Publications

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Journal Article
Locke DP, Hillier LDW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang S-P, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Valle GDella, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, De Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 ;469(7331):529-33.
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, K Durbin J, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MAF, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 ;15(1):1-18.
Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörgo B, Pósfai G, Weinstock GM, Blattner FR. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 ;190(7):2597-606.
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.
Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJP, Kitts P, Lynch JA, Murphy T, Oliveira DCSG, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MMG, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi J-H, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Forêt S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC, Hurst GDD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FMF, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu L-L, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZLP, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010 ;327(5963):343-8.
Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, M Soares B, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJM, Marra MA. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 ;99(26):16899-903.
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.
Xing J, W Watkins S, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F. Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol. 2010 ;11(11):R113.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KYih, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Nadaf SAl, Wu C, Feng Z-P, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJuana, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song X-Z, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JAM, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011 ;12(8):R81.
Yuan B, Pehlivan D, Karaca E, Patel N, Charng W-L, Gambin T, Gonzaga-Jauregui C, V Sutton R, Yesil G, Bozdogan STug, Tos T, Koparir A, Koparir E, Beck CR, Gu S, Aslan H, Yuregir OOzalp, Rubeaan KAl, Alnaqeb D, Alshammari MJ, Bayram Y, Atik MM, Aydin H, B Geckinli B, Seven M, Ulucan H, Fenercioglu E, Ozen M, Jhangiani S, Muzny DM, Boerwinkle E, Tuysuz B, Alkuraya FS, Gibbs RA, Lupski JR. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. J Clin Invest. 2015 ;125(2):636-51.
Boone PM, Yuan B, Gu S, Ma Z, Gambin T, Gonzaga-Jauregui C, Jain M, Murdock TJ, White JJ, Jhangiani SN, Walker K, Wang Q, Muzny DM, Gibbs RA, J Hejtmancik F, Lupski JR, Posey JE, Lewis RA. Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death. Mol Genet Genomic Med. 2016 ;4(1):77-94.
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.
Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Akdemir ZCoban, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SWai, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 ;168(5):830-842.e7.
Stray-Pedersen A, Sorte HSørmo, Samarakoon P, Gambin T, Chinn IK, Akdemir ZHCoban, Erichsen HChristian, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OKristin, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AGrete, Skogen V, Osnes LTN, Kulseth MAnn, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MSoledad, Bezrodnik L, Reyes SOswaldo Lu, Rosales FJEspinosa, Guerrero-Cursaru NDenisse, Pedroza LAlberto, Poli CM, Franco JL, Vargas CMTrujillo, Becerra JCarlos Ald, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MMusa, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, I Hanson C, Zhang VW, Wong L-J, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol. 2017 ;139(1):232-245.
Harel T, Yoon WHee, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RAlan, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet. 2016 ;99(4):831-845.
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 ;455(7216):1069-75.
Highlander SK, Hultén KG, Qin X, Jiang H, Yerrapragada S, Mason EO, Shang Y, Williams TM, Fortunov RM, Liu Y, Igboeli O, Petrosino J, Tirumalai M, Uzman A, Fox GE, Cardenas AMaria, Muzny DM, Hemphill L, Ding Y, Dugan S, Blyth PR, Buhay CJ, Dinh HH, Hawes AC, Holder M, Kovar CL, Lee SL, Liu W, Nazareth LV, Wang Q, Zhou J, Kaplan SL, Weinstock GM. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007 ;7:99.
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.
Murdock DR, Clark GD, Bainbridge MN, Newsham I, Wu Y-Q, Muzny DM, Cheung SWai, Gibbs RA, Ramocki MB. Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyria. Am J Med Genet A. 2011 ;155A(9):2071-7.