Publications

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2014
Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AMaria, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim Y-A, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.
Wang F, Wang H, Tuan H-F, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, Pei J, Khan A, Ren H, Wang K, Lopez I, Qamar R, Zenteno JC, Ayala-Ramirez R, Buentello-Volante B, Fu Q, Simpson DA, Li Y, Sui R, Silvestri G, Daiger SP, Koenekoop RK, Zhang K, Chen R. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet. 2014 ;133(3):331-45.
2013
Vatta M, Niu Z, Lupski JR, Putnam P, Spoonamore KG, Fang P, Eng CM, Willis AS. Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome. Am J Med Genet A. 2013 ;161A(12):3182-6.
Agopian AJ, Bhalla AD, Boerwinkle E, Finnell RH, Grove ML, Hixson JE, Shimmin LC, Sewda A, Stuart C, Zhong Y, Zhu H, Mitchell LE. Exon sequencing of PAX3 and T (brachyury) in cases with spina bifida. Birth Defects Res A Clin Mol Teratol. 2013 ;97(9):597-601.
Hanchard NA, Murdock DR, Magoulas PL, Bainbridge MN, Muzny DM, Wu Y, Wang M, Lupski JR, Gibbs RA, Brown CW. Exploring the utility of whole-exome sequencing as a diagnostic tool in a child with atypical episodic muscle weakness. Clin Genet. 2013 ;83(5):457-461.
Wiszniewski W, Hunter JV, Hanchard NA, Willer JR, Shaw C, Tian Q, Illner A, Wang X, Cheung SW, Patel A, Campbell IM, Gelowani V, Hixson P, Ester AR, Azamian MS, Potocki L, Zapata G, Hernandez PP, Ramocki MB, Santos-Cortez RLP, Wang G, York MK, Justice MJ, Chu ZD, Bader PI, Omo-Griffith L, Madduri NS, Scharer G, Crawford HP, Yanatatsaneejit P, Eifert A, Kerr J, Bacino CA, Franklin AIA, Goin-Kochel RP, Simpson G, Immken L, Haque ME, Stosic M, Williams MD, Morgan TM, Pruthi S, Omary R, Boyadjiev SA, Win KK, Thida A, Hurles M, Hibberd MLloyd, Khor CChuen, Chau NVan Vinh, Gallagher TE, Mutirangura A, Stankiewicz P, Beaudet AL, Maletic-Savatic M, Rosenfeld JA, Shaffer LG, Davis EE, Belmont JW, Dunstan S, Simmons CP, Bonnen PE, Leal SM, Katsanis N, Lupski JR, Lalani SR. TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. Am J Hum Genet. 2013 ;93(2):197-210.
2012
Tu Q, R Cameron A, Worley KC, Gibbs RA, Davidson EH. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res. 2012 ;22(10):2079-87.
Hong X, Doddapaneni H, 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.
Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin C-F, Stevens C, San Wang L-, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 ;485(7397):242-5.
Ritter DI, Dong Z, Guo S, Chuang JH. Transcriptional enhancers in protein-coding exons of vertebrate developmental genes. PLoS One. 2012 ;7(5):e35202.
2011
Wang H, Chen X, Dudinsky L, Patenia C, Chen Y, Li Y, Wei Y, Abboud EB, Al-Rajhi AA, Lewis RAlan, Lupski JR, Mardon G, Gibbs RA, Perkins BD, Chen R. Exome capture sequencing identifies a novel mutation in BBS4. Mol Vis. 2011 ;17:3529-40.
Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie T-X, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 ;333(6046):1154-7.
Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, Shibata T. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet. 2011 ;43(5):464-9.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, W Kent J, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CWhye, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 ;478(7370):476-82.
Bainbridge MN, Wang M, Wu Y, Newsham I, Muzny DM, Jefferies JL, Albert TJ, Burgess DL, Gibbs RA. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol. 2011 ;12(7):R68.
2010
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WSiang, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, B Pugh F, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 ;463(7283):943-7.
Cole SA, Butte NF, V Voruganti S, Cai G, Haack K, Kent JW, Blangero J, Comuzzie AG, McPherson JD, Gibbs RA. Evidence that multiple genetic variants of MC4R play a functional role in the regulation of energy expenditure and appetite in Hispanic children. Am J Clin Nutr. 2010 ;91(1):191-9.
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 D, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 2010 ;11(6):R62.
2009
Maheshwari M, Shi J, Badner JA, Skol A, Willour VL, Muzny DM, Wheeler DA, Gerald FR, Detera-Wadleigh S, McMahon FJ, Potash JB, Gershon ES, Liu C, Gibbs RA. Common and rare variants of DAOA in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet. 2009 ;150B(7):960-6.
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
Martinez-Moczygemba M, Doan ML, Elidemir O, Fan LL, Cheung SWai, Lei JT, Moore JP, Tavana G, Lewis LR, Zhu Y, Muzny DM, Gibbs RA, Huston DP. Pulmonary alveolar proteinosis caused by deletion of the GM-CSFRalpha gene in the X chromosome pseudoautosomal region 1. J Exp Med. 2008 ;205(12):2711-6.
2007
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SCJ, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao XD, Srinivasan KG, Sung W-K, Ooi HSain, Chiu KPing, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SWoh, Choo CYu, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei C-L, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, W Kent J, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim THoon, Wang K, Qu C, Hon G, Luna R, Glass CK, M Rosenfeld G, Aldred SForce, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, De Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 ;447(7146):799-816.
2005
Wang M, Futamura M, Wang Y, You M. Pas1c1 is a candidate for the mouse pulmonary adenoma susceptibility 1 locus. Oncogene. 2005 ;24(11):1958-63.
Yu F, Sabeti PC, Hardenbol P, Fu Q, Fry B, Lu X, Ghose S, Vega R, Perez A, Pasternak S, Leal SM, Willis TD, Nelson DL, Belmont J, Gibbs RA. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene. PLoS Genet. 2005 ;1(3):e41.
Yakub I, Lillibridge KM, Moran A, Gonzalez OY, Belmont J, Gibbs RA, Tweardy DJ. Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infection. J Infect Dis. 2005 ;192(10):1741-8.