Browsing HMS Scholarly Articles by Author "Nusbaum, Chad"

Now showing items 1-11 of 11

    • Comprehensive variation discovery in single human genomes 

      Weisenfeld, Neil I.; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S.; MacCallum, Iain; Jaffe, David B. (2014)
      Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and ...

    • Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica 

      Jiang, Rays H. Y.; de Bruijn, Irene; Haas, Brian J.; Belmonte, Rodrigo; Löbach, Lars; Christie, James; van den Ackerveken, Guido; Bottin, Arnaud; Bulone, Vincent; Díaz-Moreno, Sara M.; Dumas, Bernard; Fan, Lin; Gaulin, Elodie; Govers, Francine; Grenville-Briggs, Laura J.; Horner, Neil R.; Levin, Joshua Z.; Mammella, Marco; Meijer, Harold J. G.; Morris, Paul; Nusbaum, Chad; Oome, Stan; Phillips, Andrew J.; van Rooyen, David; Rzeszutek, Elzbieta; Saraiva, Marcia; Secombes, Chris J.; Seidl, Michael F.; Snel, Berend; Stassen, Joost H. M.; Sykes, Sean; Tripathy, Sucheta; van den Berg, Herbert; Vega-Arreguin, Julio C.; Wawra, Stephan; Young, Sarah K.; Zeng, Qiandong; Dieguez-Uribeondo, Javier; Russ, Carsten; Tyler, Brett M.; van West, Pieter (Public Library of Science, 2013)
      Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ...

    • A Framework for Human Microbiome Research 

      Methé, Barbara A.; Nelson, Karen E.; Pop, Mihai; Creasy, Heather H.; Giglio, Michelle G.; Gevers, Dirk; Petrosino, Joseph F.; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Earl, Ashlee M.; Fulton, Robert S.; Hallsworth-Pepin, Kymberlie; Lobos, Elizabeth A.; Madupu, Ramana; Magrini, Vincent; Mitreva, Makedonka; Muzny, Donna M.; Sodergren, Erica J.; Versalovic, James; Wollam, Aye M.; Worley, Kim C.; Wortman, Jennifer R.; Zeng, Qiandong; Aagaard, Kjersti M.; Abolude, Olukemi O.; Allen-Vercoe, Emma; Alm, Eric J.; Alvarado, Lucia; Andersen, Gary L.; Appelbaum, Elizabeth; Arachchi, Harindra M.; Armitage, Gary; Arze, Cesar A.; Ayvaz, Tulin; Baker, Carl C.; Begg, Lisa; Belachew, Tsegahiwot; Bhonagiri, Veena; Bihan, Monika; Blaser, Martin J.; Bloom, Toby; Vivien Bonazzi, J.; Brooks, Paul; Buck, Gregory A.; Buhay, Christian J.; Busam, Dana A.; Campbell, Joseph L.; Canon, Shane R.; Cantarel, Brandi L.; Chain, Patrick S.; Chen, I-Min A.; Chen, Lei; Chhibba, Shaila; Ciulla, Dawn M.; Clemente, Jose C.; Clifton, Sandra W.; Conlan, Sean; Crabtree, Jonathan; Cutting, Mary A.; Davidovics, Noam J.; Davis, Catherine C.; DeSantis, Todd Z.; Deal, Carolyn; Delehaunty, Kimberley D.; Deych, Elena; Dooling, David J.; Dugan, Shannon P.; Farmer, Candace N.; Faust, Karoline; Feldgarden, Michael; Felix, Victor M.; Fisher, Sheila; Fodor, Anthony A.; Forney, Larry; Foster, Leslie; Di Francesco, Valentina; Friedman, Jonathan; Friedrich, Dennis C.; Fronick, Catrina C.; Fulton, Lucinda L.; Gao, Hongyu; Garcia, Nathalia; Giannoukos, Georgia; Giblin, Christina; Giovanni, Maria Y.; Goll, Johannes; Gonzalez, Antonio; Griggs, Allison; Gujja, Sharvari; Haas, Brian J.; Hamilton, Holli A.; Hepburn, Theresa A.; Herter, Brandi; Hoffmann, Diane E.; Holder, Michael E.; Howarth, Clinton; Huse, Susan M.; Jansson, Janet K.; Jiang, Huaiyang; Jordan, Catherine; Joshi, Vandita; Katancik, James A.; Keitel, Wendy A.; Kelley, Scott T.; Kells, Cristyn; Kinder-Haake, Susan; King, Nicholas B.; Knight, Rob; Kong, Heidi H.; Koren, Omry; Koren, Sergey; Kota, Karthik C.; Kovar, Christie L.; Kyrpides, Nikos C.; La Rosa, Patricio S.; Lewis, Cecil M.; Lewis, Lora; Ley, Ruth E.; Li, Kelvin; Liolios, Konstantinos; Lo, Chien-Chi; Lozupone, Catherine A.; Lunsford, R. Dwayne; Madden, Tessa; Mahurkar, Anup A.; Mannon, Peter J.; Mardis, Elaine R.; Markowitz, Victor M.; Mavrommatis, Konstantinos; McCorrison, Jamison M.; McEwen, Jean; McGuire, Amy L.; McInnes, Pamela; Mehta, Teena; Mihindukulasuriya, Kathie A.; Minx, Patrick J.; Newsham, Irene; Nusbaum, Chad; O’Laughlin, Michelle; Orvis, Joshua; Pagani, Ioanna; Palaniappan, Krishna; Patel, Shital M.; Peterson, Jane; Podar, Mircea; Pohl, Craig; Pollard, Katherine S.; Priest, Margaret E.; Proctor, Lita M.; Qin, Xiang; Raes, Jeroen; Ravel, Jacques; Reid, Jeffrey G.; Rho, Mina; Rhodes, Rosamond; Riehle, Kevin P.; Rivera, Maria C.; Rodriguez-Mueller, Beltran; Rogers, Yu-Hui; Ross, Matthew C.; Russ, Carsten; Sanka, Ravi K.; Pamela Sankar, J.; Sathirapongsasuti, Fah; Schloss, Jeffery A.; Schloss, Patrick D.; Scholz, Matthew; Schriml, Lynn; Schubert, Alyxandria M.; Segata, Nicola; Segre, Julia A.; Shannon, William D.; Sharp, Richard R.; Sharpton, Thomas J.; Shenoy, Narmada; Sheth, Nihar U.; Simone, Gina A.; Singh, Indresh; Sobel, Jack D.; Sommer, Daniel D.; Spicer, Paul; Sutton, Granger G.; Tabbaa, Diana G.; Thiagarajan, Mathangi; Tomlinson, Chad M.; Torralba, Manolito; Treangen, Todd J.; Truty, Rebecca M.; Vishnivetskaya, Tatiana A.; Walker, Jason; Wang, Zhengyuan; Ward, Doyle V.; Warren, Wesley; Watson, Mark A.; Wellington, Christopher; Wetterstrand, Kris A.; Wilczek-Boney, Katarzyna; Wu, Yuan Qing; Wylie, Kristine M.; Wylie, Todd; Yandava, Chandri; Ye, Yuzhen; Yooseph, Shibu; Youmans, Bonnie P.; Zhou, Yanjiao; Zhu, Yiming; Zoloth, Laurie; Birren, Bruce W.; Gibbs, Richard A.; Highlander, Sarah K.; Weinstock, George M.; White, Owen; Huttenhower, Curtis; FitzGerald, Michael G.; Martin, John C.; Young, Sarah K.; Anderson, Scott; Chu, Ken; Dewhirst, Floyd Everett; Ding, Yan; Dunne, Wm. Michael; Durkin, A. Scott; Edgar, Robert C.; Erlich, Rachel L.; Farrell, Ruth M.; Goldberg, Jonathan M.; Harris, Emily L.; Huang, Katherine H.; Izard, Jacques Georges; Knights, Dan; Lee, Sandra L.; Lemon, Katherine Paige; Lennon, Niall; Liu, Bo; Liu, Yue; McDonald, Daniel; Miller, Jason R.; Pearson, Matthew; Schmidt, Thomas M.; Smillie, Chris Scott; Sykes, Sean M.; Wang, Lu; White, James R.; Ye, Liang; Zhang, Lan; Zucker, Jeremy Daniel Hofeld; Wilson, Richard K. (Nature Publishing Group, 2012)
      A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established ...

    • Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts 

      Ma, Liang; Chen, Zehua; Huang, Da Wei; Kutty, Geetha; Ishihara, Mayumi; Wang, Honghui; Abouelleil, Amr; Bishop, Lisa; Davey, Emma; Deng, Rebecca; Deng, Xilong; Fan, Lin; Fantoni, Giovanna; Fitzgerald, Michael; Gogineni, Emile; Goldberg, Jonathan M.; Handley, Grace; Hu, Xiaojun; Huber, Charles; Jiao, Xiaoli; Jones, Kristine; Levin, Joshua Z.; Liu, Yueqin; Macdonald, Pendexter; Melnikov, Alexandre; Raley, Castle; Sassi, Monica; Sherman, Brad T.; Song, Xiaohong; Sykes, Sean; Tran, Bao; Walsh, Laura; Xia, Yun; Yang, Jun; Young, Sarah; Zeng, Qiandong; Zheng, Xin; Stephens, Robert; Nusbaum, Chad; Birren, Bruce W.; Azadi, Parastoo; Lempicki, Richard A.; Cuomo, Christina A.; Kovacs, Joseph A. (Nature Publishing Group, 2016)
      Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal ...

    • How Deep Is Deep enough for RNA-Seq Profiling of Bacterial Transcriptomes? 

      Haas, Brian J; Chin, Melissa; Nusbaum, Chad; Birren, Bruce W; Livny, Jonathan (BioMed Central, 2012)
      Background: High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating ...

    • Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA 

      Miranda, Kevin C.; Bond, Daniel T.; Levin, Joshua Z.; Adiconis, Xian; Sivachenko, Andrey; Russ, Carsten; Brown, Dennis; Nusbaum, Chad; Russo, Leileata M. (Public Library of Science, 2014)
      Intact RNA from exosomes/microvesicles (collectively referred to as microvesicles) has sparked much interest as potential biomarkers for the non-invasive analysis of disease. Here we use the Illumina Genome Analyzer to ...

    • Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing 

      Kirby, Andrew; Gnirke, Andreas; Jaffe, David B.; Barešová, Veronika; Pochet, Nathalie; Blumenstiel, Brendan; Ye, Chun; Aird, Daniel; Stevens, Christine; Robinson, James T.; Cabili, Moran N.; Gat-Viks, Irit; Kelliher, Edward; Daza, Riza; DeFelice, Matthew; Hůlková, Helena; Sovová, Jana; Vylet’al, Petr; Antignac, Corinne; Guttman, Mitchell; Handsaker, Robert E.; Perrin, Danielle; Steelman, Scott; Sigurdsson, Snaevar; Scheinman, Steven J.; Sougnez, Carrie; Cibulskis, Kristian; Parkin, Melissa; Green, Todd; Rossin, Elizabeth; Zody, Michael C.; Xavier, Ramnik J.; Pollak, Martin R.; Alper, Seth L.; Lindblad-Toh, Kerstin; Gabriel, Stacey; Hart, P. Suzanne; Regev, Aviv; Nusbaum, Chad; Kmoch, Stanislav; Bleyer, Anthony J.; Lander, Eric S.; Daly, Mark J. (2014)
      While genetic lesions responsible for some Mendelian disorders can be rapidly discovered through massively parallel sequencing (MPS) of whole genomes or exomes, not all diseases readily yield to such efforts. We describe ...

    • Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo 

      Korber, Bette; Russ, Carsten; Lo, Chien-Chi; Leitner, Thomas; Gaschen, Brian; Theiler, James; Paredes, Roger; Su, Zhaohui; Gulick, Roy M.; Greaves, Wayne; Coakley, Eoin; Flexner, Charles; Nusbaum, Chad; Tsibris, Athe Michael Noel; Arnaout, Ramy; Hughes, Michael David; Kuritzkes, Daniel Robert (Public Library of Science, 2009)
      High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected ...

    • Semiconductor-based DNA sequencing of histone modification states 

      Cheng, Christine S.; Rai, Kunal; Garber, Manuel; Hollinger, Andrew; Robbins, Dana; Anderson, Scott; Macbeth, Alyssa; Tzou, Austin; Carneiro, Mauricio O.; Raychowdhury, Raktima; Russ, Carsten; Hacohen, Nir; Gershenwald, Jeffrey E.; Lennon, Niall; Nusbaum, Chad; Chin, Lynda; Regev, Aviv; Amit, Ido (2013)
      The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing ...

    • Short-Term Genome Evolution of Listeria Monocytogenes in a Non-Controlled Environment 

      Orsi, Renato H; Lauer, Peter; Nusbaum, Chad; Birren, Bruce W; Ivy, Reid A; Graves, Lewis M; Swaminathan, Bala; Wiedmann, Martin; Borowsky, Mark L; Young, Sarah K.; Galagan, James E; Sun, Qi (BioMed Central, 2008)
      Background: While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses ...

    • Targeted Next-Generation Sequencing of a Cancer Transcriptome Enhances Detection of Sequence Variants and Novel Fusion Transcripts 

      Levin, Joshua Z; Berger, Michael F; Adiconis, Xian; Rogov, Peter; Melnikov, Alexandre; Fennell, Timothy; Nusbaum, Chad; Garraway, Levi Alexander; Gnirke, Andreas (BioMed Central, 2009)
      Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide ...