Publications

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2017
Saha S, Hosmani PS, Villalobos-Ayala K, Miller S, Shippy T, Flores M, Rosendale A, Cordola C, Bell T, Mann H, DeAvila G, DeAvila D, Moore Z, Buller K, Ciolkevich K, Nandyal S, Mahoney R, Van Voorhis J, Dunlevy M, Farrow D, Hunter D, Morgan T, Shore K, Guzman V, Izsak A, Dixon DE, Cridge A, Cano L, Cao X, Jiang H, Leng N, Johnson S, Cantarel BL, Richards S, English A, Shatters RG, Childers C, Chen M-J, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D'Elia T, Brown SJ. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Database (Oxford). 2017 ;2017.
Zhang Y, Ng PKwok-Shing, Kucherlapati M, Chen F, Liu Y, Tsang YHuen, De Velasco G, Jeong KJin, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CSimon, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 ;31(6):820-832.e3.
2016
Becnel LB, Pereira S, Drummond JA, Gingras M-C, Covington KR, Kovar CL, Doddapaneni HV, Hu J, Muzny DM, McGuire AL, Wheeler DA, Gibbs RA. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data. 2016 ;3:160010.
2015
Appadurai V, DeBarber A, Chiang P-W, Patel SB, Steiner RD, Tyler C, Bonnen PE. Apparent underdiagnosis of Cerebrotendinous Xanthomatosis revealed by analysis of ~60,000 human exomes. Mol Genet Metab. 2015 ;116(4):298-304.
English AC, Salerno WJ, Hampton OA, Gonzaga-Jauregui C, Ambreth S, Ritter DI, Beck CR, Davis CF, Dahdouli M, Ma S, Carroll A, Veeraraghavan N, Bruestle J, Drees B, Hastie A, Lam ET, White S, Mishra P, Wang M, Han Y, Zhang F, Stankiewicz P, Wheeler DA, Reid JG, Muzny DM, Rogers J, Sabo A, Worley KC, Lupski JR, Boerwinkle E, Gibbs RA. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics. 2015 ;16:286.
Wang F, Jiang L, Chen Y, Haelterman NA, Bellen HJ, Chen R. FlyVar: a database for genetic variation in Drosophila melanogaster. Database (Oxford). 2015 ;2015.
Karaca E, Harel T, Pehlivan D, Jhangiani SN, Gambin T, Akdemir ZCoban, Gonzaga-Jauregui C, Erdin S, Bayram Y, Campbell IM, Hunter JV, Atik MM, Van Esch H, Yuan B, Wiszniewski W, Isikay S, Yesil G, Yuregir OO, Bozdogan STug, Aslan H, Aydin H, Tos T, Aksoy A, De Vivo DC, Jain P, B Geckinli B, Sezer O, Gul D, Durmaz B, Cogulu O, Ozkinay F, Topcu V, Candan S, Cebi AHan, Ikbal M, Gulec EYilmaz, Gezdirici A, Koparir E, Ekici F, Coskun S, Cicek S, Karaer K, Koparir A, Duz MBugrahan, Kirat E, Fenercioglu E, Ulucan H, Seven M, Guran T, Elcioglu N, Yildirim MSelman, Aktas D, Alikaşifoğlu M, Ture M, Yakut T, Overton JD, Yuksel A, Ozen M, Muzny DM, Adams DR, Boerwinkle E, Chung WK, Gibbs RA, Lupski JR. Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. Neuron. 2015 ;88(3):499-513.
Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Camara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MMG, Blaxter ML, Bourke AFG, Brown MJF, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, Plessis Ldu, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FCP, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, F Kraus B, H Lattorff MG, Leask M, Lockett GA, Mallon EB, Antonio DSMarco, Marxer M, Meeus I, Moritz RFA, Nair A, Näpflin K, Nissen I, Niu J, Nunes FMF, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZLP, Soares MPM, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu L-L, Saada N, Santibanez J, Simmons DN, Thornton R, Venkat A, Walden KKO, Wu Y-Q, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol. 2015 ;16:76.
Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SOM, Dunnen JT den, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 ;36(10):915-21.
Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny DM, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res. 2015 ;43(Database issue):D737-42.
2014
Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, Brautbar A, Brilliant MH, Carrell DS, Connolly JJ, Crosslin DR, Doheny KF, Gallego CJ, Gottesman O, Kim DS, Leppig KA, Li R, Lin S, Manzi S, Mejia AR, Pacheco JA, Pan V, Pathak J, Perry CL, Peterson JF, Prows CA, Ralston J, Rasmussen LV, Ritchie MD, Sadhasivam S, Scott SA, Smith M, Vega A, Vinks AA, Volpi S, Wolf WA, Bottinger E, Chisholm RL, Chute CG, Haines JL, Harley JB, Keating B, Holm IA, Kullo IJ, Jarvik GP, Larson EB, Manolio T, McCarty CA, Nickerson DA, Scherer SE, Williams MS, Roden DM, Denny JC. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems. Clin Pharmacol Ther. 2014 ;96(4):482-9.
Shinbrot E, Henninger EE, Weinhold N, Covington KR, A Göksenin Y, Schultz N, Chao H, Doddapaneni HV, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 2014 ;24(11):1740-50.
Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong X-Z, Ehrlich DS, Fraser C, Gibbs RA, Gilbert J, Gilna P, Glöckner FOliver, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee J-S, Li W-J, Ma J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K-I, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou Y-G, Field D, Whitman WB, Garrity GM, Klenk H-P. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014 ;12(8):e1001920.
Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S-B, Yang L, Ko M, Chen R, Göttgens B, Lee J-S, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014 ;46(1):17-23.
2013
Wang QY, Song J, Gibbs RA, Boerwinkle E, Dong JF, Yu F. Characterizing polymorphisms and allelic diversity of von Willebrand factor gene in the 1000 Genomes. J Thromb Haemost. 2013 ;11(2):261-9.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 2013 ;23(2):341-51.
Boone PM, Campbell IM, Baggett BC, Soens ZT, Rao MM, Hixson PM, Patel A, Bi W, Cheung SWai, Lalani SR, Beaudet AL, Stankiewicz P, Shaw CA, Lupski JR. Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles. Genome Res. 2013 ;23(9):1383-94.
Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni HV, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM, J Manak R. OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Res. 2013 ;41(Database issue):D845-53.
Morrison AC, Voorman A, Johnson AD, Liu X, Yu J, Li A, Muzny DM, Yu F, Rice K, Zhu C, Bis J, Heiss G, O'Donnell CJ, Psaty BM, L Cupples A, Gibbs RA, Boerwinkle E. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet. 2013 ;45(8):899-901.
2012
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P. The 1000 Genomes Project: data management and community access. Nat Methods. 2012 ;9(5):459-62.
Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F. Atlas2 Cloud: a framework for personal genome analysis in the cloud. BMC Genomics. 2012 ;13 Suppl 6:S19.
Hong X, Doddapaneni HV, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, Bolei F, Metpally R, Richmond TA, Albert TJ, Manak JR. Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster. G3 (Bethesda). 2012 ;2(8):873-82.
English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012 ;7(11):e47768.
2011
Luo L, Boerwinkle E, Xiong M. Association studies for next-generation sequencing. Genome Res. 2011 ;21(7):1099-108.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PLuigi, Chain PSG, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FOliver. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 ;29(5):415-20.