Publications

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2010
Kochunov P, Glahn DC, Fox PT, Lancaster JL, Saleem K, Shelledy W, Zilles K, Thompson PM, Coulon O, Mangin JF, Blangero J, Rogers J. Genetics of primary cerebral gyrification: Heritability of length, depth and area of primary sulci in an extended pedigree of Papio baboons. Neuroimage. 2010 ;53(3):1126-34.
Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010 ;8(2):e1000313.
Firozi P, Zhang W, Chen L, Quiocho FA, Worley KC, Templeton NS. Identification and removal of colanic acid from plasmid DNA preparations: implications for gene therapy. Gene Ther. 2010 ;17(12):1484-99.
Bose T, V Voruganti S, M Tejero E, J Proffit M, Cox LA, VandeBerg JL, Mahaney MC, Rogers J, Freeland-Graves JH, Cole SA, Comuzzie AG. Identification of a QTL for adipocyte volume and of shared genetic effects with aspartate aminotransferase. Biochem Genet. 2010 ;48(5-6):538-47.
Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol. 2010 ;27(10):2322-32.
Han S-J, Hu J, Pierce B, Weng Z, Renne R. Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. J Gen Virol. 2010 ;91(Pt 9):2203-15.
Chen M, Matsuda H, Wang L, Watanabe T, Kimura MT, Igarashi J, Wang X, Sakimoto T, Fukuda N, Sawa M, Nagase H. Pretranscriptional regulation of Tgf-beta1 by PI polyamide prevents scarring and accelerates wound healing of the cornea after exposure to alkali. Mol Ther. 2010 ;18(3):519-27.
Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs RA, Zhang K, Chen R. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 ;20(7):981-8.
Li Q, Ritter D, Yang N, Dong Z, Li H, Chuang JH, Guo S. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 ;337(2):484-95.
2009
Liu Y, Qin X, Song X-ZHenry, Jiang H, Shen Y, K Durbin J, Lien S, Kent MPeter, Sodeland M, Ren Y, Zhang L, Sodergren E, Havlak P, Worley KC, Weinstock GM, Gibbs RA. Bos taurus genome assembly. BMC Genomics. 2009 ;10:180.
Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, Hollander AI den, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet. 2009 ;41(6):739-45.
Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact. 2009 ;22(8):1011-20.
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.
Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, Bustamante CD. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet. 2009 ;5(1):e1000346.
Wang C, Mavrogianis PA, Fazleabas AT. Endometriosis is associated with progesterone resistance in the baboon (Papio anubis) oviduct: evidence based on the localization of oviductal glycoprotein 1 (OVGP1). Biol Reprod. 2009 ;80(2):272-8.
You M, Wang D, Liu P, Vikis H, James M, Lu Y, Wang Y, Wang M, Chen Q, Jia D, Liu Y, Wen W, Yang P, Sun Z, Pinney SM, Zheng W, Shu X-O, Long J, Gao Y-T, Xiang Y-B, Chow W-H, Rothman N, Petersen GM, de Andrade M, Wu Y, Cunningham JM, Wiest JS, Fain PR, Schwartz AG, Girard L, Gazdar A, Gaba C, Rothschild H, Mandal D, Coons T, Lee J, Kupert E, Seminara D, Minna J, Bailey-Wilson JE, Amos CI, Anderson MW. Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene. Clin Cancer Res. 2009 ;15(8):2666-74.
Willmore KE, Roseman CC, Rogers J, Richtsmeier JT, Cheverud JM. Genetic variation in baboon craniofacial sexual dimorphism. Evolution. 2009 ;63(3):799-806.
Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen H-C, Chrast J, Camara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FSL, Lau LPL, Whiteside MD, Walker A, Wheeler TT, Casey T, J German B, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CTA, Iivanainen A, Lahmers KK, Bennett AK, C Dickens M, Gilbert JGR, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JFernando, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJM, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MDiep, Dinh HH, Gabisi RAyiesha, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu Y-S, Lopez J, Morgan MB, Nguyen NBich, Okwuonu GO, Ruiz SJuana, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens MEdward, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, K Durbin J, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SNicole, Davis C, Johnson AJolivet, Lee S, Nazareth LV, Patel BMayurkumar, Pu L-L, Vattathil S, Williams RLee, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo ARR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IKF de Mir, de Oliveira CJF, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu Z-L, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC-M, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MFG, Olsaker I, Pant SD, Panzitta F, Pastor RCP, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YStrandberg, Sweedler JV, Tammen I, Telugu BPrakash V, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao F-Q. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 ;324(5926):522-8.
Dmitrieva RI, Hinojos CA, Grove ML, Bell RJ, Boerwinkle E, Fornage M, Doris PA. Genome-wide identification of allelic expression in hypertensive rats. Circ Cardiovasc Genet. 2009 ;2(2):106-15.
Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JFernando, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LOC, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song X-Z, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, da Silva MBarbosa, Lau LPL, Liu GE, Lynn DJ, Panzitta F, Dodds KG. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 ;324(5926):528-32.
Daines B, Wang H, Li Y, Han Y, Gibbs RA, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009 ;182(4):935-41.
Wang Y, Brahmakshatriya V, Zhu H, Lupiani B, Reddy SM, Yoon B-J, Gunaratne PH, Kim JHwan, Chen R, Wang J, Zhou H. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009 ;10:512.
Hu J, Liu E, Renne R. Involvement of SSRP1 in latent replication of Kaposi's sarcoma-associated herpesvirus. J Virol. 2009 ;83(21):11051-63.
Rainwater DL, Cox LA, Rogers J, VandeBerg JL, Mahaney MC. Localization of multiple pleiotropic genes for lipoprotein metabolism in baboons. J Lipid Res. 2009 ;50(7):1420-8.
Patel SG, Zhou G, Liu S-H, Li M, Jeong J-W, DeMayo FJ, Gingras M-C, Gibbs RA, Fisher WE, F Brunicardi C. Microarray analysis of somatostatin receptor 5-regulated gene expression profiles in murine pancreas. World J Surg. 2009 ;33(4):630-7.