Publications

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2016
Deiros DRio, Gibbs RA, Rogers J. DNAism: exploring genomic datasets on the web with Horizon Charts. BMC Bioinformatics. 2016 ;17:49.
2015
Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics. 2015 ;16:214.
McMichael G, Bainbridge MN, Haan E, Corbett M, Gardner A, Thompson S, van Bon BWM, van Eyk CL, Broadbent J, Reynolds C, O'Callaghan ME, Nguyen LS, Adelson DL, Russo R, Jhangiani S, Doddapaneni HV, Muzny DM, Gibbs RA, Gecz J, MacLennan AH. Whole-exome sequencing points to considerable genetic heterogeneity of cerebral palsy. Mol Psychiatry. 2015 ;20(2):176-82.
2012
Deng Z, Huang W, Bakkalbasi E, Brown NG, Adamski CJ, Rice K, Muzny DM, Gibbs RA, Palzkill T. Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution. J Mol Biol. 2012 ;424(3-4):150-67.
2010
Shigenobu S, Richards S, Cree AG, Morioka M, Fukatsu T, Kudo T, Miyagishima S, Gibbs RA, Stern DL, Nakabachi A. A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum. Insect Mol Biol. 2010 ;19 Suppl 2:23-31.
Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu Y-Q, Newsham I, Richmond TA, Jeddeloh JA, Muzny DM, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010 ;11(6):R62.
2009
Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CLG, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny DM, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 ;19(12):2324-33.
Rodriguez JA, Guiteau JJ, Nazareth L, Reid JG, Goss JA, Gibbs RA, Gingras M-C. Sequencing the full-length of the phosphatase and tensin homolog (PTEN) gene in hepatocellular carcinoma (HCC) using the 454 GS20 and Illumina GA DNA sequencing platforms. World J Surg. 2009 ;33(4):647-52.
2008
Park Y, Aikins J, Wang LJ, Beeman RW, Oppert B, Lord JC, Brown SJ, Lorenzen MD, Richards S, Weinstock GM, Gibbs RA. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem Mol Biol. 2008 ;38(4):380-6.
2007
Lin H, Doddapaneni HV, Takahashi Y, M Walker A. Comparative analysis of ESTs involved in grape responses to Xylella fastidiosa infection. BMC Plant Biol. 2007 ;7:8.
Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler DA, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007 ;4(11):903-5.
2004
McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, C Harkins R, 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. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet. 2004 ;36(12):1268-74.
Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, M Soares B, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MSH, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CLin, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJM, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 ;14(10B):2121-7.
2002
Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, M Soares B, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJM, Marra MA. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 ;99(26):16899-903.
2000
Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, Tabor PE, Bailey MR, DeShazo DR, Catanese J, Mammoser A, Osoegawa K, de Jong PJ, Celniker SE, Gibbs RA, Rubin GM, Scherer SE. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science. 2000 ;287(5461):2271-4.
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science. 2000 ;287(5461):2185-95.
1998
Bouck J, Miller W, Gorrell JH, Muzny DM, Gibbs RA. Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res. 1998 ;8(10):1074-84.
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 ;217(1-2):101-6.
1997
Andersson B, Lu J, Shen Y, Wentland MA, Gibbs RA. Simultaneous shotgun sequencing of multiple cDNA clones. DNA Seq. 1997 ;7(2):63-70.
1993
Guo W, Worley KC, Adams V, Mason J, Sylvester-Jackson D, Zhang YH, Towbin JA, Fogt DD, Madu S, Wheeler DA. Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene. Nat Genet. 1993 ;4(4):367-72.
Povinelli CM, Gibbs RA. Large-scale sequencing library production: an adaptor-based strategy. Anal Biochem. 1993 ;210(1):16-26.
Worley KC, Ellison KA, Zhang YH, Wang DF, Mason J, Roth EJ, Adams V, Fogt DD, Zhu XM, Towbin JA. Yeast artificial chromosome cloning in the glycerol kinase and adrenal hypoplasia congenita region of Xp21. Genomics. 1993 ;16(2):407-16.
1992
Worley KC, Towbin JA, Zhu XM, Barker DF, Ballabio A, Chamberlain J, Biesecker LG, Blethen SL, Brosnan P, Fox JE. Identification of new markers in Xp21 between DXS28 (C7) and DMD. Genomics. 1992 ;13(4):957-61.