An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA von Geml, József, Timling, Ina, Robinson, Clare H., Lennon, Niall, Nusbaum, H. Chad, Brochmann, Christian, Noordeloos, Machiel E., Taylor, D. Lee

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

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SvABA: genome-wide detection of structural variants and indels by local assembly von Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen

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A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning von Taylor, D. Lee, Hollingsworth, Teresa N., Mcfarland, Jack W., Lennon, Niall J., Nusbaum, Chad, Ruess, Roger 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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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs von Guttman, Mitchell, Garber, Manuel, Regev, Aviv, Levin, Joshua Z, Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J, Gnirke, Andreas, Nusbaum, Chad, Rinn, John L, Lander, Eric S

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High-quality draft assemblies of mammalian genomes from massively parallel sequence data von Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Burton, Joshua N, 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, Lander, Eric S, Jaffe, David B

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Genome-scale DNA methylation maps of pluripotent and differentiated cells von Jaenisch, Rudolf, Lander, Eric S, Meissner, Alexander, Mikkelsen, Tarjei S, Gu, Hongcang, Wernig, Marius, Hanna, Jacob, Sivachenko, Andrey, Zhang, Xiaolan, Bernstein, Bradley E, Nusbaum, Chad, Jaffe, David B, Gnirke, Andreas

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Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains von Ku, Manching, Koche, Richard P, Rheinbay, Esther, Mendenhall, Eric M, Endoh, Mitsuhiro, Mikkelsen, Tarjei S, Presser, Aviva, Nusbaum, Chad, Xie, Xiaohui, Chi, Andrew S, Adli, Mazhar, Kasif, Simon, Ptaszek, Leon M, Cowan, Chad A, Lander, Eric S, Koseki, Haruhiko, Bernstein, Bradley E

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Mammalian microRNAs: experimental evaluation of novel and previously annotated genes von Chiang, H Rosaria, Schoenfeld, Lori W, Ruby, J Graham, Auyeung, Vincent C, Spies, Noah, Baek, Daehyun, Johnston, Wendy K, Russ, Carsten, Luo, Shujun, Babiarz, Joshua E, Blelloch, Robert, Schroth, Gary P, Nusbaum, Chad, Bartel, David P

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ALLPATHS: de novo assembly of whole-genome shotgun microreads von Butler, Jonathan, MacCallum, Iain, Kleber, Michael, Shlyakhter, Ilya A, Belmonte, Matthew K, Lander, Eric S, Nusbaum, Chad, Jaffe, David B

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

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Characterizing and measuring bias in sequence data von Ross, Michael G, Russ, Carsten, Costello, Maura, Hollinger, Andrew, Lennon, Niall J, Hegarty, Ryan, Nusbaum, Chad, Jaffe, David B

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

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Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage von Raffaele, Sylvain, Farrer, Rhys A, Cano, Liliana M, Studholme, David J, MacLean, Daniel, Thines, Marco, Jiang, Rays H.Y, Zody, Michael C, Kunjeti, Sridhara G, Donofrio, Nicole M, Meyers, Blake C, Nusbaum, Chad, Kamoun, Sophien

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells von Presser, Aviva, Kim, Tae-Kyung, Issac, Biju, O'Donovan, Aisling, Giannoukos, Georgia, Lander, Eric S, Jaffe, David B, Jaenisch, Rudolf, Xie, Xiaohui, Alvarez, Pablo, Russ, Carsten, Wernig, Marius, Lee, William, Meissner, Alexander, Mikkelsen, Tarjei S, Nusbaum, Chad, Mendenhall, Eric, Ku, Manching, Lieberman, Erez, Brockman, William, Bernstein, Bradley E, Koche, Richard P

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Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta von Fairclough, Stephen R, Chen, Zehua, Kramer, Eric, Zeng, Qiandong, Young, Sarah, Robertson, Hugh M, Begovic, Emina, Richter, Daniel J, Russ, Carsten, Westbrook, M Jody, Manning, Gerard, Lang, B Franz, Haas, Brian, Nusbaum, Chad, King, Nicole

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High-resolution description of antibody heavy-chain repertoires in humans von Arnaout, Ramy, Lee, William, Cahill, Patrick, Honan, Tracey, Sparrow, Todd, Weiand, Michael, Nusbaum, Chad, Rajewsky, Klaus, Koralov, Sergei B

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Finished bacterial genomes from shotgun sequence data von Ribeiro, Filipe J, Przybylski, Dariusz, Yin, Shuangye, Sharpe, Ted, Gnerre, Sante, Abouelleil, Amr, Berlin, Aaron M, Montmayeur, Anna, Shea, Terrance P, Walker, Bruce J, Young, Sarah K, Russ, Carsten, Nusbaum, Chad, MacCallum, Iain, Jaffe, David B

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