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Bovine HapMap Consortium, Gibbs, RA, Taylor, JF, Van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.  Science  2009 Apr 24; 324(5926):528-32. [PubMed]

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Petrosino, JF, Highlander, S, Luna, RA, Gibbs, RA, Versalovic, J. Metagenomic Pyrosequencing and Microbial Identification.  Clin. Chem.  2009 Mar 5; . [PubMed]

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Ding, L, Getz, G, Wheeler, DA, Mardis, ER, McLellan, MD, Cibulskis, K, Sougnez, C, Greulich, H, Muzny, DM, et al. Somatic mutations affect key pathways in lung adenocarcinoma.   Nature  2008 Oct 23; 455(7216): 1069-75 . [PubMed]

Li, Y, Wang, H, Peng, J, Gibbs, RA, Lewis, RA, Lupski, JR, Mardon, G, Chen, R. Mutation Survey of Known LCA Genes and Loci in the Saudi Arabian Population.  Invest. Ophthalmol. Vis. Sci.  2008 Oct 20; . [PubMed]

Srivatsan, A, Han, Y, Peng, J, Tehranchi, AK, Gibbs, R, Wang, JD, Chen, R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies.  PLoS Genet.  2008; 4(8):e1000139. [PubMed]

Liu, S, Ballian, N, Belaguli, NS, Patel, S, Li, M, Templeton, NS, Gingras, MC, Gibbs, R, Fisher, W et al. PDX-1 acts as a potential molecular target for treatment of human pancreatic cancer.  Pancreas  2008 Aug; 37(2):210-20. [PubMed]

Gu, P, Reid, JG, Gao, X, Shaw, CA, Creighton, C, Tran, PL, Zhou, X, Drabek, RB, Steffen, DL et al. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.  PLoS ONE  2008; 3(7):e2548. [PubMed]

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Twigger, SN, Pruitt, KD, Fernandez-Suarez, XM, Karolchik, D, Worley, KC, Maglott, DR, Brown, G, Weinstock, G, Gibbs, RA et al. What everybody should know about the rat genome and its online resources.  Nat. Genet.  2008 May; 40(5):523-7. [PubMed]

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Worley, KC, Weinstock, GM, Gibbs, RA. Rats in the genomic era.  Physiol. Genomics  2008 Feb 19; 32(3):273-82. [PubMed]

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Wu, W, Stupi, BP, Litosh, VA, Mansouri, D, Farley, D, Morris, S, Metzker, S, Metzker, ML. Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.  Nucleic Acids Res.  2007; 35(19):6339-49. [PubMed]

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International HapMap Consortium, Frazer, KA, Ballinger, DG, Cox, DR, Hinds, DA, Stuve, LL, Gibbs, RA, Belmont, JW, Boudreau, A et al. A second generation human haplotype map of over 3.1 million SNPs.  Nature  2007 Oct 18; 449(7164):851-61. [PubMed]

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Price, AL, Patterson, N, Yu, F, Cox, DR, Waliszewska, A, McDonald, GJ, Tandon, A, Schirmer, C, Neubauer, J et al. A genomewide admixture map for Latino populations.  Am. J. Hum. Genet.  2007 Jun; 80(6):1024-36. [PubMed]

Yu, F, Hill, RS, Schaffner, SF, Sabeti, PC, Wang, ET, Mignault, AA, Ferland, RJ, Moyzis, RK, Walsh, CA et al. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens".  Science  2007 Apr 20; 316(5823):370. [PubMed]

Hernandez, RD, Hubisz, MJ, Wheeler, DA, Smith, DG, Ferguson, B, Rogers, J, Nazareth, L, Indap, A, Bourquin, T et al. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.  Science  2007 Apr 13; 316(5822):240-3. [PubMed]

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs, RA, Rogers, J, Katze, MG, Bumgarner, R, Weinstock, GM, Mardis, ER, Remington, KA, Strausberg, RL et al. Evolutionary and biomedical insights from the rhesus macaque genome.  Science  2007 Apr 13; 316(5822):222-34. [PubMed]

Harris, RA, Rogers, J, Milosavljevic, A. Human-specific changes of genome structure detected by genomic triangulation.  Science  2007 Apr 13; 316(5822):235-7. [PubMed]

McGuire, AL, Gibbs, RA. Meeting the growing demands of genetic research.  The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics  2006; 34(4):809-12. [PubMed]

Mukherjee, A, Soyal, SM, Wheeler, DA, Fernandez-Valdivia, R, Nguyen, J, DeMayo, FJ, Lydon, JP. Targeting iCre expression to murine progesterone receptor cell-lineages using bacterial artificial chromosome transgenesis.  Genesis  2006 Dec; 44(12):601-10. [PubMed]

Sodergren, E, Shen, Y, Song, X, Zhang, L, Gibbs, RA, Weinstock, GM. Shedding genomic light on Aristotle's lantern.  Dev. Biol.  2006 Dec 1; 300(1):2-8. [PubMed]

Johnson, ME, National Institute of Health Intramural Sequencing Center Comparative Sequencing Program, Cheng, Z, Morrison, VA, Scherer, S, Ventura, M, Gibbs, RA, Green, ED, Eichler, EE. Recurrent duplication-driven transposition of DNA during hominoid evolution.  Proc. Natl. Acad. Sci. U.S.A.  2006 Nov 21; 103(47):17626-31. [PubMed]

Sea Urchin Genome Sequencing Consortium, Sodergren, E, Weinstock, GM, Davidson, EH, Cameron, RA, Gibbs, RA, Angerer, RC, Angerer, LM, Arnone, MI et al. The genome of the sea urchin Strongylocentrotus purpuratus.  Science  2006 Nov 10; 314(5801):941-52. [PubMed]

Savard, J, Tautz, D, Richards, S, Weinstock, GM, Gibbs, RA, Werren, JH, Tettelin, H, Lercher, MJ. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects.  Genome Res.  2006 Nov; 16(11):1334-8. [PubMed]

Elsik, CG, Worley, KC, Zhang, L, Milshina, NV, Jiang, H, Reese, JT, Childs, KL, Venkatraman, A, Dickens, CM et al. Community annotation: procedures, protocols, and supporting tools.  Genome Res.  2006 Nov; 16(11):1329-33. [PubMed]

Qin, X, Evans, JD, Aronstein, KA, Murray, KD, Weinstock, GM. Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis.  Insect Mol. Biol.  2006 Oct; 15(5):715-8. [PubMed]

Robinson, GE, Evans, JD, Maleszka, R, Robertson, HM, Weaver, DB, Worley, K, Gibbs, RA, Weinstock, GM. Sweetness and light: illuminating the honey bee genome.  Insect Mol. Biol.  2006 Oct; 15(5):535-9. [PubMed]

Honeybee Genome Sequencing Consortium, Insights into social insects from the genome of the honeybee Apis mellifera.  Nature  2006 Oct 26; 443(7114):931-49. [PubMed]

Zhao, Y, Yang, Z, Phelan, JK, Wheeler, DA, Lin, S, McCabe, ER. Zebrafish dax1 is required for development of the interrenal organ, the adrenal cortex equivalent.  Mol. Endocrinol.  2006 Nov; 20(11):2630-40. [PubMed]

Gioia, J, Qin, X, Jiang, H, Clinkenbeard, K, Lo, R, Liu, Y, Fox, GE, Yerrapragada, S, McLeod, MP et al. The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny.  J. Bacteriol.  2006 Oct; 188(20):7257-66. [PubMed]

Yang, Z, Bowles, NE, Scherer, SE, Taylor, MD, Kearney, DL, Ge, S, Nadvoretskiy, VV, DeFreitas, G, Carabello, B et al. Desmosomal dysfunction due to mutations in desmoplakin causes arrhythmogenic right ventricular dysplasia/cardiomyopathy.  Circ. Res.  2006 Sep 15; 99(6):646-55. [PubMed]

Highlander, SK, Weissenberger, S, Alvarez, LE, Weinstock, GM, Berget, PB. Complete nucleotide sequence of a P2 family lysogenic bacteriophage, varphiMhaA1-PHL101, from Mannheimia haemolytica serotype A1.  Virology  2006 Jun 20; 350(1):79-89. [PubMed]

Muzny, DM, Scherer, SE, Kaul, R, Wang, J, Yu, J, Sudbrak, R, Buhay, CJ, Chen, R, Cree, A et al. The DNA sequence, annotation and analysis of human chromosome 3.  Nature  2006 Apr 27; 440(7088):1194-8. [PubMed]

Smajs, D, Matejkova, P, Weinstock, GM. Recognition of pore-forming colicin Y by its cognate immunity protein.  FEMS Microbiol. Lett.  2006 May; 258(1):108-13. [PubMed]

McGuire, AL, Gibbs, RA. Genetics. No longer de-identified.  Science  2006 Apr 21; 312(5772):370-1. [PubMed]

Ostrin, EJ, Li, Y, Hoffman, K, Liu, J, Wang, K, Zhang, L, Mardon, G, Chen, R. Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless.  Genome Res.  2006 Apr; 16(4):466-76. [PubMed]

Childers, CP, Newkirk, HL, Honeycutt, DA, Ramlachan, N, Muzney, DM, Sodergren, E, Gibbs, RA, Weinstock, GM, Womack, JE et al. Comparative analysis of the bovine MHC class IIb sequence identifies inversion breakpoints and three unexpected genes.  Anim. Genet.  2006 Apr; 37(2):121-9. [PubMed]

Scherer, SE, Muzny, DM, Buhay, CJ, Chen, R, Cree, A, Ding, Y, Dugan-Rocha, S, Gill, R, Gunaratne, P et al. The finished DNA sequence of human chromosome 12.  Nature  2006 Mar 16; 440(7082):346-51. [PubMed]

Brinkman, MB, McKevitt, M, McLoughlin, M, Perez, C, Howell, J, Weinstock, GM, Norris, SJ, Palzkill, T. Reactivity of antibodies from syphilis patients to a protein array representing the Treponema pallidum proteome.  J. Clin. Microbiol.  2006 Mar; 44(3):888-91. [PubMed]

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Fernandez-Valdivia, R, Zhang, Y, Pai, S, Metzker, ML, Schumacher, A. l7Rn6 encodes a novel protein required for clara cell function in mouse lung development.  Genetics  2006 Jan; 172(1):389-99. [PubMed]

Kim, MS, Jeong, J, Majewski, T, Kram, A, Yoon, DS, Zhang, RD, Li, JZ, Ptaszynski, K, Kuang, TC et al. Evidence for alternative candidate genes near RB1 involved in clonal expansion of in situ urothelial neoplasia.  Lab. Invest.  2006 Feb; 86(2):175-90. [PubMed]

Gibbs, RA. Trp modification signals a quorum.  Nat. Chem. Biol.  2005 Jun; 1(1):7-8. [PubMed]

Lalani, SR, Safiullah, AM, Fernbach, SD, Harutyunyan, KG, Thaller, C, Peterson, LE, McPherson, JD, Gibbs, RA, White, LD et al. Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation.  Am. J. Hum. Genet.  2006 Feb; 78(2):303-14. [PubMed]

Metzker, ML. Emerging technologies in DNA sequencing.  Genome Res.  2005 Dec; 15(12):1767-76. [PubMed]

Zhang, J, Wheeler, DA, Yakub, I, Wei, S, Sood, R, Rowe, W, Liu, PP, Gibbs, RA, Buetow, KH. SNPdetector: a software tool for sensitive and accurate SNP detection.  PLoS Comput. Biol.  2005 Oct; 1(5):e53. [PubMed]

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Gibbs, R. Deeper into the genome.  Nature  2005 Oct 27; 437(7063):1233-4. [PubMed]

Yakub, I, Lillibridge, KM, Moran, A, Gonzalez, OY, Belmont, J, Gibbs, RA, Tweardy, DJ. Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infection.  J. Infect. Dis.  2005 Nov 15; 192(10):1741-8. [PubMed]

Martin, KA, Siefert, JL, Yerrapragada, S, Lu, Y, McNeill, TZ, Moreno, PA, Weinstock, GM, Widger, WR, Fox, GE. Cyanobacterial signature genes.  Photosyn. Res.  2003; 75(3):211-21. [PubMed]

Yu, F, Sabeti, PC, Hardenbol, P, Fu, Q, Fry, B, Lu, X, Ghose, S, Vega, R, Perez, A et al. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene.  PLoS Genet.  2005 Sep; 1(3):e41. [PubMed]

Al-Lamki, Z, Wali, YA, Wasifuddin, SM, Zachariah, M, Al-Mjeni, R, Li, C, Muralitharan, S, Al-Kharusi, K, Gunaratne, P et al. Identification of prognosis markers in pediatric high-risk acute lymphoblastic leukemia.  Pediatric hematology and oncology  ; 22(7):629-43. [PubMed]

Gu, P, LeMenuet, D, Chung, AC, Mancini, M, Wheeler, DA, Cooney, AJ. Orphan nuclear receptor GCNF is required for the repression of pluripotency genes during retinoic acid-induced embryonic stem cell differentiation.  Mol. Cell. Biol.  2005 Oct; 25(19):8507-19. [PubMed]

Nallapareddy, SR, Wenxiang, H, Weinstock, GM, Murray, BE. Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island.  J. Bacteriol.  2005 Aug; 187(16):5709-18. [PubMed]

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Koekkoek, SK, Yamaguchi, K, Milojkovic, BA, Dortland, BR, Ruigrok, TJ, Maex, R, De Graaf, W, Smit, AE, VanderWerf, F et al. Deletion of FMR1 in Purkinje cells enhances parallel fiber LTD, enlarges spines, and attenuates cerebellar eyelid conditioning in Fragile X syndrome.  Neuron  2005 Aug 4; 47(3):339-52. [PubMed]

Alford, RL, Morris, KE, Rives, CM, Scherer, SE, Weinstock, G, Gibbs, RA, Ghonima, K, Belcher, M, Valdes, H et al. Genetic testing, biotechnology, and GMOs: A snapshot of public opinion, 2003 through 2004.  Genet. Med.  ; 7(6):454-5. [PubMed]

Horvath, JE, Gulden, CL, Vallente, RU, Eichler, MY, Ventura, M, McPherson, JD, Graves, TA, Wilson, RK, Schwartz, S et al. Punctuated duplication seeding events during the evolution of human chromosome 2p11.  Genome Res.  2005 Jul; 15(7):914-27. [PubMed]

McKevitt, M, Brinkman, MB, McLoughlin, M, Perez, C, Howell, JK, Weinstock, GM, Norris, SJ, Palzkill, T. Genome scale identification of Treponema pallidum antigens.  Infect. Immun.  2005 Jul; 73(7):4445-50. [PubMed]

Chen, R, Mardon, G. Keeping an eye on the fly genome.  Dev. Biol.  2005 Jun 15; 282(2):285-93. [PubMed]

Pappu, KS, Ostrin, EJ, Middlebrooks, BW, Sili, BT, Chen, R, Atkins, MR, Gibbs, R, Mardon, G. Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund.  Development  2005 Jun; 132(12):2895-905. [PubMed]

Eichinger, L, Pachebat, JA, Glockner, G, Rajandream, MA, Sucgang, R, Berriman, M, Song, J, Olsen, R, Szafranski, K et al. The genome of the social amoeba Dictyostelium discoideum.  Nature  2005 May 5; 435(7038):43-57. [PubMed]

Gu, P, Goodwin, B, Chung, AC, Xu, X, Wheeler, DA, Price, RR, Galardi, C, Peng, L, Latour, AM et al. Orphan nuclear receptor LRH-1 is required to maintain Oct4 expression at the epiblast stage of embryonic development.  Mol. Cell. Biol.  2005 May; 25(9):3492-505. [PubMed]

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