The Human Microbiome Project: a community resource for the healthy human microbiome von Gevers, Dirk, Knight, Rob, Petrosino, Joseph F, Huang, Katherine, McGuire, Amy L, Birren, Bruce W, Nelson, Karen E, White, Owen, Methé, Barbara A, Huttenhower, Curtis

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How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? von Haas, Brian J, Chin, Melissa, Nusbaum, Chad, Birren, Bruce W, Livny, Jonathan

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Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters von Cimermancic, Peter, Medema, Marnix H., Claesen, Jan, Kurita, Kenji, Wieland Brown, Laura C., Mavrommatis, Konstantinos, Pati, Amrita, Godfrey, Paul A., Koehrsen, Michael, Clardy, Jon, Birren, Bruce W., Takano, Eriko, Sali, Andrej, Linington, Roger G., Fischbach, Michael A.

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Whole genome amplification and de novo assembly of single bacterial cells von Rodrigue, Sébastien, Malmstrom, Rex R, Berlin, Aaron M, Birren, Bruce W, Henn, Matthew R, Chisholm, Sallie W

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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons von Haas, Brian J, Gevers, Dirk, Earl, Ashlee M, Feldgarden, Mike, Ward, Doyle V, Giannoukos, Georgia, Ciulla, Dawn, Tabbaa, Diana, Highlander, Sarah K, Sodergren, Erica, Methé, Barbara, DeSantis, Todd Z, Petrosino, Joseph F, Knight, Rob, Birren, Bruce W

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Full-length transcriptome assembly from RNA-Seq data without a reference genome von Friedman, Nir, Regev, Aviv, Grabherr, Manfred G, Haas, Brian J, Yassour, Moran, Levin, Joshua Z, Thompson, Dawn A, Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, di Palma, Federica, Birren, Bruce W, Nusbaum, Chad, Lindblad-Toh, Kerstin

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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes von Giannoukos, Georgia, Ciulla, Dawn M, Huang, Katherine, Haas, Brian J, Izard, Jacques, Levin, Joshua Z, Livny, Jonathan, Earl, Ashlee M, Gevers, Dirk, Ward, Doyle V, Nusbaum, Chad, Birren, Bruce W, Gnirke, Andreas

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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae von Kellis, Manolis, Lander, Eric S, Birren, Bruce W

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Genomic analysis identifies association of Fusobacterium with colorectal carcinoma von Kostic, Aleksandar D, Gevers, Dirk, Pedamallu, Chandra Sekhar, Michaud, Monia, Duke, Fujiko, Earl, Ashlee M, Ojesina, Akinyemi I, Jung, Joonil, Bass, Adam J, Tabernero, Josep, Baselga, José, Liu, Chen, Shivdasani, Ramesh A, Ogino, Shuji, Birren, Bruce W, Huttenhower, Curtis, Garrett, Wendy S, Meyerson, Matthew

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Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance von Cerqueira, Gustavo C, Cheeseman, Ian H, Schaffner, Steve F, Nair, Shalini, McDew-White, Marina, Phyo, Aung Pyae, Ashley, Elizabeth A, Melnikov, Alexandre, Rogov, Peter, Birren, Bruce W, Nosten, François, Anderson, Timothy J C, Neafsey, Daniel E

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Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes von Yassour, Moran, Lim, Mi Young, Yun, Hyun Sun, Tickle, Timothy L, Sung, Joohon, Song, Yun-Mi, Lee, Kayoung, Franzosa, Eric A, Morgan, Xochitl C, Gevers, Dirk, Lander, Eric S, Xavier, Ramnik J, Birren, Bruce W, Ko, GwangPyo, Huttenhower, Curtis

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Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development von Holder, Jason W, Ulrich, Jil C, DeBono, Anthony C, Godfrey, Paul A, Desjardins, Christopher A, Zucker, Jeremy, Zeng, Qiandong, Leach, Alex L B, Ghiviriga, Ion, Dancel, Christine, Abeel, Thomas, Gevers, Dirk, Kodira, Chinnappa D, Desany, Brian, Affourtit, Jason P, Birren, Bruce W, Sinskey, Anthony J

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The "most wanted" taxa from the human microbiome for whole genome sequencing von Fodor, Anthony A, DeSantis, Todd Z, Wylie, Kristine M, Badger, Jonathan H, Ye, Yuzhen, Hepburn, Theresa, Hu, Ping, Sodergren, Erica, Liolios, Konstantinos, Huot-Creasy, Heather, Birren, Bruce W, Earl, Ashlee M

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Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia von Vu, Thi Ty Hang, Holmes, Edward C, Duong, Veasna, Nguyen, Thien Quy, Tran, Tinh Hien, Quail, Michael, Churcher, Carol, Parkhill, Julian, Cardosa, Jane, Farrar, Jeremy, Wills, Bridget, Lennon, Niall J, Birren, Bruce W, Buchy, Philippe, Henn, Matthew R, Simmons, Cameron P

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The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum von Neafsey, Daniel E, Galinsky, Kevin, Jiang, Rays H Y, Young, Lauren, Sykes, Sean M, Saif, Sakina, Gujja, Sharvari, Goldberg, Jonathan M, Young, Sarah, Zeng, Qiandong, Chapman, Sinéad B, Dash, Aditya P, Anvikar, Anupkumar R, Sutton, Patrick L, Birren, Bruce W, Escalante, Ananias A, Barnwell, John W, Carlton, Jane M

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Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data von Macalalad, Alexander R, Zody, Michael C, Charlebois, Patrick, Lennon, Niall J, Newman, Ruchi M, Malboeuf, Christine M, Ryan, Elizabeth M, Boutwell, Christian L, Power, Karen A, Brackney, Doug E, Pesko, Kendra N, Levin, Joshua Z, Ebel, Gregory D, Allen, Todd M, Birren, Bruce W, Henn, Matthew R

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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment von Orsi, Renato H, Borowsky, Mark L, Lauer, Peter, Young, Sarah K, Nusbaum, Chad, Galagan, James E, Birren, Bruce W, Ivy, Reid A, Sun, Qi, Graves, Lewis M, Swaminathan, Bala, Wiedmann, Martin

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Evolutionary dynamics of the accessory genome of Listeria monocytogenes von den Bakker, Henk C, Desjardins, Christopher A, Griggs, Allison D, Peters, Joseph E, Zeng, Qiandong, Young, Sarah K, Kodira, Chinnappa D, Yandava, Chandri, Hepburn, Theresa A, Haas, Brian J, Birren, Bruce W, Wiedmann, Martin

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Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance von Desjardins, Christopher A, Cohen, Keira A, Munsamy, Vanisha, Abeel, Thomas, Maharaj, Kashmeel, Walker, Bruce J, Shea, Terrance P, Almeida, Deepak V, Manson, Abigail L, Salazar, Alex, Padayatchi, Nesri, O'Donnell, Max R, Mlisana, Koleka P, Wortman, Jennifer, Birren, Bruce W, Grosset, Jacques, Earl, Ashlee M, Pym, Alexander S

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Genomics of Loa loa, a Wolbachia-free filarial parasite of humans von Desjardins, Christopher A, Cerqueira, Gustavo C, Goldberg, Jonathan M, Hotopp, Julie C Dunning, Haas, Brian J, Zucker, Jeremy, Ribeiro, José M C, Saif, Sakina, Levin, Joshua Z, Fan, Lin, Zeng, Qiandong, Russ, Carsten, Wortman, Jennifer R, Fink, Doran L, Birren, Bruce W, Nutman, Thomas B

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