Publications

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1996
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 ;175(1-2):209-13.
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.
Bouck JB, Metzker ML, Gibbs RA. Shotgun sample sequence comparisons between mouse and human genomes. Nat Genet. 2000 ;25(1):31-3.
2001
Cai WW, Chen R, Gibbs RA, Bradley A. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 2001 ;11(10):1619-23.
Chen R, Bouck JB, Weinstock GM, Gibbs RA. Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 2001 ;11(11):1807-16.
Kram A, Li L, Zhang RD, Yoon DS, Ro JY, Johnston D, Grossman HB, Scherer S, Czerniak B. Mapping and genome sequence analysis of chromosome 5 regions involved in bladder cancer progression. Lab Invest. 2001 ;81(7):1039-48.
2002
Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci U S A. 2002 ;99(22):14326-31.
Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, Hodgson A, George RA, Hoskins RA, Laverty T, Muzny DM, Nelson CR, Pacleb JM, Park S, Pfeiffer BD, Richards S, Sodergren EJ, Svirskas R, Tabor PE, Wan K, Stapleton M, Sutton GG, Venter C, Weinstock G, Scherer SE, Myers EW, Gibbs RA, Rubin GM. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 2002 ;3(12):RESEARCH0079.
Dederich DA, Okwuonu G, Garner T, Denn A, Sutton A, Escotto M, Martindale A, Delgado O, Muzny DM, Gibbs RA, Metzker ML. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. Nucleic Acids Res. 2002 ;30(7):e32.
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LDW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, L Johnson S, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, W Kent J, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, W McCombie R, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang S-P, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 ;420(6915):520-62.
2003
Csuros M, Li B, Milosavljevic A. Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments. Genome Inform. 2003 ;14:186-95.
Gibbs RA, Weinstock GM. Evolving methods for the assembly of large genomes. Cold Spring Harb Symp Quant Biol. 2003 ;68:189-94.
Richards S. How is the Drosophila research community making use of the genome sequence?. Genome Biol. 2003 ;4(5):319.
Gibbs RA, Nelson DL. Human genetics. Primate shadow play. Science. 2003 ;299(5611):1331-3.
Gibson-Brown JJ, Osoegawa K, McPherson JD, Waterston RH, De Jong PJ, Rokhsar DS, Holland LZ. A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of Energy. J Exp Zool B Mol Dev Evol. 2003 ;300(1):5-22.
2004
Gunaratne PH. Advances in genome biology and technology. Expert Rev Mol Diagn. 2004 ;4(6):757-60.
Havlak P, Chen R, K Durbin J, Egan A, Ren Y, Song X-Z, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res. 2004 ;14(4):721-32.
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 ;14(4):679-84.
Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, Wilson RK, Spieth J. EAnnot: a genome annotation tool using experimental evidence. Genome Res. 2004 ;14(12):2503-9.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, J Venter C, Woodage T, Smith D, Lee H-M, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, K Durbin J, Simons R, Ren Y, Song X-Z, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQian, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, M Albà M, Abril JF, Guigó R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee Y-A, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, T Andrews D, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, J Venter C, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VBing, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 ;428(6982):493-521.
Belmont JW, Gibbs RA. Genome-wide linkage disequilibrium and haplotype maps. Am J Pharmacogenomics. 2004 ;4(4):253-62.
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 ;14(4):580-90.
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 LD, 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. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 2004 ;14(4):766-79.
Kalafus KJ, Jackson AR, Milosavljevic A. Pash: efficient genome-scale sequence anchoring by Positional Hashing. Genome Res. 2004 ;14(4):672-8.