Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins von Turnbaugh, Peter J, Quince, Christopher, Faith, Jeremiah J, McHardy, Alice C, Yatsunenko, Tanya, Niazi, Faheem, Affourtit, Jason, Egholm, Michael, Henrissat, Bernard, Knight, Rob, Gordon, Jeffrey I

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A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing von Green, Richard E., Malaspinas, Anna-Sapfo, Krause, Johannes, Briggs, Adrian W., Johnson, Philip L.F., Uhler, Caroline, Meyer, Matthias, Good, Jeffrey M., Maricic, Tomislav, Stenzel, Udo, Prüfer, Kay, Siebauer, Michael, Burbano, Hernán A., Ronan, Michael, Rothberg, Jonathan M., Egholm, Michael, Rudan, Pavao, Brajković, Dejana, Kućan, Željko, Gušić, Ivan, Wikström, Mårten, Laakkonen, Liisa, Kelso, Janet, Slatkin, Montgomery, Pääbo, Svante

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Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder von Cox-Foster, Diana L, Conlan, Sean, Holmes, Edward C, Palacios, Gustavo, Evans, Jay D, Moran, Nancy A, Quan, Phenix-Lan, Briese, Thomas, Hornig, Mady, Geiser, David M, Martinson, Vince, vanEngelsdorp, Dennis, Kalkstein, Abby L, Drysdale, Andrew, Hui, Jeffrey, Zhai, Junhui, Cui, Liwang, Hutchison, Stephen K, Simons, Jan Fredrik, Egholm, Michael, Pettis, Jeffery S, Lipkin, W. Ian

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Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes von Simen, Birgitte B., Simons, Jan Fredrik, Hullsiek, Katherine Huppler, Novak, Richard M., MacArthur, Rodger D., Baxter, John D., Huang, Chunli, Lubeski, Christine, Turenchalk, Gregory S., Braverman, Michael S., Desany, Brian, Rothberg, Jonathan M., Egholm, Michael

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Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae von Borneman, Anthony R, Desany, Brian A, Riches, David, Affourtit, Jason P, Forgan, Angus H, Pretorius, Isak S, Egholm, Michael, Chambers, Paul J

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High-resolution antibody dynamics of vaccine-induced immune responses von Laserson, Uri, Vigneault, Francois, Gadala-Maria, Daniel, Yaari, Gur, Uduman, Mohamed, Heiden, Jason A. Vander, Kelton, William, Jung, Sang Taek, Liu, Yi, Laserson, Jonathan, Chari, Raj, Lee, Je-Hyuk, Bachelet, Ido, Hickey, Brendan, Lieberman-Aiden, Erez, Hanczaruk, Bozena, Simen, Birgitte B., Egholm, Michael, Koller, Daphne, Georgiou, George, Kleinstein, Steven H., Church, George M.

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Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa von Briese, Thomas, Paweska, Janusz T, McMullan, Laura K, Hutchison, Stephen K, Street, Craig, Palacios, Gustavo, Khristova, Marina L, Weyer, Jacqueline, Swanepoel, Robert, Egholm, Michael, Nichol, Stuart T, Lipkin, W Ian

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Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome von Korbel, Jan O, Urban, Alexander Eckehart, Affourtit, Jason P, Godwin, Brian, Grubert, Fabian, Simons, Jan Fredrik, Kim, Philip M, Palejev, Dean, Carriero, Nicholas J, Du, Lei, Taillon, Bruce E, Chen, Zhoutao, Tanzer, Andrea, Saunders, A.C. Eugenia, Chi, Jianxiang, Yang, Fengtang, Carter, Nigel P, Hurles, Matthew E, Weissman, Sherman M, Harkins, Timothy T, Gerstein, Mark B, Egholm, Michael, Snyder, Michael

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Analysis of one million base pairs of Neanderthal DNA von Ronan, Michael T, Egholm, Michael, Paunovic, Maja, Pääbo, Svante, Green, Richard E, Ptak, Susan E, Rothberg, Jonathan M, Briggs, Adrian W, Simons, Jan F, Krause, Johannes, Du, Lei

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The complete genome of an individual by massively parallel DNA sequencing von Lupski, James R, Rothberg, Jonathan M, Shen, Yufeng, Chen, Yi-Ju, Turcotte, Cynthia L, Tartaro, Karrie, Irzyk, Gerard P, Wheeler, David A, Gomes, Xavier, Yuan, Ye, Qin, Xiang, Chinault, Craig, Weinstock, George M, Song, Xing-zhi, Chen, Lei, Srinivasan, Maithreyan, He, Wen, Liu, Yue, Muzny, Donna M, Gibbs, Richard A, Niazi, Faheem, Margulies, Marcel, Roth, G. Thomas, Makhijani, Vinod, Nazareth, Lynne, McGuire, Amy, Egholm, Michael

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Astrovirus encephalitis in boy with X-linked agammaglobulinemia von Quan, Phenix Lan, Wagner, Thor A, Briese, Thomas, Torgerson, Troy R, Hornig, Mady, Tashmukhamedova, Alla, Firth, Cadhla, Palacios, Gustavo, Baisre-De-Leon, Ada, Paddock, Christopher D, Hutchison, Stephen K, Egholm, Michael, Zaki, Sherif R, Goldman, James E, Ochs, Hans D, Lipkin, W Ian

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Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing von Pinard, Robert, de Winter, Alex, Sarkis, Gary J, Gerstein, Mark B, Tartaro, Karrie R, Plant, Ramona N, Egholm, Michael, Rothberg, Jonathan M, Leamon, John H

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Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing von Wu, Jia Qian, Habegger, Lukas, Noisa, Parinya, Szekely, Anna, Qiu, Caihong, Hutchison, Stephen, Raha, Debasish, Egholm, Michael, Lin, Haifan, Weissman, Sherman, Cui, Wei, Gerstein, Mark, Snyder, Michael

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Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus von Palacios, Gustavo, Lovoll, Marie, Tengs, Torstein, Hornig, Mady, Hutchison, Stephen, Hui, Jeffrey, Kongtorp, Ruth-Torill, Savji, Nazir, Bussetti, Ana V, Solovyov, Alexander, Kristoffersen, Anja B, Celone, Christopher, Street, Craig, Trifonov, Vladimir, Hirschberg, David L, Rabadan, Raul, Egholm, Michael, Rimstad, Espen, Lipkin, W Ian

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Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements von Boyd, Scott D, Gaëta, Bruno A, Jackson, Katherine J, Fire, Andrew Z, Marshall, Eleanor L, Merker, Jason D, Maniar, Jay M, Zhang, Lyndon N, Sahaf, Bita, Jones, Carol D, Simen, Birgitte B, Hanczaruk, Bozena, Nguyen, Khoa D, Nadeau, Kari C, Egholm, Michael, Miklos, David B, Zehnder, James L, Collins, Andrew M

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Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)–Treated Patients and NRTI-Naive Patients von Margeridon-Thermet, Severine, Shulman, Nancy S., Ahmed, Aijaz, Shahriar, Rajin, Liu, Tommy, Wang, Chunlin, Holmes, Susan P., Babrzadeh, Farbod, Gharizadeh, Baback, Hanczaruk, Bozena, Simen, Birgitte B., Egholm, Michael, Shafer, Robert W.

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Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees von Cornman, R. Scott, Chen, Yan Ping, Schatz, Michael C, Street, Craig, Zhao, Yan, Desany, Brian, Egholm, Michael, Hutchison, Stephen, Pettis, Jeffery S, Lipkin, W. Ian, Evans, Jay D

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Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study von Lataillade, Max, Chiarella, Jennifer, Yang, Rong, Schnittman, Steven, Wirtz, Victoria, Uy, Jonathan, Seekins, Daniel, Krystal, Mark, Mancini, Marco, McGrath, Donnie, Simen, Birgitte, Egholm, Michael, Kozal, Michael

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Human metapneumovirus infection in wild mountain gorillas, Rwanda von Palacios, Gustavo, Lowenstine, Linda J, Cranfield, Michael R, Gilardi, Kirsten V K, Spelman, Lucy, Lukasik-Braum, Magda, Kinani, Jean Felix, Mudakikwa, Antoine, Nyirakaragire, Elisabeth, Bussetti, Ana Valeria, Savji, Nazir, Hutchison, Stephen, Egholm, Michael, Lipkin, W Ian

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Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use von Le, Thuy, Chiarella, Jennifer, Simen, Birgitte B, Hanczaruk, Bozena, Egholm, Michael, Landry, Marie L, Dieckhaus, Kevin, Rosen, Marc I, Kozal, Michael J

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