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1.

An integrated semiconductor device enabling non-optical genome sequencing.

Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James.

Nature ; 475(7356): 348-52, 2011 Jul 20.

Article in English | MEDLINE | ID: mdl-21776081

2.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Pleasance, Erin D; Stephens, Philip J; O'Meara, Sarah; McBride, David J; Meynert, Alison; Jones, David; Lin, Meng-Lay; Beare, David; Lau, King Wai; Greenman, Chris; Varela, Ignacio; Nik-Zainal, Serena; Davies, Helen R; Ordoñez, Gonzalo R; Mudie, Laura J; Latimer, Calli; Edkins, Sarah; Stebbings, Lucy; Chen, Lina; Jia, Mingming; Leroy, Catherine; Marshall, John; Menzies, Andrew; Butler, Adam; Teague, Jon W; Mangion, Jonathon; Sun, Yongming A; McLaughlin, Stephen F; Peckham, Heather E; Tsung, Eric F; Costa, Gina L; Lee, Clarence C; Minna, John D; Gazdar, Adi; Birney, Ewan; Rhodes, Michael D; McKernan, Kevin J; Stratton, Michael R; Futreal, P Andrew; Campbell, Peter J.

Nature ; 463(7278): 184-90, 2010 Jan 14.

Article in English | MEDLINE | ID: mdl-20016488

3.

Mutation in the nuclear-encoded mitochondrial isoleucyl-tRNA synthetase IARS2 in patients with cataracts, growth hormone deficiency with short stature, partial sensorineural deafness, and peripheral neuropathy or with Leigh syndrome.

Schwartzentruber, Jeremy; Buhas, Daniela; Majewski, Jacek; Sasarman, Florin; Papillon-Cavanagh, Simon; Thiffault, Isabelle; Thiffaut, Isabelle; Sheldon, Katherine M; Massicotte, Christine; Patry, Lysanne; Simon, Mariella; Zare, Amir S; McKernan, Kevin J; Michaud, Jacques; Boles, Richard G; Deal, Cheri L; Desilets, Valerie; Shoubridge, Eric A; Samuels, Mark E.

Hum Mutat ; 35(11): 1285-9, 2014 Nov.

Article in English | MEDLINE | ID: mdl-25130867

4.

Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Cloonan, Nicole; Forrest, Alistair R R; Kolle, Gabriel; Gardiner, Brooke B A; Faulkner, Geoffrey J; Brown, Mellissa K; Taylor, Darrin F; Steptoe, Anita L; Wani, Shivangi; Bethel, Graeme; Robertson, Alan J; Perkins, Andrew C; Bruce, Stephen J; Lee, Clarence C; Ranade, Swati S; Peckham, Heather E; Manning, Jonathan M; McKernan, Kevin J; Grimmond, Sean M.

Nat Methods ; 5(7): 613-9, 2008 Jul.

Article in English | MEDLINE | ID: mdl-18516046

5.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Jaillon, Olivier; Aury, Jean-Marc; Brunet, Frédéric; Petit, Jean-Louis; Stange-Thomann, Nicole; Mauceli, Evan; Bouneau, Laurence; Fischer, Cécile; Ozouf-Costaz, Catherine; Bernot, Alain; Nicaud, Sophie; Jaffe, David; Fisher, Sheila; Lutfalla, Georges; Dossat, Carole; Segurens, Béatrice; Dasilva, Corinne; Salanoubat, Marcel; Levy, Michael; Boudet, Nathalie; Castellano, Sergi; Anthouard, Véronique; Jubin, Claire; Castelli, Vanina; Katinka, Michael; Vacherie, Benoît; Biémont, Christian; Skalli, Zineb; Cattolico, Laurence; Poulain, Julie; De Berardinis, Véronique; Cruaud, Corinne; Duprat, Simone; Brottier, Philippe; Coutanceau, Jean-Pierre; Gouzy, Jérôme; Parra, Genis; Lardier, Guillaume; Chapple, Charles; McKernan, Kevin J; McEwan, Paul; Bosak, Stephanie; Kellis, Manolis; Volff, Jean-Nicolas; Guigó, Roderic; Zody, Michael C; Mesirov, Jill; Lindblad-Toh, Kerstin; Birren, Bruce; Nusbaum, Chad.

Nature ; 431(7011): 946-57, 2004 Oct 21.

Article in English | MEDLINE | ID: mdl-15496914

6.

Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica.

Malek, Joel A; Wierzbowski, Jamey M; Tao, Wei; Bosak, Stephanie A; Saranga, David J; Doucette-Stamm, Lynn; Smith, Douglas R; McEwan, Paul J; McKernan, Kevin J.

Nucleic Acids Res ; 32(3): 1059-64, 2004.

Article in English | MEDLINE | ID: mdl-14872061

7.

Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic "functional" symptomatology including pain, fatigue and gastrointestinal dysmotility.

Boles, Richard G; Hornung, Holly A; Moody, Alastair E; Ortiz, Thomas B; Wong, Stacey A; Eggington, Julie M; Stanley, Christine M; Gao, Mu; Zhou, Hongyi; McLaughlin, Stephen; Zare, Amir S; Sheldon, Katherine M; Skolnick, Jeffrey; McKernan, Kevin J.

Mitochondrion ; 23: 64-70, 2015 Jul.

Article in English | MEDLINE | ID: mdl-26022780

8.

Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment.

McKernan, Kevin J; Spangler, Jessica; Zhang, Lei; Tadigotla, Vasisht; McLaughlin, Stephen; Warner, Jason; Zare, Amir; Boles, Richard G.

PLoS One ; 9(5): e96492, 2014.

Article in English | MEDLINE | ID: mdl-24788618

9.

Whole methylome analysis by ultra-deep sequencing using two-base encoding.

Bormann Chung, Christina A; Boyd, Victoria L; McKernan, Kevin J; Fu, Yutao; Monighetti, Cinna; Peckham, Heather E; Barker, Melissa.

PLoS One ; 5(2): e9320, 2010 Feb 22.

Article in English | MEDLINE | ID: mdl-20179767

10.

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.

Motallebipour, Mehdi; Ameur, Adam; Reddy Bysani, Madhu Sudhan; Patra, Kalicharan; Wallerman, Ola; Mangion, Jonathan; Barker, Melissa A; McKernan, Kevin J; Komorowski, Jan; Wadelius, Claes.

Genome Biol ; 10(11): R129, 2009.

Article in English | MEDLINE | ID: mdl-19919681

11.

Polymorphism discovery in high-throughput resequenced microarray-enriched human genomic loci.

Antipova, Alena A; Sokolsky, Tanya D; Clouser, Christopher R; Dimalanta, Eileen T; Hendrickson, Cynthia L; Kosnopo, Cisilya; Lee, Clarence C; Ranade, Swati S; Zhang, Lei; Blanchard, Alan P; McKernan, Kevin J.

J Biomol Tech ; 20(5): 253-7, 2009 Dec.

Article in English | MEDLINE | ID: mdl-19949697

12.

DREAMing of a patent-free human genome for clinical sequencing.

McKernan, Kevin J; Spangler, Jessica; Helbert, Yvonne; Zhang, Lei; Tadigotla, Vasisht.

Nat Biotechnol ; 31(10): 884-7, 2013 Oct.

Article in English | MEDLINE | ID: mdl-24104751

13.

Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Smith, Douglas R; Quinlan, Aaron R; Peckham, Heather E; Makowsky, Kathryn; Tao, Wei; Woolf, Betty; Shen, Lei; Donahue, William F; Tusneem, Nadeem; Stromberg, Michael P; Stewart, Donald A; Zhang, Lu; Ranade, Swati S; Warner, Jason B; Lee, Clarence C; Coleman, Brittney E; Zhang, Zheng; McLaughlin, Stephen F; Malek, Joel A; Sorenson, Jon M; Blanchard, Alan P; Chapman, Jarrod; Hillman, David; Chen, Feng; Rokhsar, Daniel S; McKernan, Kevin J; Jeffries, Thomas W; Marth, Gabor T; Richardson, Paul M.

Genome Res ; 18(10): 1638-42, 2008 Oct.

Article in English | MEDLINE | ID: mdl-18775913

14.

Sample preparation.

McKernan, Kevin J.

Curr Protoc Hum Genet ; Chapter 16: Unit 16.1, 2004 May.

Article in English | MEDLINE | ID: mdl-18428359

15.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Strausberg, Robert L; Feingold, Elise A; Grouse, Lynette H; Derge, Jeffery G; Klausner, Richard D; Collins, Francis S; Wagner, Lukas; Shenmen, Carolyn M; Schuler, Gregory D; Altschul, Stephen F; Zeeberg, Barry; Buetow, Kenneth H; Schaefer, Carl F; Bhat, Narayan K; Hopkins, Ralph F; Jordan, Heather; Moore, Troy; Max, Steve I; Wang, Jun; Hsieh, Florence; Diatchenko, Luda; Marusina, Kate; Farmer, Andrew A; Rubin, Gerald M; Hong, Ling; Stapleton, Mark; Soares, M Bento; Bonaldo, Maria F; Casavant, Tom L; Scheetz, Todd E; Brownstein, Michael J; Usdin, Ted B; Toshiyuki, Shiraki; Carninci, Piero; Prange, Christa; Raha, Sam S; Loquellano, Naomi A; Peters, Garrick J; Abramson, Rick D; Mullahy, Sara J; Bosak, Stephanie A; McEwan, Paul J; McKernan, Kevin J; Malek, Joel A; Gunaratne, Preethi H; Richards, Stephen; Worley, Kim C; Hale, Sarah; Garcia, Angela M; Gay, Laura J.

Proc Natl Acad Sci U S A ; 99(26): 16899-903, 2002 Dec 24.

Article in English | MEDLINE | ID: mdl-12477932

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