ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter by Jackman, Shaun D, Vandervalk, Benjamin P, Mohamadi, Hamid, Chu, Justin, Yeo, Sarah, Hammond, S Austin, Jahesh, Golnaz, Khan, Hamza, Coombe, Lauren, Warren, Rene L, Birol, Inanc

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ABySS: a parallel assembler for short read sequence data by Simpson, Jared T, Wong, Kim, Jackman, Shaun D, Schein, Jacqueline E, Jones, Steven J M, Birol, Inanç

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Tigmint: correcting assembly errors using linked reads from large molecules by Jackman, Shaun D, Coombe, Lauren, Chu, Justin, Warren, Rene L, Vandervalk, Benjamin P, Yeo, Sarah, Xue, Zhuyi, Mohamadi, Hamid, Bohlmann, Joerg, Jones, Steven J M, Birol, Inanc

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ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers by Coombe, Lauren, Zhang, Jessica, Vandervalk, Benjamin P, Chu, Justin, Jackman, Shaun D, Birol, Inanc, Warren, René L

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Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data by Birol, Inanc, Raymond, Anthony, Jackman, Shaun D, Pleasance, Stephen, Coope, Robin, Taylor, Greg A, Yuen, Macaire Man Saint, Keeling, Christopher I, Brand, Dana, Vandervalk, Benjamin P, Kirk, Heather, Pandoh, Pawan, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Jaquish, Barry, Yanchuk, Alvin, Ritland, Carol, Boyle, Brian, Bousquet, Jean, Ritland, Kermit, Mackay, John, Bohlmann, Jörg, Jones, Steven J M

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Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure by Jackman, Shaun D, Coombe, Lauren, Warren, René L, Kirk, Heather, Trinh, Eva, MacLeod, Tina, Pleasance, Stephen, Pandoh, Pawan, Zhao, Yongjun, Coope, Robin J, Bousquet, Jean, Bohlmann, Joerg, Jones, Steven J M, Birol, Inanc

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Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism by Warren, René L., Keeling, Christopher I., Yuen, Macaire Man Saint, Raymond, Anthony, Taylor, Greg A., Vandervalk, Benjamin P., Mohamadi, Hamid, Paulino, Daniel, Chiu, Readman, Jackman, Shaun D., Robertson, Gordon, Yang, Chen, Boyle, Brian, Hoffmann, Margarete, Weigel, Detlef, Nelson, David R., Ritland, Carol, Isabel, Nathalie, Jaquish, Barry, Yanchuk, Alvin, Bousquet, Jean, Jones, Steven J. M., MacKay, John, Birol, Inanc, Bohlmann, Joerg

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BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters by Chu, Justin, Sadeghi, Sara, Raymond, Anthony, Jackman, Shaun D, Nip, Ka Ming, Mar, Richard, Mohamadi, Hamid, Butterfield, Yaron S, Robertson, A Gordon, Birol, Inanç

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Sealer: a scalable gap-closing application for finishing draft genomes by Paulino, Daniel, Warren, René L, Vandervalk, Benjamin P, Raymond, Anthony, Jackman, Shaun D, Birol, Inanç

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Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data by Coombe, Lauren, Warren, René L, Jackman, Shaun D, Yang, Chen, Vandervalk, Benjamin P, Moore, Richard A, Pleasance, Stephen, Coope, Robin J, Bohlmann, Joerg, Holt, Robert A, Jones, Steven J M, Birol, Inanc

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Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest by Keeling, Christopher I, Yuen, Macaire MS, Liao, Nancy Y, Roderick Docking, T, Chan, Simon K, Taylor, Greg A, Palmquist, Diana L, Jackman, Shaun D, Nguyen, Anh, Li, Maria, Henderson, Hannah, Janes, Jasmine K, Zhao, Yongjun, Pandoh, Pawan, Moore, Richard, Sperling, Felix AH, W Huber, Dezene P, Birol, Inanc, Jones, Steven JM, Bohlmann, Joerg

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Frequent mutation of histone―modifying genes in non―Hodgkin lymphoma by MORIN, Ryan D, MENDEZ-LAGO, Maria, JACKMAN, Shaun, KRZYWINSKI, Martin, SCOTT, David W, TRINH, Diane L, TAMURA-WELLS, Jessica, SA LI, FIRME, Marlo R, ROGIC, Sanja, GRIFFITH, Malachi, CHAN, Susanna, MUNGALL, Andrew J, YAKOVENKO, Oleksandr, MEYER, Irmtraud M, ZHAO, Eric Y, SMAILUS, Duane, MOKSA, Michelle, CHITTARANJAN, Suganthi, RIMSZA, Lisa, BROOKS-WILSON, Angela, SPINELLI, John J, BEN-NERIAH, Susana, GOYA, Rodrigo, MEISSNER, Barbara, WOOLCOCK, Bruce, BOYLE, Merrill, MCDONALD, Helen, TAM, Angela, YONGJUN ZHAO, DELANEY, Allen, ZENG, Thomas, TSE, Kane, BUTTERFIELD, Yaron, MUNGALL, Karen L, BIROL, Inanç, HOLT, Rob, SCHEIN, Jacqueline, HORSMAN, Douglas E, MOORE, Richard, JONES, Steven J. M, CONNORS, Joseph M, HIRST, Martin, GASCOYNE, Randy D, MARRA, Marco A, CORBETT, Richard D, JOHNSON, Nathalie A, SEVERSON, Tesa M, CHIU, Readman, FIELD, Matthew

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The western redcedar genome reveals low genetic diversity in a self-compatible conifer by Shalev, Tal J., Gamal El-Dien, Omnia, Yuen, Macaire M.S., Shengqiang, Shu, Jackman, Shaun D., Warren, René L., Coombe, Lauren, van der Merwe, Lise, Stewart, Ada, Boston, Lori B., Plott, Christopher, Jenkins, Jerry, He, Guifen, Yan, Juying, Yan, Mi, Guo, Jie, Breinholt, Jesse W., Neves, Leandro G., Grimwood, Jane, Rieseberg, Loren H., Schmutz, Jeremy, Birol, Inanc, Kirst, Matias, Yanchuk, Alvin D., Ritland, Carol, Russell, John H., Bohlmann, Joerg

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DIDA: Distributed Indexing Dispatched Alignment by Mohamadi, Hamid, Vandervalk, Benjamin P, Raymond, Anthony, Jackman, Shaun D, Chu, Justin, Breshears, Clay P, Birol, Inanc

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UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation by Jackman, Shaun D, Bohlmann, Joerg, Birol, İnanç

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De novo transcriptome assembly with ABySS by Birol, Inanç, Jackman, Shaun D., Nielsen, Cydney B., Qian, Jenny Q., Varhol, Richard, Stazyk, Greg, Morin, Ryan D., Zhao, Yongjun, Hirst, Martin, Schein, Jacqueline E., Horsman, Doug E., Connors, Joseph M., Gascoyne, Randy D., Marra, Marco A., Jones, Steven J. M.

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ORCA: a comprehensive bioinformatics container environment for education and research by Jackman, Shaun D, Mozgacheva, Tatyana, Chen, Susie, O’Huiginn, Brendan, Bailey, Lance, Birol, Inanc, Jones, Steven J M

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Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers by Yip, Stephen, Butterfield, Yaron S, Morozova, Olena, Chittaranjan, Suganthi, Blough, Michael D, An, Jianghong, Birol, Inanc, Chesnelong, Charles, Chiu, Readman, Chuah, Eric, Corbett, Richard, Docking, Rod, Firme, Marlo, Hirst, Martin, Jackman, Shaun, Karsan, Aly, Li, Haiyan, Louis, David N, Maslova, Alexandra, Moore, Richard, Moradian, Annie, Mungall, Karen L, Perizzolo, Marco, Qian, Jenny, Roldan, Gloria, Smith, Eric E, Tamura-Wells, Jessica, Thiessen, Nina, Varhol, Richard, Weiss, Samuel, Wu, Wei, Young, Sean, Zhao, Yongjun, Mungall, Andrew J, Jones, Steven JM, Morin, Gregg B, Chan, Jennifer A, Cairncross, J Gregory, Marra, Marco A

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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species by Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Elénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, Maccallum, Iain, Macmanes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J Graham, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, Korf, Ian F

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Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii by Lenassi, Metka, Gostinčar, Cene, Jackman, Shaun, Turk, Martina, Sadowski, Ivan, Nislow, Corey, Jones, Steven, Birol, Inanc, Cimerman, Nina Gunde, Plemenitaš, Ana

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