Pacific biosciences sequencing technology for genotyping and variation discovery in human data by Carneiro Mauricio O, Russ Carsten, Ross Michael G, Gabriel Stacey B, Nusbaum Chad, DePristo Mark A

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Comprehensive comparative analysis of strand-specific RNA sequencing methods by Regev, Aviv, Levin, Joshua Z., Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas

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Closing gaps in the human genome using sequencing by synthesis by Arachchi, Harindra M., Green, Lisa M., Zody, Michael C., Lennon, Niall, Gnerre, Sante, Berlin, Aaron M., Nusbaum, Chad, Garber, Manuel

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Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species by Yassour, Moran, Pfiffner, Jenna, Levin, Joshua Z., Adiconis, Xian, Gnirke, Andreas, Nusbaum, Chad, Thompson, Dawn-Anne, Friedman, Nir, Regev, Aviv, Yassour, Moran

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Development and evaluation of RNA-seq methods by Levin, Joshua Z., Adiconis, Xian, Yassour, Moran, Thompson, Dawn, Guttman, Mitchell, Berger, Michael F., Fan, Lin, Friedman, Nir, Nusbaum, Chad, Gnirke, Andreas, Regev, Aviv

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Model-based Analysis of ChIP-Seq (MACS) by Zhang, Yong, Liu, Tao, Meyer, Clifford A., Eeckhoute, Jerome, Johnson, David S., Nusbaum, Chad, Myers, Richard M., Brown, Myles, Li, Wei, Liu, Xiaole S., Bernstein, Bradley E.

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells by Rabani, Michal, Levin, Joshua Z., Fan, Lin, Adiconis, Xian, Raychowdhury, Raktima, Garber, Manuel, Gnirke, Andreas, Nusbaum, Chad, Hacohen, Nir, Friedman, Nir, Amit, Ido, Regev, Aviv

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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs by Guttman, Mitchell, Garber, Manuel, Levin, Joshua Z., Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J., Gnirke, Andreas, Nusbaum, Chad, Rinn, John L., Regev, Aviv, Lander, Eric Steven

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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment by 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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Comprehensive variation discovery in single human genomes by Weisenfeld, Neil I, Yin, Shuangye, Sharpe, Ted, Lau, Bayo, Hegarty, Ryan, Holmes, Laurie, Sogoloff, Brian, Tabbaa, Diana, Williams, Louise, Russ, Carsten, Nusbaum, Chad, MacCallum, Iain, Jaffe, David B., Lander, Eric Steven

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Genome-wide identification and characterization of replication origins by deep sequencing by Xu, Jia, Yanagisawa, Yoshimi, Tsankov, Alexander M, Hart, Christopher, Aoki, Keita, Kommajosyula, Naveen, Steinmann, Kathleen E., Bochicchio, James, Russ, Carsten, Regev, Aviv, Rando, Oliver J, Nusbaum, Chad, Niki, Hironori, Milos, Patrice M., Weng, Zhiping, Rhind, Nicholas, Regev, Aviv

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Semiconductor-based DNA sequencing of histone modification states by 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

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Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes by Chisholm, Sallie (Penny), Sullivan, Matthew B., Birren, Bruce W., Nusbaum, Chad, Young, Sarah K., Giannoukos, Georgia, Saif, akina, Sparrow, Todd, Weiand, Michael, Zeng, Qiandong, Kodira, Chinnappa D., Yandava, Chandri, Kelly, Libusha, Berlin, Aaron M., Osburne, Marcia, Stange-Thomann, Nicole, Henn, Matthew R.

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Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany by Grad, Y. H., Lipsitch, M., Griggs, Allison, Haas, Brian J., Shea, T. P., McCowan, C., Montmayeur, A., FitzGerald, M., Wortman, J. R., Krogfelt, K. A., Bingen, E., Weill, F.-X., Tietze, E., Flieger, A., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., Hanage, W. P.

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High-quality draft assemblies of mammalian genomes from massively parallel sequence data by Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Felipe J., Burton, Joshua, Walker, Bruce J., Sharpe, Ted, Hall, Giles, Shea, Terrance P., Sykes, Sean, Berlin, Aaron M., Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Jaffe, David B., Lander, Eric Steven

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A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals by Garber, Manuel, Yosef, Nir, Goren, Alon, Raychowdhury, Raktima, Thielke, Anne, Guttman, Mitchell, Robinson, James, Minie, Brian, Chevrier, Nicolas, Itzhaki, Zohar, Blecher-Gonen, Ronnie, Bornstein, Chamutal, Amann-Zalcenstein, Daniela, Weiner, Assaf, Friedrich, Dennis C., Meldrim, James C., Ram, Oren, Cheng, Christine S., Gnirke, Andreas, Fisher, Sheila, Friedman, Nir, Wong, Bang, Bernstein, Bradley E., Nusbaum, Chad, Hacohen, Nir, Regev, Aviv, Amit, Ido

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Integrative analysis of the melanoma transcriptome by Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert, Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew L., Jaffe, David B., Gabriel, Stacey B., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A., Lander, Eric Steven

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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing by Kirby, Andrew, Gnirke, Andreas, Jaffe, David B., Baresova, 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, Hulkova, Helena, Sovova, 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 B., Hart, P. Suzanne, Regev, Aviv, Nusbaum, Chad, Kmoch, Stanislav, Bleyer, Anthony J., Daly, Mark J., Lander, Eric Steven

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