Richard Gibbs, Ph.D.

Liu, Y, Qin, X, Song, XZ, Jiang, H, Shen, Y, Durbin, KJ, Lien, S, Kent, MP, Sodeland, M et al. Bos taurus genome assembly.  BMC Genomics  2009; 10():180. [PubMed]

Bovine Genome Sequencing and Analysis Consortium, Elsik, CG, Tellam, RL, Worley, KC, Gibbs, RA, Muzny, DM, Weinstock, GM, Adelson, DL, Eichler, EE et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution.  Science  2009 Apr 24; 324(5926):522-8. [PubMed]

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]

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

Hampton, OA, Den Hollander, P, Miller, CA, Delgado, DA, Li, J, Coarfa, C, Harris, RA, Richards, S, Scherer, SE et al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.  Genome Res.  2008 Dec 3; . [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]

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]

Tribolium Genome Sequencing Consortium, Richards, S, Gibbs, RA, Weinstock, GM, Brown, SJ, Denell, R, Beeman, RW, Gibbs, R, Beeman, RW et al. The genome of the model beetle and pest Tribolium castaneum.  Nature  2008 Apr 24; 452(7190):949-55. [PubMed]

Wheeler, DA, Srinivasan, M, Egholm, M, Shen, Y, Chen, L, McGuire, A, He, W, Chen, YJ, Makhijani, V et al. The complete genome of an individual by massively parallel DNA sequencing.  Nature  2008 Apr 17; 452(7189):872-6. [PubMed]

Durfee, T, Nelson, R, Baldwin, S, Plunkett, G, Burland, V, Mau, B, Petrosino, JF, Qin, X, Muzny, DM et al. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.  J. Bacteriol.  2008 Apr; 190(7):2597-606. [PubMed]

Park, Y, Aikins, J, Wang, LJ, Beeman, RW, Oppert, B, Lord, JC, Brown, SJ, Lorenzen, MD, Richards, S et al. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum.  Insect Biochem. Mol. Biol.  2008 Apr; 38(4):380-6. [PubMed]

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

Miller, W, Rosenbloom, K, Hardison, RC, Hou, M, Taylor, J, Raney, B, Burhans, R, King, DC, Baertsch, R et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser.  Genome Res.  2007 Dec; 17(12):1797-808. [PubMed]

Weir, BA, Woo, MS, Getz, G, Perner, S, Ding, L, Beroukhim, R, Lin, WM, Province, MA, Kraja, A et al. Characterizing the cancer genome in lung adenocarcinoma.  Nature  2007 Dec 6; 450(7171):893-8. [PubMed]

Albert, TJ, Molla, MN, Muzny, DM, Nazareth, L, Wheeler, D, Song, X, Richmond, TA, Middle, CM, Rodesch, MJ et al. Direct selection of human genomic loci by microarray hybridization.  Nat. Methods  2007 Nov; 4(11):903-5. [PubMed]

Sabeti, PC, Varilly, P, Fry, B, Lohmueller, J, Hostetter, E, Cotsapas, C, Xie, X, Byrne, EH, McCarroll, SA et al. Genome-wide detection and characterization of positive selection in human populations.  Nature  2007 Oct 18; 449(7164):913-8. [PubMed]

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]

Detera-Wadleigh, SD, Liu, CY, Maheshwari, M, Cardona, I, Corona, W, Akula, N, Steele, CJ, Badner, JA, Kundu, M et al. Sequence variation in DOCK9 and heterogeneity in bipolar disorder.  Psychiatr. Genet.  2007 Oct; 17(5):274-86. [PubMed]

ENCODE Project Consortium, Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigo, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature  2007 Jun 14; 447(7146):799-816. [PubMed]

Margulies, EH, Cooper, GM, Asimenos, G, Thomas, DJ, Dewey, CN, Siepel, A, Birney, E, Keefe, D, Schwartz, AS et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.  Genome Res.  2007 Jun; 17(6):760-74. [PubMed]

Solignac, M, Zhang, L, Mougel, F, Li, B, Vautrin, D, Monnerot, M, Cornuet, JM, Worley, KC, Weinstock, GM et al. The genome of Apis mellifera: dialog between linkage mapping and sequence assembly.  Genome Biol.  2007; 8(3):403. [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]

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]

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]

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]

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]

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]

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]

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]

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

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]

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]

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]

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]

Siepel, A, Bejerano, G, Pedersen, JS, Hinrichs, AS, Hou, M, Rosenbloom, K, Clawson, H, Spieth, J, Hillier, LW et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.  Genome Res.  2005 Aug; 15(8):1034-50. [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]

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]

Ross, MT, Grafham, DV, Coffey, AJ, Scherer, S, McLay, K, Muzny, D, Platzer, M, Howell, GR, Burrows, C et al. The DNA sequence of the human X chromosome.  Nature  2005 Mar 17; 434(7031):325-37. [PubMed]

Milosavljevic, A, Harris, RA, Sodergren, EJ, Jackson, AR, Kalafus, KJ, Hodgson, A, Cree, A, Dai, W, Csuros, M et al. Pooled genomic indexing of rhesus macaque.  Genome Res.  2005 Feb; 15(2):292-301. [PubMed]

Hardenbol, P, Yu, F, Belmont, J, Mackenzie, J, Bruckner, C, Brundage, T, Boudreau, A, Chow, S, Eberle, J et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.  Genome Res.  2005 Feb; 15(2):269-75. [PubMed]

Richards, S, Liu, Y, Bettencourt, BR, Hradecky, P, Letovsky, S, Nielsen, R, Thornton, K, Hubisz, MJ, Chen, R et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.  Genome Res.  2005 Jan; 15(1):1-18. [PubMed]

Nelson, DL, Gibbs, RA. Genetics. The critical region in trisomy 21.  Science  2004 Oct 22; 306(5696):619-21. [PubMed]

Gerhard, DS, Wagner, L, Feingold, EA, Shenmen, CM, Grouse, LH, Schuler, G, Klein, SL, Old, S, Rasooly, R et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).  Genome Res.  2004 Oct; 14(10B):2121-7. [PubMed]

Gibbs, RA, Weinstock, GM. Evolving methods for the assembly of large genomes.  Cold Spring Harb. Symp. Quant. Biol.  2003; 68():189-94. [PubMed]

Li, J, Jiang, T, Mao, JH, Balmain, A, Peterson, L, Harris, C, Rao, PH, Havlak, P, Gibbs, R et al. Genomic segmental polymorphisms in inbred mouse strains.  Nat. Genet.  2004 Sep; 36(9):952-4. [PubMed]

Egan, MF, Straub, RE, Goldberg, TE, Yakub, I, Callicott, JH, Hariri, AR, Mattay, VS, Bertolino, A, Hyde, TM et al. Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia.  Proc. Natl. Acad. Sci. U.S.A.  2004 Aug 24; 101(34):12604-9. [PubMed]

McLeod, MP, Qin, X, Karpathy, SE, Gioia, J, Highlander, SK, Fox, GE, McNeill, TZ, Jiang, H, Muzny, D et al. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.  J. Bacteriol.  2004 Sep; 186(17):5842-55. [PubMed]

Wu, JQ, Garcia, AM, Hulyk, S, Sneed, A, Kowis, C, Yuan, Y, Steffen, D, McPherson, JD, Gunaratne, PH et al. Large-scale RT-PCR recovery of full-length cDNA clones.  BioTechniques  2004 Apr; 36(4):690-6, 698-700. [PubMed]

Wu, JQ, Shteynberg, D, Arumugam, M, Gibbs, RA, Brent, MR. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.  Genome Res.  2004 Apr; 14(4):665-71. [PubMed]

Chen, R, Sodergren, E, Weinstock, GM, Gibbs, RA. Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project.  Genome Res.  2004 Apr; 14(4):679-84. [PubMed]

Havlak, P, Chen, R, Durbin, KJ, Egan, A, Ren, Y, Song, XZ, Weinstock, GM, Gibbs, RA. The Atlas genome assembly system.  Genome Res.  2004 Apr; 14(4):721-32. [PubMed]

Zhang, Z, Burch, PE, Cooney, AJ, Lanz, RB, Pereira, FA, Wu, J, Gibbs, RA, Weinstock, G, Wheeler, DA. Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome.  Genome Res.  2004 Apr; 14(4):580-90. [PubMed]

Gibbs, RA, Weinstock, GM, Metzker, ML, Muzny, DM, Sodergren, EJ, Scherer, S, Scott, G, Steffen, D, Worley, KC et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution.  Nature  2004 Apr 1; 428(6982):493-521. [PubMed]

Gunaratne, PH, Wu, JQ, Garcia, AM, Hulyk, S, Worley, KC, Margolin, JF, Gibbs, RA. Concatenation cDNA sequencing for transcriptome analysis.  C. R. Biol.  ; 326(10-11):971-7. [PubMed]

The International HapMap Consortium, The International HapMap Project.  Nature  2003 Dec 18; 426(6968):789-96. [PubMed]

Qiu, J, Gunaratne, P, Peterson, LE, Khurana, D, Walsham, N, Loulseged, H, Karni, RJ, Roussel, E, Gibbs, RA et al. Novel potential ALL low-risk markers revealed by gene expression profiling with new high-throughput SSH-CCS-PCR.  Leukemia  2003 Sep; 17(9):1891-900. [PubMed]

Shah, G, Brugada, R, Gonzalez, O, Czernuszewicz, G, Gibbs, RA, Bachinski, L, Roberts, R. The cloning, genomic organization and tissue expression profile of the human DLG5 gene: Correction.  BMC Genomics  2002 Jun 11; 3(1):14. [PubMed]

Maheshwari, M, Christian, SL, Liu, C, Badner, JA, Detera-Wadleigh, S, Gershon, ES, Gibbs, RA. Mutation screening of two candidate genes from 13q32 in families affected with Bipolar disorder: human peptide transporter (SLC15A1) and human glypican5 (GPC5).  BMC Genomics  2002 Oct 22; 3(1):30. [PubMed]

Shah, G, Brugada, R, Gonzalez, O, Czernuszewicz, G, Gibbs, RA, Bachinski, L, Roberts, R. The cloning, genomic organization and tissue expression profile of the human DLG5 gene.  BMC Genomics  2002; 3(1):6. [PubMed]

Sucgang, R, Chen, G, Liu, W, Lindsay, R, Lu, J, Muzny, D, Shaulsky, G, Loomis, W, Gibbs, R et al. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium.  Nucleic Acids Res.  2003 May 1; 31(9):2361-8. [PubMed]

Hattori, E, Liu, C, Badner, JA, Bonner, TI, Christian, SL, Maheshwari, M, Detera-Wadleigh, SD, Gibbs, RA, Gershon, ES. Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series.  Am. J. Hum. Genet.  2003 May; 72(5):1131-40. [PubMed]

Gibbs, RA, Nelson, DL. Human genetics. Primate shadow play.  Science  2003 Feb 28; 299(5611):1331-3. [PubMed]

Celniker, SE, Wheeler, DA, Kronmiller, B, Carlson, JW, Halpern, A, Patel, S, Adams, M, Champe, M, Dugan, SP et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.  Genome Biol.  2002; 3(12):RESEARCH0079. [PubMed]

Strausberg, RL, Feingold, EA, Grouse, LH, Derge, JG, Klausner, RD, Collins, FS, Wagner, L, Shenmen, CM, Schuler, GD et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.  Proc. Natl. Acad. Sci. U.S.A.  2002 Dec 24; 99(26):16899-903. [PubMed]

Mouse Genome Sequencing Consortium, Waterston, RH, Lindblad-Toh, K, Birney, E, Rogers, J, Abril, JF, Agarwal, P, Agarwala, R, Ainscough, R et al. Initial sequencing and comparative analysis of the mouse genome.  Nature  2002 Dec 5; 420(6915):520-62. [PubMed]

Metzker, ML, Mindell, DP, Liu, XM, Ptak, RG, Gibbs, RA, Hillis, DM. Molecular evidence of HIV-1 transmission in a criminal case.  Proc. Natl. Acad. Sci. U.S.A.  2002 Oct 29; 99(22):14292-7. [PubMed]

Maheshwari, M, Belmont, J, Fernbach, S, Ho, T, Molinari, L, Yakub, I, Yu, F, Combes, A, Towbin, J et al. PTPN11 mutations in Noonan syndrome type I: detection of recurrent mutations in exons 3 and 13.  Hum. Mutat.  2002 Oct; 20(4):298-304. [PubMed]

Sgourou, A, Papachatzopoulou, A, Psiouri, L, Antoniou, M, Zoumbos, N, Gibbs, R, Athanassiadou, A. The beta-globin C-->G mutation at 6 bp 3' to the termination codon causes beta-thalassaemia by decreasing the mRNA level.  Br. J. Haematol.  2002 Aug; 118(2):671-6. [PubMed]

Scott, GB, Steffen, DL, Edgar, D, Warren, JT, Kovar, CL, Scherer, SE, Havlak, PH, Gibbs, RA. Loader Lite: a new software tool for the ABI PRISM 3700 DNA sequencer.  BioTechniques  2002 Jun; 32(6):1366, 1368, 1370-1. [PubMed]

Dederich, DA, Okwuonu, G, Garner, T, Denn, A, Sutton, A, Escotto, M, Martindale, A, Delgado, O, Muzny, DM et al. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes.  Nucleic Acids Res.  2002 Apr 1; 30(7):e32. [PubMed]

Chen, R, Bouck, JB, Weinstock, GM, Gibbs, RA. Comparing vertebrate whole-genome shotgun reads to the human genome.  Genome Res.  2001 Nov; 11(11):1807-16. [PubMed]

Cai, WW, Chen, R, Gibbs, RA, Bradley, A. A clone-array pooled shotgun strategy for sequencing large genomes.  Genome Res.  2001 Oct; 11(10):1619-23. [PubMed]

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M et al. Initial sequencing and analysis of the human genome.  Nature  2001 Feb 15; 409(6822):860-921. [PubMed]

McPherson, JD, Marra, M, Hillier, L, Waterston, RH, Chinwalla, A, Wallis, J, Sekhon, M, Wylie, K, Mardis, ER et al. A physical map of the human genome.  Nature  2001 Feb 15; 409(6822):934-41. [PubMed]

Montgomery, KT, Lee, E, Miller, A, Lau, S, Shim, C, Decker, J, Chiu, D, Emerling, S, Sekhon, M et al. A high-resolution map of human chromosome 12.  Nature  2001 Feb 15; 409(6822):945-6. [PubMed]

Pacheco, SE, Gibbs, RA, Ansari-Lari, A, Rogers, P. Intranasal immunization with HIV reverse transcriptase: effect of dose in the induction of helper T cell type 1 and 2 immunity.  AIDS Res. Hum. Retroviruses  2000 Dec 10; 16(18):2009-17. [PubMed]

Bouck, J, McLeod, MP, Worley, K, Gibbs, RA. The human transcript database: a catalogue of full length cDNA inserts.  Bioinformatics  2000 Feb; 16(2):176-7. [PubMed]

Bowles, KR, Abraham, SE, Brugada, R, Zintz, C, Comeaux, J, Sorajja, D, Tsubata, S, Li, H, Brandon, L et al. Construction of a high-resolution physical map of the chromosome 10q22-q23 dilated cardiomyopathy locus and analysis of candidate genes.  Genomics  2000 Jul 15; 67(2):109-27. [PubMed]

Bouck, JB, Metzker, ML, Gibbs, RA. Shotgun sample sequence comparisons between mouse and human genomes.  Nat. Genet.  2000 May; 25(1):31-3. [PubMed]

Schwartz, S, Zhang, Z, Frazer, KA, Smit, A, Riemer, C, Bouck, J, Gibbs, R, Hardison, R, Miller, W. PipMaker--a web server for aligning two genomic DNA sequences.  Genome Res.  2000 Apr; 10(4):577-86. [PubMed]

Hoskins, RA, Nelson, CR, Berman, BP, Laverty, TR, George, RA, Ciesiolka, L, Naeemuddin, M, Arenson, AD, Durbin, J et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster.  Science  2000 Mar 24; 287(5461):2271-4. [PubMed]

Adams, MD, Celniker, SE, Holt, RA, Evans, CA, Gocayne, JD, Amanatides, PG, Scherer, SE, Li, PW, Hoskins, RA et al. The genome sequence of Drosophila melanogaster.  Science  2000 Mar 24; 287(5461):2185-95. [PubMed]

Bidichandani, SI, Purandare, SM, Taylor, EE, Gumin, G, Machkhas, H, Harati, Y, Gibbs, RA, Ashizawa, T, Patel, PI. Somatic sequence variation at the Friedreich ataxia locus includes complete contraction of the expanded GAA triplet repeat, significant length variation in serially passaged lymphoblasts and enhanced mutagenesis in the flanking sequence.  Hum. Mol. Genet.  1999 Dec; 8(13):2425-36. [PubMed]

Gibbs, RA. The weed paves the way.  Nat. Genet.  1999 Jul; 22(3):219-20. [PubMed]

Bouck, J, Yu, W, Gibbs, R, Worley, K. Comparison of gene indexing databases.  Trends Genet.  1999 Apr; 15(4):159-62. [PubMed]

Martinez, CI, Thoresen, LH, Gibbs, RA, Burgess, K. An allylic/acyclic adenosine nucleoside triphosphate for termination of DNA synthesis by DNA template-dependent polymerases.  Nucleic Acids Res.  1999 Mar 1; 27(5):1271-4. [PubMed]

Muzny, DM, Metzker, ML, Bouck, J, Gorrell, JH, Ding, Y, Maxim, E, Gibbs, RA. Using BODIPY dye-primer chemistry in large-scale sequencing.  IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society  ; 17(6):88-93. [PubMed]

Metzker, ML, Raghavachari, R, Burgess, K, Gibbs, RA. Elimination of residual natural nucleotides from 3'-O-modified-dNTP syntheses by enzymatic mop-up.  BioTechniques  1998 Nov; 25(5):814-7. [PubMed]

Bouck, J, Miller, W, Gorrell, JH, Muzny, D, Gibbs, RA. Analysis of the quality and utility of random shotgun sequencing at low redundancies.  Genome Res.  1998 Oct; 8(10):1074-84. [PubMed]

Metzker, ML, Ansari-Lari, MA, Liu, XM, Holder, DJ, Gibbs, RA. Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers.  BioTechniques  1998 Sep; 25(3):446-7, 450-2, 454, passim. [PubMed]

Timms, KM, Ansari-Lari, MA, Morris, W, Brown, SN, Gibbs, RA. The genomic organization of Isopeptidase T-3 (ISOT-3), a new member of the ubiquitin specific protease family (UBP).  Gene  1998 Sep 14; 217(1-2):101-6. [PubMed]

Timms, KM, Edwards, FJ, Belmont, JW, Yates, JR, Gibbs, RA. Reassessment of biochemically determined Hunter syndrome carrier status by DNA testing.  J. Med. Genet.  1998 Aug; 35(8):646-9. [PubMed]

Timms, KM, Huckett, LE, Belmont, JW, Shapira, SK, Gibbs, RA. DNA deletion confined to the iduronate-2-sulfatase promoter abolishes IDS gene expression.  Hum. Mutat.  1998; 11(2):121-6. [PubMed]

Jacutin, S, Zhang, AJ, Russell, DH, Gibbs, RA, Burgess, K. Test of the potential of a dATP surrogate for sequencing via MALDI-MS.  Nucleic Acids Res.  1997 Dec 15; 25(24):5072-6. [PubMed]

Ansari-Lari, MA, Oeltjen, JC, Schwartz, S, Zhang, Z, Muzny, DM, Lu, J, Gorrell, JH, Chinault, AC, Belmont, JW et al. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.  Genome Res.  1998 Jan; 8(1):29-40. [PubMed]

Reiter, LT, Murakami, T, Koeuth, T, Gibbs, RA, Lupski, JR. The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs.  Hum. Mol. Genet.  1997 Sep; 6(9):1595-603. [PubMed]

Gibbs, RA. Hares and tortoises in the race to sequence the human genome: expectations and realities.  Trends Genet.  1997 Oct; 13(10):381-3. [PubMed]

Huq, AH, Sutcliffe, JS, Nakao, M, Shen, Y, Gibbs, RA, Beaudet, AL. Sequencing and functional analysis of the SNRPN promoter: in vitro methylation abolishes promoter activity.  Genome Res.  1997 Jun; 7(6):642-8. [PubMed]

Ansari-Lari, MA, Liu, XM, Metzker, ML, Rut, AR, Gibbs, RA. The extent of genetic variation in the CCR5 gene.  Nat. Genet.  1997 Jul; 16(3):221-2. [PubMed]

Oeltjen, JC, Malley, TM, Muzny, DM, Miller, W, Gibbs, RA, Belmont, JW. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.  Genome Res.  1997 Apr; 7(4):315-29. [PubMed]

Yu, W, Andersson, B, Worley, KC, Muzny, DM, Ding, Y, Liu, W, Ricafrente, JY, Wentland, MA, Lennon, G et al. Large-scale concatenation cDNA sequencing.  Genome Res.  1997 Apr; 7(4):353-8. [PubMed]

Andersson, B, Lu, J, Shen, Y, Wentland, MA, Gibbs, RA. Simultaneous shotgun sequencing of multiple cDNA clones.  DNA Seq.  1997; 7(2):63-70. [PubMed]

Ansari-Lari, MA, Shen, Y, Muzny, DM, Lee, W, Gibbs, RA. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.  Genome Res.  1997 Mar; 7(3):268-80. [PubMed]

Timms, KM, Bondeson, ML, Ansari-Lari, MA, Lagerstedt, K, Muzny, DM, Dugan-Rocha, SP, Nelson, DL, Pettersson, U, Gibbs, RA. Molecular and phenotypic variation in patients with severe Hunter syndrome.  Hum. Mol. Genet.  1997 Mar; 6(3):479-86. [PubMed]

Ansari-Lari, MA, Jones, SN, Timms, KM, Gibbs, RA. Improved ligation-anchored PCR strategy for identification of 5' ends of transcripts.  BioTechniques  1996 Jul; 21(1):34-6, 38. [PubMed]

Eichler, EE, Lu, F, Shen, Y, Antonacci, R, Jurecic, V, Doggett, NA, Moyzis, RK, Baldini, A, Gibbs, RA et al. Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution.  Hum. Mol. Genet.  1996 Jul; 5(7):899-912. [PubMed]

Andersson, B, Lu, J, Edwards, KE, Muzny, DM, Gibbs, RA. Method for 96-well M13 DNA template preparations for large-scale sequencing.  BioTechniques  1996 Jun; 20(6):1022-7. [PubMed]

Jones, SN, Ansari-Lari, MA, Hancock, AR, Jones, WJ, Gibbs, RA, Donehower, LA, Bradley, A. Genomic organization of the mouse double minute 2 gene.  Gene  1996 Oct 10; 175(1-2):209-13. [PubMed]

Timms, KM, Lu, F, Shen, Y, Pierson, CA, Muzny, DM, Gu, Y, Nelson, DL, Gibbs, RA. 130 kb of DNA sequence reveals two new genes and a regional duplication distal to the human iduronate-2-sulfate sulfatase locus.  Genome Res.  1995 Aug; 5(1):71-8. [PubMed]

Ansari-Lari, MA, Muzny, DM, Lu, J, Lu, F, Lilley, CE, Spanos, S, Malley, T, Gibbs, RA. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.  Genome Res.  1996 Apr; 6(4):314-26. [PubMed]

Gu, Y, Shen, Y, Gibbs, RA, Nelson, DL. Identification of FMR2, a novel gene associated with the FRAXE CCG repeat and CpG island.  Nat. Genet.  1996 May; 13(1):109-13. [PubMed]

Ansari-Lari, MA, Gibbs, RA. Expression of human immunodeficiency virus type 1 reverse transcriptase in trans during virion release and after infection.  J. Virol.  1996 Jun; 70(6):3870-5. [PubMed]

Andersson, B, Wentland, MA, Ricafrente, JY, Liu, W, Gibbs, RA. A "double adaptor" method for improved shotgun library construction.  Anal. Biochem.  1996 Apr 5; 236(1):107-13. [PubMed]

Metzker, ML, Lu, J, Gibbs, RA. Electrophoretically uniform fluorescent dyes for automated DNA sequencing.  Science  1996 Mar 8; 271(5254):1420-2. [PubMed]

Reiter, LT, Murakami, T, Koeuth, T, Pentao, L, Muzny, DM, Gibbs, RA, Lupski, JR. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element.  Nat. Genet.  1996 Mar; 12(3):288-97. [PubMed]

Gibbs, RA. Pressing ahead with human genome sequencing.  Nat. Genet.  1995 Oct; 11(2):121-5. [PubMed]

Ansari-Lari, MA, Donehower, LA, Gibbs, RA. Analysis of human immunodeficiency virus type 1 integrase mutants.  Virology  1995 Aug 1; 211(1):332-5. [PubMed]

Andersson, B, Lu, F, Muzny, DM, Warren, ST, Gibbs, RA. Complete sequence of a 38.4-kb human cosmid insert containing the polymorphic marker DXS455 from Xq28.  DNA Seq.  1995; 5(4):219-23. [PubMed]

Oeltjen, JC, Liu, X, Lu, J, Allen, RC, Muzny, D, Belmont, JW, Gibbs, RA. Sixty-nine kilobases of contiguous human genomic sequence containing the alpha-galactosidase A and Bruton's tyrosine kinase loci.  Mamm. Genome  1995 May; 6(5):334-8. [PubMed]

Metzker, ML, Allain, KM, Gibbs, RA. Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0).  Comput. Appl. Biosci.  1995 Apr; 11(2):187-94. [PubMed]

Gibbs, RA, Cockerill, M. Working on the assembly line.  Trends Biochem. Sci.  1995 Apr; 20(4):162-3. [PubMed]

Ansari-Lari, MA, Gibbs, RA. Analysis of HIV type 1 reverse transcriptase expression in a human cell line.  AIDS Res. Hum. Retroviruses  1994 Sep; 10(9):1117-24. [PubMed]

Athanassiadou, A, Papachatzopoulou, A, Zoumbos, N, Maniatis, GM, Gibbs, R. A novel beta-thalassaemia mutation in the 5' untranslated region of the beta-globin gene.  Br. J. Haematol.  1994 Oct; 88(2):307-10. [PubMed]

Metzker, ML, Raghavachari, R, Richards, S, Jacutin, SE, Civitello, A, Burgess, K, Gibbs, RA. Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates.  Nucleic Acids Res.  1994 Oct 11; 22(20):4259-67. [PubMed]

Andersson, B, Povinelli, CM, Wentland, MA, Shen, Y, Muzny, DM, Gibbs, RA. Adaptor-based uracil DNA glycosylase cloning simplifies shotgun library construction for large-scale sequencing.  Anal. Biochem.  1994 May 1; 218(2):300-8. [PubMed]

Edwards, MC, Gibbs, RA. Multiplex PCR: advantages, development, and applications.  PCR Methods Appl.  1994 Feb; 3(4):S65-75. [PubMed]

Eichler, EE, Richards, S, Gibbs, RA, Nelson, DL. Fine structure of the human FMR1 gene.  Hum. Mol. Genet.  1993 Aug; 2(8):1147-53. [PubMed]

Zu, Z, Yu, Y, Gibbs, RA, Caskey, CT, Hsie, AW. Multiplex DNA amplification and solid-phase direct sequencing for mutation analysis at the hprt locus in Chinese hamster cells.  Mutat. Res.  1993 Aug; 288(2):237-48. [PubMed]

Andersson, B, Ying, JH, Lewis, DE, Gibbs, RA. Rapid characterization of HIV-1 sequence diversity using denaturing gradient gel electrophoresis and direct automated DNA sequencing of PCR products.  PCR Methods Appl.  1993 May; 2(4):293-300. [PubMed]

Povinelli, CM, Gibbs, RA. Large-scale sequencing library production: an adaptor-based strategy.  Anal. Biochem.  1993 Apr; 210(1):16-26. [PubMed]

Winnard, AV, Jia-Hsu, Y, Gibbs, RA, Mendell, JR, Burghes, AH. Identification of a 2 base pair nonsense mutation causing a cryptic splice site in a DMD patient.  Hum. Mol. Genet.  1992 Nov; 1(8):645-6. [PubMed]

Fu, YH, Friedman, DL, Richards, S, Pearlman, JA, Gibbs, RA, Pizzuti, A, Ashizawa, T, Perryman, MB, Scarlato, G et al. Decreased expression of myotonin-protein kinase messenger RNA and protein in adult form of myotonic dystrophy.  Science  1993 Apr 9; 260(5105):235-8. [PubMed]

Lewis, DE, Gibbs, RA. Detection and significance of HIV sequences in HIV infection.  Prog. Med. Virol.  1993; 40():19-47. [PubMed]

Civitello, AB, Richards, S, Gibbs, RA. A simple protocol for the automation of DNA cycle sequencing reactions and polymerase chain reactions.  DNA Seq.  1992; 3(1):17-23. [PubMed]

Edwards, MC, Gibbs, RA. A human dimorphism resulting from loss of an Alu.  Genomics  1992 Nov; 14(3):590-7. [PubMed]

Pizzuti, A, Pieretti, M, Fenwick, RG, Gibbs, RA, Caskey, CT. A transposon-like element in the deletion-prone region of the dystrophin gene.  Genomics  1992 Jul; 13(3):594-600. [PubMed]

Yu, YJ, Xu, Z, Gibbs, RA, Hsie, AW. Polymerase chain reaction-based comprehensive procedure for the analysis of the mutation spectrum at the hypoxanthine-guanine phosphoribosyltransferase locus in Chinese hamster cells.  Environ. Mol. Mutagen.  1992; 19(4):267-73. [PubMed]

Descartes, M, Huang, Y, Zhang, YH, McCabe, LL, Gibbs, R, Therrell, BL, McCabe, ER. Genotypic confirmation from the original dried blood specimens in a neonatal hemoglobinopathy screening program.  Pediatr. Res.  1992 Mar; 31(3):217-21. [PubMed]

Gibbs, RA. Polymerase chain reaction techniques.  Curr. Opin. Biotechnol.  1991 Feb; 2(1):69-75. [PubMed]

Clemens, PR, Fenwick, RG, Chamberlain, JS, Gibbs, RA, de Andrade, M, Chakraborty, R, Caskey, CT. Carrier detection and prenatal diagnosis in Duchenne and Becker muscular dystrophy families, using dinucleotide repeat polymorphisms.  Am. J. Hum. Genet.  1991 Nov; 49(5):951-60. [PubMed]

Zheng, H, Hasty, P, Brenneman, MA, Grompe, M, Gibbs, RA, Wilson, JH, Bradley, A. Fidelity of targeted recombination in human fibroblasts and murine embryonic stem cells.  Proc. Natl. Acad. Sci. U.S.A.  1991 Sep 15; 88(18):8067-71. [PubMed]

Edwards, MC, Clemens, PR, Tristan, M, Pizzuti, A, Gibbs, RA. Pentanucleotide repeat length polymorphism at the human CD4 locus.  Nucleic Acids Res.  1991 Sep 11; 19(17):4791. [PubMed]

Nelson, DL, Ballabio, A, Victoria, MF, Pieretti, M, Bies, RD, Gibbs, RA, Maley, JA, Chinault, AC, Webster, TD et al. Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus.  Proc. Natl. Acad. Sci. U.S.A.  1991 Jul 15; 88(14):6157-61. [PubMed]

Gibbs, RA. DNA amplification by the polymerase chain reaction.  Anal. Chem.  1990 Jul 1; 62(13):1202-14. [PubMed]

Edwards, A, Gibbs, RA, Nguyen, PN, Ansorge, W, Caskey, CT. Automated DNA sequencing methods for detection and analysis of mutations: applications to the Lesch-Nyhan syndrome.  Trans. Assoc. Am. Physicians  1989; 102():185-94. [PubMed]

Donehower, LA, Bohannon, RC, Ford, RJ, Gibbs, RA. The use of primers from highly conserved pol regions to identify uncharacterized retroviruses by the polymerase chain reaction.  J. Virol. Methods  1990 Apr; 28(1):33-46. [PubMed]

Grompe, M, Gibbs, RA, Chamberlain, JS, Caskey, CT. Detection of new mutation disease in man and mouse.  Mol. Biol. Med.  1989 Dec; 6(6):511-21. [PubMed]

Ballabio, A, Gibbs, RA, Caskey, CT. PCR test for cystic fibrosis deletion.  Nature  1990 Jan 18; 343(6255):220. [PubMed]

McBride, LJ, Koepf, SM, Gibbs, RA, Salser, W, Mayrand, PE, Hunkapiller, MW, Kronick, MN. Automated DNA sequencing methods involving polymerase chain reaction.  Clin. Chem.  1989 Nov; 35(11):2196-201. [PubMed]

Gibbs, RA, Caskey, CT. The application of recombinant DNA technology for genetic probing in epidemiology.  Annual review of public health  1989; 10():27-48. [PubMed]

Gibbs, RA, Nguyen, PN, Caskey, CT. Detection of single DNA base differences by competitive oligonucleotide priming.  Nucleic Acids Res.  1989 Apr 11; 17(7):2437-48. [PubMed]

Gibbs, RA, Nguyen, PN, McBride, LJ, Koepf, SM, Caskey, CT. Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA.  Proc. Natl. Acad. Sci. U.S.A.  1989 Mar; 86(6):1919-23. [PubMed]

Chamberlain, JS, Gibbs, RA, Ranier, JE, Nguyen, PN, Caskey, CT. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification.  Nucleic Acids Res.  1988 Dec 9; 16(23):11141-56. [PubMed]

Caskey, CT, Gibbs, RA, Witkowski, JA, Hejtmancik, JF. Diagnosis of human heritable defects by recombinant DNA methods.  Philos. Trans. R. Soc. Lond., B, Biol. Sci.  1988 Jun 15; 319(1194):353-60. [PubMed]

Chamberlain, JS, Pearlman, JA, Muzny, DM, Gibbs, RA, Ranier, JE, Caskey, CT, Reeves, AA. Expression of the murine Duchenne muscular dystrophy gene in muscle and brain.  Science  1988 Mar 18; 239(4846):1416-8. [PubMed]

Lee, CC, Wu, XW, Gibbs, RA, Cook, RG, Muzny, DM, Caskey, CT. Generation of cDNA probes directed by amino acid sequence: cloning of urate oxidase.  Science  1988 Mar 11; 239(4845):1288-91. [PubMed]

Veres, G, Gibbs, RA, Scherer, SE, Caskey, CT. The molecular basis of the sparse fur mouse mutation.  Science  1987 Jul 24; 237(4813):415-7. [PubMed]

Gibbs, RA, Caskey, CT. Identification and localization of mutations at the Lesch-Nyhan locus by ribonuclease A cleavage.  Science  1987 Apr 17; 236(4799):303-5. [PubMed]

Gibbs, RA, Camakaris, J, Hodgson, GS, Martin, RF. Molecular characterization of 125I decay and X-ray-induced HPRT mutants in CHO cells.  Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med.  1987 Feb; 51(2):193-9. [PubMed]