Author Report for: Karolchik D No contact information in database for Karolchik D
Title: Evolutionary and biomedical insights from the rhesus macaque genomeGibbs RA , Rogers J , Katze MG , Bumgarner R , Weinstock GM , Mardis ER , Remington KA , Strausberg RL , Venter JC and Zwieg AS <166 more author(s)> 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 YS , Moore SM , Muzny D , Nazareth LV , Ngo DN , Okwuonu GO , Pai G , Parker D , Paul HA , Pfannkoch C , Pohl CS , Rogers YH , 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 SP , Jones SM , Marra MA , Rocchi M , Schein JE , Baertsch R , Clarke L , Csuros M , Glasscock J , Harris RA , Havlak P , Jackson AR , Jiang H , Liu Y , Messina DN , Shen Y , Song HX , Wylie T , Zhang L , Birney E , Han K , Konkel MK , Lee J , Smit AF , 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 SG , 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 LL , 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 W E , Prufer K , Stenson PD , Wallace JC , Ke H , Liu XM , Wang P , Xiang AP , Yang F , Barber GP , Haussler D , Karolchik D , Kern AD , Kuhn RM , Smith KE , Zwieg AS (- 166) Ref: Science, 316 :222, 2007 : PubMed Abstract ESTHER: Gibbs_2007_Science_316_222 PubMedSearch: Gibbs 2007 Science 316 222 PubMedID: 17431167 Gene_locus related to this paper: macmu-3neur ,
macmu-ACHE ,
macmu-BCHE ,
macmu-f6rul6 ,
macmu-f6sz31 ,
macmu-f6the6 ,
macmu-f6unj2 ,
macmu-f6wtx1 ,
macmu-f6zkq5 ,
macmu-f7aa58 ,
macmu-f7ai42 ,
macmu-f7aim4 ,
macmu-f7buk8 ,
macmu-f7cfi8 ,
macmu-f7cnr2 ,
macmu-f7cu68 ,
macmu-f7flv1 ,
macmu-f7ggk1 ,
macmu-f7hir7 ,
macmu-g7n054 ,
macmu-KANSL3 ,
macmu-TEX30 ,
macmu-Y4neur ,
macmu-g7n4x3 ,
macmu-i2cy02 ,
macmu-f7ba84 ,
macmu-CES2 ,
macmu-h9er02 ,
macmu-a0a1d5rbr3 ,
macmu-a0a1d5q4k5 ,
macmu-g7mxj6 ,
macmu-f7dn71 ,
macmu-f7hkw9 ,
macmu-f7hm08 ,
macmu-g7mke4 ,
macmu-a0a1d5rh04 ,
macmu-h9fud6 ,
macmu-f6qwx1 ,
macmu-f7h4t2 ,
macmu-h9zaw9 ,
macmu-f7h550 ,
macmu-a0a1d5q9w1 ,
macmu-f7gkb9 ,
macmu-f7hp78 ,
macmu-a0a1d5qvu5 Abstract
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
Title: Genome sequence of the Brown Norway rat yields insights into mammalian evolutionGibbs RA , Weinstock GM , Metzker ML , Muzny DM , Sodergren EJ , Scherer S , Scott G , Steffen D , Worley KC and Collins F <218 more author(s)> 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 , Celera , 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 , Venter JC , Woodage T , Smith D , Lee HM , 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 , Durbin KJ , Egan A , Ren Y , Song XZ , Li B , Liu Y , Qin X , Cawley S , Cooney AJ , D'Souza LM , Martin K , Wu JQ , 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 , Mar Alba M , Abril JF , Guigo R , Smit A , Dubchak I , Rubin EM , Couronne O , Poliakov A , Hubner N , Ganten D , Goesele C , Hummel O , Kreitler T , Lee YA , 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 , Andrews TD , Caccamo M , Clamp M , Clarke L , Curwen V , Durbin R , Eyras E , Searle SM , Cooper GM , Batzoglou S , Brudno M , Sidow A , Stone EA , Payseur BA , Bourque G , Lopez-Otin C , Puente XS , Chakrabarti K , Chatterji S , Dewey C , Pachter L , Bray N , Yap VB , 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 (- 218) Ref: Nature, 428 :493, 2004 : PubMed Abstract ESTHER: Gibbs_2004_Nature_428_493 PubMedSearch: Gibbs 2004 Nature 428 493 PubMedID: 15057822 Gene_locus related to this paper: rat-abhea ,
rat-abheb ,
rat-cd029 ,
rat-d3zaw4 ,
rat-dpp9 ,
rat-d3zhq1 ,
rat-d3zkp8 ,
rat-d3zuq1 ,
rat-d3zxw8 ,
rat-d4a4w4 ,
rat-d4a7w1 ,
rat-d4a9l7 ,
rat-d4a071 ,
rat-d4aa31 ,
rat-d4aa33 ,
rat-d4aa61 ,
rat-dglb ,
rat-f1lz91 ,
rat-Kansl3 ,
rat-nceh1 ,
rat-Tex30 ,
ratno-1hlip ,
ratno-1neur ,
ratno-1plip ,
ratno-2neur ,
ratno-3neur ,
ratno-3plip ,
ratno-ABH15 ,
ratno-ACHE ,
ratno-balip ,
ratno-BCHE ,
ratno-cauxin ,
ratno-Ces1d ,
ratno-Ces1e ,
ratno-Ces2f ,
ratno-d3ze31 ,
ratno-d3zp14 ,
ratno-d3zxi3 ,
ratno-d3zxq0 ,
ratno-d3zxq1 ,
ratno-d4a3d4 ,
ratno-d4aa05 ,
ratno-dpp4 ,
ratno-dpp6 ,
ratno-est8 ,
ratno-FAP ,
ratno-hyep ,
ratno-hyes ,
ratno-kmcxe ,
ratno-lmcxe ,
ratno-LOC246252 ,
ratno-MGLL ,
ratno-pbcxe ,
ratno-phebest ,
ratno-Ppgb ,
ratno-q4qr68 ,
ratno-q6ayr2 ,
ratno-q6q629 ,
ratno-SPG21 ,
ratno-thyro ,
rat-m0rc77 ,
rat-a0a0g2k9y7 ,
rat-a0a0g2kb83 ,
rat-d3zba8 ,
rat-d3zbj1 ,
rat-d3zcr8 ,
rat-d3zxw5 ,
rat-d4a340 ,
rat-f1lvg7 ,
rat-m0r509 ,
rat-m0r5d4 ,
rat-b5den3 ,
rat-d3zxk4 ,
rat-d4a1b6 ,
rat-d3zmg4 ,
rat-ab17c Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
