Publications

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2019
Hollister EB, Oezguen N, Chumpitazi BP, Luna RAnn, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta T-A, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn. 2019 ;21(3):449-461.
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.
2011
Saulnier DM, Riehle K, Mistretta T-A, Diaz M-A, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 ;141(5):1782-91.
2014
Lindstrand A, Davis EE, Carvalho CMB, Pehlivan D, Willer JR, Tsai I-C, Ramanathan S, Zuppan C, Sabo A, Muzny D, Gibbs R, Liu P, Lewis RA, Banin E, Lupski JR, Clark R, Katsanis N. Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am J Hum Genet. 2014 ;94(5):745-54.
2016
Lindstrand A, Frangakis S, Carvalho CMB, Richardson EB, McFadden KA, Willer JR, Pehlivan D, Liu P, Pediaditakis IL, Sabo A, Lewis RAlan, Banin E, Lupski JR, Davis EE, Katsanis N. Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. Am J Hum Genet. 2016 ;99(2):318-36.
2020
Surendran P, Feofanova EV, Lahrouchi N, Ntalla I, Karthikeyan S, Cook J, Chen L, Mifsud B, Yao C, Kraja AT, Cartwright JH, Hellwege JN, Giri A, Tragante V, Thorleifsson G, Liu DJ, Prins BP, Stewart ID, Cabrera CP, Eales JM, Akbarov A, Auer PL, Bielak LF, Bis JC, Braithwaite VS, Brody JA, E Daw W, Warren HR, Drenos F, Nielsen SFallgaard, Faul JD, Fauman EB, Fava C, Ferreira T, Foley CN, Franceschini N, Gao H, Giannakopoulou O, Giulianini F, Gudbjartsson DF, Guo X, Harris SE, Havulinna AS, Helgadottir A, Huffman JE, Hwang S-J, Kanoni S, Kontto J, Larson MG, Li-Gao R, Lindström J, Lotta LA, Lu Y, Luan J'an, Mahajan A, Malerba G, Masca NGD, Mei H, Menni C, Mook-Kanamori DO, Mosen-Ansorena D, Müller-Nurasyid M, Paré G, Paul DS, Perola M, Poveda A, Rauramaa R, Richard M, Richardson TG, Sepúlveda N, Sim X, Smith AV, Smith JA, Staley JR, Stanáková A, Sulem P, Thériault S, Thorsteinsdottir U, Trompet S, Varga TV, Edwards DRVelez, Veronesi G, Weiss S, Willems SM, Yao J, Young R, Yu B, Zhang W, Zhao J-H, Zhao W, Zhao W, Evangelou E, Aeschbacher S, Asllanaj E, Blankenberg S, Bonnycastle LL, Bork-Jensen J, Brandslund I, Braund PS, Burgess S, Cho K, Christensen C, Connell J, de Mutsert R, Dominiczak AF, Dörr M, Eiriksdottir G, Farmaki A-E, J Gaziano M, Grarup N, Grove ML, Hallmans G, Hansen T, Have CT, Heiss G, Jørgensen ME, Jousilahti P, Kajantie E, Kamat M, Käräjämäki A, Karpe F, Koistinen HA, Kovesdy CP, Kuulasmaa K, Laatikainen T, Lannfelt L, Lee I-T, Lee W-J, Linneberg A, Martin LW, Moitry M, Nadkarni G, Neville MJ, Palmer CNA, Papanicolaou GJ, Pedersen O, Peters J, Poulter N, Rasheed A, Rasmussen KL, N Rayner W, Mägi R, Renstrom F, Rettig R, Rossouw J, Schreiner PJ, Sever PS, Sigurdsson EL, Skaaby T, Sun YV, Sundström J, Thorgeirsson G, Esko T, Trabetti E, Tsao PS, Tuomi T, Turner ST, Tzoulaki I, Vaartjes I, Vergnaud A-C, Willer CJ, Wilson PWF, Witte DR, Yonova-Doing E, Zhang H, Aliya N, Almgren P, Amouyel P, Asselbergs FW, Barnes MR, Blakemore AI, Boehnke M, Bots ML, Bottinger EP, Buring JE, Chambers JC, Chen Y-DIda, Chowdhury, iv R, Conen D, Correa A, Smith GDavey, de Boer RA, Deary IJ, Dedoussis G, Deloukas P, Di Angelantonio E, Elliott P, Felix SB, Ferrieres J, Ford I, Fornage M, Franks PW, Franks S, Frossard P, Gambaro G, Gaunt TR, Groop L, Gudnason V, Harris TB, Hayward C, Hennig BJ, Herzig K-H, Ingelsson E, Tuomilehto J, Jarvelin M-R, J Jukema W, Kardia SLR, Kee F, Kooner JS, Kooperberg C, Launer LJ, Lind L, Loos RJF, Majumder AAl Shafi, Laakso M, McCarthy MI, Melander O, Mohlke KL, Murray AD, Nordestgaard BGrønne, Orho-Melander M, Packard CJ, Padmanabhan S, Palmas W, Polasek O, Porteous DJ, Prentice AM, Province MA, Relton CL, Rice K, Ridker PM, Rolandsson O, Rosendaal FR, Rotter JI, Rudan I, Salomaa V, Samani NJ, Sattar N, Sheu WH-H, Smith BH, Soranzo N, Spector TD, Starr JM, Sebert S, Taylor KD, Lakka TA, Timpson NJ, Tobin MD, van der Harst P, van der Meer P, Ramachandran VS, Verweij N, Virtamo J, Völker U, Weir DR, Zeggini E, Charchar FJ, Wareham NJ, Langenberg C, Tomaszewski M, Butterworth AS, Caulfield MJ, Danesh J, Edwards TL, Holm H, Hung AM, Lindgren CM, Liu C, Manning AK, Morris AP, Morrison AC, O'Donnell CJ, Psaty BM, Saleheen D, Stefansson K, Boerwinkle E, Chasman DI, Levy D, Newton-Cheh C, Munroe PB, Howson JMM. Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals. Nat Genet. 2020 ;52(12):1314-1332.
2019
Leija-Salazar M, Sedlazeck FJ, Toffoli M, Mullin S, Mokretar K, Athanasopoulou M, Donald A, Sharma R, Hughes D, Schapira AHV, Proukakis C. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION. Mol Genet Genomic Med. 2019 ;7(3):e564.
2015
Bailey AL, Lauck M, Mohns M, Peterson EJ, Beheler K, Brunner KG, Crosno K, Mejia A, Mutschler J, Gehrke M, Greene J, Ericsen AJ, Weiler A, Lehrer-Brey G, Friedrich TC, Sibley SD, Kallas EG, Capuano S, Rogers J, Goldberg TL, Simmons HA, O'Connor DH. Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection. Sci Transl Med. 2015 ;7(305):305ra144.
2001
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 ;409(6822):860-921.
2002
Sifri CD, Mylonakis E, Singh KV, Qin X, Garsin DA, Murray BE, Ausubel FM, Calderwood SB. Virulence effect of Enterococcus faecalis protease genes and the quorum-sensing locus fsr in Caenorhabditis elegans and mice. Infect Immun. 2002 ;70(10):5647-50.
2001
Qin X, Singh KV, Weinstock GM, Murray BE. Characterization of fsr, a regulator controlling expression of gelatinase and serine protease in Enterococcus faecalis OG1RF. J Bacteriol. 2001 ;183(11):3372-82.
1998
Singh KV, Qin X, Weinstock GM, Murray BE. Generation and testing of mutants of Enterococcus faecalis in a mouse peritonitis model. J Infect Dis. 1998 ;178(5):1416-20.
2000
Qin X, Singh KV, Weinstock GM, Murray BE. Effects of Enterococcus faecalis fsr genes on production of gelatinase and a serine protease and virulence. Infect Immun. 2000 ;68(5):2579-86.
2011
Galloway-Peña JR, Bourgogne A, Qin X, Murray BE. Diversity of the fsr-gelE region of the Enterococcus faecalis genome but conservation in strains with partial deletions of the fsr operon. Appl Environ Microbiol. 2011 ;77(2):442-51.
2003
Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LDW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003 ;13(5):940-53.
2011
Fisher WE. The promise of a personalized genomic approach to pancreatic cancer and why targeted therapies have missed the mark. World J Surg. 2011 ;35(8):1766-9.
2015
Burrage LC, Charng W-L, Eldomery MK, Willer JR, Davis EE, Lugtenberg D, Zhu W, Leduc MS, Akdemir ZC, Azamian M, Zapata G, Hernandez PP, Schoots J, de Munnik SA, Roepman R, Pearring JN, Jhangiani S, Katsanis N, Vissers LELM, Brunner HG, Beaudet AL, Rosenfeld JA, Muzny DM, Gibbs RA, Eng CM, Xia F, Lalani SR, Lupski JR, Bongers EMHF, Yang Y. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet. 2015 ;97(6):904-13.
2012
Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M. Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology. 2012 ;432(1):162-72.
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho T-J, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature. 2012 ;483(7387):82-6.
1990
Donehower LA, Bohannon RC, Ford RJ, Gibbs RA. The use of primers from highly conserved pol regions to identify uncharacterized retroviruses by the polymerase chain reaction. J Virol Methods. 1990 ;28(1):33-46.
2000
Zhang Y, Dipple KM, Vilain E, Huang BL, Finlayson G, Therrell BL, Worley KC, Deininger P, McCabe ER. AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency. Hum Mutat. 2000 ;15(4):316-23.
2003
Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier LD, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou S-F, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang S-P, Waterston RH, Wilson RK, Rozen S, Page DC. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 ;423(6942):825-37.
1990
Gibbs RA. DNA amplification by the polymerase chain reaction. Anal Chem. 1990 ;62(13):1202-14.
1988
Lee CC, Wu XW, Gibbs RA, Cook RG, Muzny DM, Caskey CT. Generation of cDNA probes directed by amino acid sequence: cloning of urate oxidase. Science. 1988 ;239(4845):1288-91.
1989
Xu ZD, Yu YJ, Hsie AW, Caskey CT, Rossiter B, Gibbs RA. Deletion screening at the hypoxanthine-guanine phosphoribosyltransferase locus in Chinese hamster cells using the polymerase chain reaction. Teratog Carcinog Mutagen. 1989 ;9(3):177-87.