. Standards in Genomic Sciences; 4(2):257-270.
Date published: January 1, 2011Featured in this article: Wes Warren.
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2010
Novel venom gene discovery in the platypus. Whittington CM, Papenfuss AT, Locke DP, Mardis ER, Wilson RK, Abubucker S, Mitreva M, Wong ESW, Hsu AL, Kuchel PW, Belov K, Warren WC. Genome Biology; 11(9):R95.
Date published: September 29, 2010Featured in this article: Wes Warren.
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Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC. Nature; 466(7306):612-616.
Date published: July 29, 2010Featured in this article: Wes Warren.
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A catalog of reference genomes from the human microbiome. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Russon Wortman J, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. Science; 328(5981):994-999.
Date published: May 21, 2010Featured in this article: Wes Warren.
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The genome of the western clawed frog xenopus tropicalis. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak L, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. Science; 328(5978):633-636.
Date published: April 30, 2010Featured in this article: Wes Warren.
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The genome of a songbird. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin Y-C, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner MB, Griffin DK, Ye L, McLauren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Chang Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang S-P, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. Nature; 464(7289):757-762.
Date published: April 1, 2010Featured in this article: Wes Warren.
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Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals. Quesada V, Velasco G, Puente XS, Warren WC, López-Otín C. BMC Genomics; 11(1):220.
Date published: April 1, 2010Featured in this article: Wes Warren.
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Gene duplication and fragmentation in the zebra finch major histocompatibility complex. Balakrishnan CN, Ekblom R, Völker M, Westerdahl H, Godinez R, Kotkiewicz H, Burt DW, Graves T, Griffin DK, Warren WC, Edwards SV. BMC Biology; 8:29.
Date published: April 1, 2010Featured in this article: Wes Warren.
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Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other cronobacter species. Kucerova E, Clifton SW, Xia X-Q, Long F, Porwollik S, Fulton L, Fronick C, Minx P, Kyung K, Warren W, Fulton R, Feng D, Wollam A, Shan N, Bhonagiri V, Nash WE, Hallsworth-Pepin K, Wilson RK, McClelland M, Forsythe SJ. PLoS ONE; 5(3):e9556.
Date published: March 8, 2010Featured in this article: Wes Warren.
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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H. Molecular Ecology; 19(SUPPL. 1):266-276.
Date published: March 1, 2010Featured in this article: Wes Warren.
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Chimpanzee and human y chromosomes are remarkably divergent in structure and gene content. Hughes JF, Skaletsky H, Pyntikova T, Graves TA, Van Daalen SKM, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC. Nature; 463(7280):536-539.
Date published: January 28, 2010Featured in this article: Wes Warren.
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2009
Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Haussler D, O'Brien SJ, Ryder OA, Keither Barker F, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, Miller W, Murphy RW, Murphy WJ, Sheldon FM, Sinervo B, Venkaesh B, Wiley EO, Allendorf FW, Amato G, Scott Baker C, Bauer A, Beja-Pereira A, Bermingham E, Bernardi G, Bonvicino CR, Brenner S, Burke T, Cracraft J, Diekhans M, Edwards S, Ericson PGP, Estes J, Fjelsda J, Flesness N, Gamble T, Gaubert P, Graphodatsky AS, Marshall Graves JA, Green ED, Gree RE, Hackett S, Hebert P, Helgen KM, Joseph L, Kessing B, Kingsley DM, Lewin HA, Luikart G, Martelli P, Moreira MAM, Nguyen N, Ortí G, Pike BL, Rawson DM, Schuster SC, Seuánez HN, Bradley Shaffer H, Springer MS, Stuart JM, Sumner J, Teeling E, Vrijenhoek RC, Ward RD, Warren WC, Wayne R, Williams TM, Wolfe ND, Zhang Y-P, Graves J, Springer M, Williams T, Wolfe N, Edwards SV, Orti G, Rawson DM, Felsenfeld A, Stuart JM, Turner S. Journal of Heredity; 100(6):659-674.
Date published: November 1, 2009Featured in this article: Wes Warren.
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Understanding and utilising mammalian venom via a platypus venom transcriptome. Whittington CM, Koh JMS, Warren WC, Pepenfuss AT, Torres AM, Kuchel PW, Belov K. Journal of Proteomics; 72(2):155-164.
Date published: March 6, 2009Featured in this article: Wes Warren.
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Higher-order genome organization in platypus and chicken sperm and repositioning of sex chromosomes during mammalian evolution. Tsend-Ayush E, Dodge N, Mohr J, Casey A, Himmelbauer H, Kremitzki CL, Schatzkamer K, Graves T, Warren WC, Griützner F. Chromosoma; 118(1):53-69.
Date published: January 1, 2009Featured in this article: Wes Warren.
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The enigma of the platypus genome. Warren WC, Grützner F. Australian Journal of Zoology; 57(4):157-165.
Date published: January 1, 2009Featured in this article: Wes Warren.
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2008
Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Pearks Wilkerson AJ, Raudsepp T, Graves T, Albracht D, Warren W, Chowdhary BP, Skow LC, Murphy WJ. Genomics; 92(5):329-338.
Date published: November 1, 2008Featured in this article: Wes Warren.
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Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183)). Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S-P, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordó̃ez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AFA, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ESW, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux J-L, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, De Jong PJ, Renfree MB, Mardis ER, Wilson RK. Nature; 455(7210):256.
Date published: September 1, 2008Featured in this article: Wes Warren.
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Evolutionary toggling of the MAPT 17q21.31 inversion region. Zody MC, Jiang Z, Fung H-C, Antonacci F, Hillier LW, Cardone MF, Graves TA, Kidd JM, Cheng Z, Abouelleil A, Chen L, Wallis J, Glasscock J, Wilson RK, Reily AD, Duckworth J, Ventura M, Hardy J, Warren WC, Eichler EE. Nature Genetics; 40(9):1076-1083.
Date published: September 1, 2008Featured in this article: Wes Warren.
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Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals. Patel VS, Cooper SJB, Deakin JE, Fulton B, Graves T, Warren WC, Wilson RK, Graves JAM. BMC Biology; 6:34.
Date published: August 1, 2008Featured in this article: Wes Warren.
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Defensins and the convergent evolution of platypus and reptile venom genes. Whittington CM, Papenfuss AT, Bansal P, Torres AM, Wong ESW, Deakin JE, Graves T, Alsop A, Schatzkamer K, Kremitzki C, Ponting CP, Temple-Smith P, Warren WC, Kuchel PW, Belov K. Genome Research; 18(6):986-994.
Date published: June 1, 2008Featured in this article: Wes Warren.
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Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, Deakin JE, Whittington CM, Schatzkamer K, Kremitzki CL, Graves T, Ferguson-Smith MA, Warren W, Marshal Graves JA. Genome Research; 18(6):965-973.
Date published: June 1, 2008Featured in this article: Wes Warren.
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Origin of INSL3-mediated testicular descent in therian mammals. Park J-I, Semyonov J, Chia LC, Yi W, Warren W, Hsu SYT. Genome Research; 18(6): 974-985.
Date published: June 1, 2008Featured in this article: Wes Warren.
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Loss of genes implicated in gastric function during platypus evolution. Ordoñez GR, Hillier LW, Warren WC, Grützner F, López-Otín C, Puente XS. Genome Biology; 9(5):R81.
Date published: May 15, 2008Featured in this article: Wes Warren.
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Genome analysis of the platypus reveals unique signatures of evolution. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang S-P, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AFA, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ESW, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Ole Kriegs J, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux J-L, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK. Nature; 453(7192):175-183.
Date published: May 8, 2008Featured in this article: Wes Warren.
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Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton SW, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schmutz J, Stacey G, Jackson S. Genome; 51(4):294-302.
Date published: April 1, 2008Featured in this article: Wes Warren, Gary Stacey.
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SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstehard TS. Nature Methods; 5(3):247-252.
Date published: March 1, 2008Featured in this article: Wes Warren.
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2007
Characterizing the chromosomes of the platypus (Ornithorhynchus anatinus). McMillan D, Miethke P, Alsop AE, Rens W, O'Brien P, Trifonov V, Veyrunes F, Schatzkamer K, Kremitzki CL, Graves T, Warren W, Grützner F, Ferguson-Smith MA, Graves JAM. Chromosome Research; 15(8):961-974.
Date published: December 1, 2007Featured in this article: Wes Warren.
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Evolutionary and biomedical insights from the rhesus macaque genome. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu Y-S, Moore SM, Muzny D, Nazareth LV, Dinh NN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers Y-H, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang S-P, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX-Z, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AFA, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han S-G, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu L-L, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'Brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu X-M, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Science; 316(5822):222-234.
Date published: April 13, 2007Featured in this article: Wes Warren.
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2006
Physical map-assisted whole-genome shotgun sequence assemblies. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJM. Genome Research; 16(6):768-775.
Date published: June 1, 2006Featured in this article: Wes Warren.
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Resources for genetic and genomic studies of Xenopus. Klein SL, Gerhard DS, Wagner L, Richardson P, Schriml LM, Sater AK, Warren WC, McPherson JD. Methods in molecular biology (Clifton, N.J.); 322:1-16.
Date published: January 1, 2006Featured in this article: Wes Warren.
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2005
Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Li B-W, Rush AC, Crosby SD, Warren WC, Williams SA, Mitreva M, Weil GJ. Molecular and Biochemical Parasitology; 143(1):49-57.
Date published: September 1, 2005Featured in this article: Wes Warren.
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Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, Van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam A-M, Maupin R, Latreille P, Wendl MC, Yang S-P, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chnwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. Nature; 434(7034):724-731.
Date published: April 7, 2005Featured in this article: Wes Warren.
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Erratum: Sequence and comparative analysis of the chicken genome provide unique perspective on vertebrate evolution (Nature (2004) 432 (695-716)). Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang S-P, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde J-M, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kauman J, Salomonsen J, Skjoedt K, Wong GK-S, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, James Kent W, Hausler D Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK. Nature; 433(7027):777.
Date published: February 17, 2005Featured in this article: Wes Warren.
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2004
A physical map of the chicken genome. Wallis JW, Aerts J, Groenen MAM, Crooljmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang S-P, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, De Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Scheln J, Hillier L, Mardis ER, Wilson RK, Warren WC. Nature; 432(7018):761-764.
Date published: December 9, 2004Featured in this article: Wes Warren.
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A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Wong GK-S, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang S-P, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RPMA, van der Poel JJ, Bovenhuis H, Groenen MAM, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning D-J, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H. Nature; 432(7018):717-722.
Date published: December 9, 2004Featured in this article: Wes Warren.
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang S-P, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde J-M, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kauman J, Salomonsen J, Skjoedt K, Wong GK-S, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, James Kent W, Hausler D Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK. Nature; 432(7018):695-716.
Date published: December 9, 2004Featured in this article: Wes Warren.
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Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, Wilson RK. Nature Genetics; 36(12):1268-1274.
Date published: December 1, 2004Featured in this article: Wes Warren.
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Fosmid-based physical mapping of the Histoplasma capsulatum genome. Magrini V, Warren WC, Wallis J, Goldman WE, Xu J, Mardis ER, McPherson JD. Genome Research; 14(8):1603-1609.
Date published: August 1, 2004Featured in this article: Wes Warren.
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Glucose and insulin treatment of insulinoma cells results in transcriptional regulation of a common set of genes. Ohsugi M, Cras-Méneur C, Zhou Y, Warren W, Bernal-Mizrachi E, Permutt MA. Diabetes; 53(6):1496-1508.
Date published: June 1, 2004Featured in this article: Wes Warren.
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Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu A-L, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hübner N, Jones S, Marra M, Schein J. Genome Research; 14(4):766-779.
Date published: April 1, 2004Featured in this article: Wes Warren.
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2002
Mapping microsatellite markers identified in porcine EST sequences. Rohrer GA, Fahrenkrug SC, Nonneman D, Tao N, Warren WC. Animal Genetics; 33(5):372-376.
Date published: October 1, 2002Featured in this article: Wes Warren.
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Development of microsatellite markers and comparative mapping for bovine chromosome 19. Kirkpatrick BW, Byla B, Kurar E, Warren WC. Animal Genetics; 33(1):65-68.
Date published: January 1, 2002Featured in this article: Wes Warren.
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2000
Construction and characterization of a new bovine bacterial artificial chromosome library with 10 genome-equivalent coverage. Warren W, Smith TPL, Rexroad III CE, Fahrenkrug SC, Allison T, Shu C-L, Catanese J, De Jong PJ. Mammalian Genome; 11(8):662-663.
Date published: January 1, 2000Featured in this article: Wes Warren.
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1999
Evaluation of the somatogenic activity of bovine placental lactogen with cell lines transfected with the bovine somatotropin receptor. Warren WC, Byatt JC, Huynh M, Paik K, Pegg G, Staten NR. Life Sciences; 65(25):2755-2767.
Date published: November 12, 1999Featured in this article: Wes Warren.
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Evaluation of two cDNA-derived bovine tandem repeat sequences, BMON112 and BMON114. Warren WC, Allison T, Tao N, Kappes SM. Animal Genetics; 30(5):401-402.
Date published: October 1, 1999Featured in this article: Wes Warren.
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1996
Cloning of the cDNAs coding for cat growth hormone and prolactin. Warren WC, Bentle KA, Bogosian G. Gene; 168(2):247-249.
Date published: February 12, 1996Featured in this article: Wes Warren.
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Increased production of peptide deformylase eliminates retention of formylmethionine in bovine somatotropin overproduced in Escherichia coli. Warren WC, Bentle KA, Schlittler MR, Schwane AC, O'Neil JP, Bogosian G. Gene; 174(2):235-238.
Date published: January 1, 1996Featured in this article: Wes Warren.
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1995
Rapid communication: nucleotide sequence of the promoter and first exon of the somatotropin receptor gene in cattle. Heap D, Lucy MC, Collier RJ, Boyd CK, Warren WC. Journal of Animal Science; 73(5):1529.
Date published: May 1, 1995Featured in this article: Wes Warren.
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1993
Spi-1: an hepatic serine protease inhibitor regulated by GH and other hormones. Warren WC, Munie GE, Glenn KC. Molecular and Cellular Endocrinology; 98(1):27-32.
Date published: December 1, 1993Featured in this article: Wes Warren.
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1992
Quantification and cellular localization of ovine placental lactogen messenger ribonucleic acid expression during mid- and late gestation. Kappes SM, Warren WC, Pratt SL, Liang R, Anthony RV. Endocrinology; 131(6):2829-2838.
Date published: December 1, 1992Featured in this article: Wes Warren.
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Tissue repair by thrombin-derived peptides in the rat. Warren WC, Mustoe TA, Glenn KC. Peptide Research; 5(6):331-335.
Date published: November 1, 1992Featured in this article: Wes Warren.
Ruminant placental lactogens: structure and biology. Byatt JC, Warren WC, Eppard PJ, Staten NR, Krivi GG, Collier RJ. Journal of Animal Science; 70(9):2911-2923.
Date published: September 1, 1992Featured in this article: Wes Warren.
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1990
Synthesis and secretion of ovine placental lactogen and its biochemical properties. Warren WC, Keisler DH, Anthony RV. Domestic Animal Endocrinology; 7(3):331-342.
Date published: July 1, 1990Featured in this article: Wes Warren.
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Purification and structural characterization of ovine placental lactogen. Warren WC, Liang R, Krivi GG, Siegel NR, Anthony RV. The Journal of Endocrinology; 126(1):141-149.
Date published: July 1, 1990Featured in this article: Wes Warren.
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