Publications

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2017
Venner E, Leduc MS, Bainbridge MN, Wu T-J, Kovar C, Chiang T, Murugan M, Salerno WJ, Muzny DM, Gibbs RA. Generating Clinical Reports from Genomic Data on the Cloud-based Neptune Platform [Internet]. Phoenix: ACMG Annual Clinical Genetics Meeting 2017; 2017. http://epostersonline.com/acmg2017/node/2480
2016
Kanost MR, Arrese EL, Cao X, Chen Y-R, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, Papanicolaou A, Qu J, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn S-J, Almeida FC, An C, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu Y, Jiang H, Kalra D, Klinner C, König C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li Z, Liang H, Lovelace S, Lu Z, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu L-L, Pyrousis I, Rao X-J, Redding A, Roesel C, Sánchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong G-H, Traut W, Walsh TK, Worley KC, Wu D, Wu W, Wu Y-Q, Zhang X, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, A Passarelli L, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu X-Q, Zhou J-J, Brown SJ, Scherer SE, Richards S, Blissard GW. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochem Mol Biol. 2016 ;76:118-47.
2015
Li AH, Morrison AC, Kovar C, L Cupples A, Brody JA, Polfus LM, Yu B, Metcalf G, Muzny DM, Veeraraghavan N, Liu X, Lumley T, Mosley TH, Gibbs RA, Boerwinkle E. Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease. Nat Genet. 2015 ;47(6):640-2.
Foote AD, Liu Y, Thomas GWC, Vinar T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, M Gilbert TP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015 ;47(3):272-5.
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.
2012
Qin X, Galloway-Peña JR, Sillanpaa J, Roh JHyeob, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE. Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol. 2012 ;12:135.
2010
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HHuot, Wortman JRusso, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MGwinn, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. A catalog of reference genomes from the human microbiome. Science. 2010 ;328(5981):994-9.
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.
2008
Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJP, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZMohid, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz S-J, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du Y-Z, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang J-jun, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen H-C, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DEK, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, H Lattorff MG, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RNunes, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJP, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KKO, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, Bucher G. The genome of the model beetle and pest Tribolium castaneum. Nature. 2008 ;452(7190):949-55.
2007
Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Moorthy PEswara, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One. 2007 ;2(9):e928.
2006
Sodergren E, Weinstock GM, Davidson EH, R Cameron A, Gibbs RA, Angerer RC, Angerer LM, Arnone MIna, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, L Smith C, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley KC, K Durbin J, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière A-M, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron K-F, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QAutumn, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su Y-H, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu S-Y, Xu R, C Brown T, Chen L, Gray RF, Lee PYun, Nam J, Oliveri P, Smith J, Muzny DM, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu L-L, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 ;314(5801):941-52.