Assembling genomes using short-read sequencing technology

Por Jackman, Shaun D, Birol, İnanç
Publicado em 2010

UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation

Por Jackman, Shaun D., Bohlmann, Joerg, Birol, İnanç
Publicado no PLoS One (2015)

Sealer: a scalable gap-closing application for finishing draft genomes

Por Paulino, Daniel, Warren, René L., Vandervalk, Benjamin P., Raymond, Anthony, Jackman, Shaun D., Birol, Inanç
Publicado no BMC Bioinformatics (2015)

ABySS: A parallel assembler for short read sequence data

Por Simpson, Jared T., Wong, Kim, Jackman, Shaun D., Schein, Jacqueline E., Jones, Steven J.M., Birol, İnanç
Publicado em 2009

DIDA: Distributed Indexing Dispatched Alignment

Por Mohamadi, Hamid, Vandervalk, Benjamin P, Raymond, Anthony, Jackman, Shaun D, Chu, Justin, Breshears, Clay P, Birol, Inanc
Publicado no PLoS One (2015)

Spaced Seed Data Structures for De Novo Assembly

Por Birol, Inanç, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D., Raghavan, Karthika, Vandervalk, Benjamin P., Raymond, Anthony, Warren, René L.
Publicado no Int J Genomics (2015)

Konnector v2.0: pseudo-long reads from paired-end sequencing data

Por Vandervalk, Benjamin P, Yang, Chen, Xue, Zhuyi, Raghavan, Karthika, Chu, Justin, Mohamadi, Hamid, Jackman, Shaun D, Chiu, Readman, Warren, René L, Birol, Inanç
Publicado no BMC Med Genomics (2015)

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

Por Chu, Justin, Sadeghi, Sara, Raymond, Anthony, Jackman, Shaun D., Nip, Ka Ming, Mar, Richard, Mohamadi, Hamid, Butterfield, Yaron S., Robertson, A. Gordon, Birol, Inanç
Publicado no Bioinformatics (2014)

KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES()

Por Birol, Inanç, Raymond, Anthony, Chiu, Readman, Nip, Ka Ming, Jackman, Shaun D, Kreitzman, Maayan, Docking, T Roderick, Ennis, Catherine A, Robertson, A Gordon, Karsan, Aly
Publicado no Pac Symp Biocomput (2015)

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data

Por 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
Publicado no PLoS One (2016)

Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees

Por Chan, Queenie WT, Cornman, R Scott, Birol, Inanc, Liao, Nancy Y, Chan, Simon K, Docking, T Roderick, Jackman, Shaun D, Taylor, Greg A, Jones, Steven JM, de Graaf, Dirk C, Evans, Jay D, Foster, Leonard J
Publicado em 2011

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

Por Jackman, Shaun D., Warren, René L., Gibb, Ewan A., Vandervalk, Benjamin P., Mohamadi, Hamid, Chu, Justin, Raymond, Anthony, Pleasance, Stephen, Coope, Robin, Wildung, Mark R., Ritland, Carol E., Bousquet, Jean, Jones, Steven J. M., Bohlmann, Joerg, Birol, Inanç
Publicado no Genome Biol Evol (2015)

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

Por 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
Publicado em 2013

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

Por 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.
Publicado em 2013

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

Por Swanson, Lucas, Robertson, Gordon, Mungall, Karen L, Butterfield, Yaron S, Chiu, Readman, Corbett, Richard D, Docking, T Roderick, Hogge, Donna, Jackman, Shaun D, Moore, Richard A, Mungall, Andrew J, Nip, Ka Ming, Parker, Jeremy DK, Qian, Jenny Qing, Raymond, Anthony, Sung, Sandy, Tam, Angela, Thiessen, Nina, Varhol, Richard, Wang, Sherry, Yorukoglu, Deniz, Zhao, YongJun, Hoodless, Pamela A, Sahinalp, S Cenk, Karsan, Aly, Birol, Inanc
Publicado em 2013

The genetic landscape of high-risk neuroblastoma

Por Pugh, Trevor J., Morozova, Olena, Attiyeh, Edward F., Asgharzadeh, Shahab, Wei, Jun S., Auclair, Daniel, Carter, Scott L., Cibulskis, Kristian, Hanna, Megan, Kiezun, Adam, Kim, Jaegil, Lawrence, Michael S., Lichenstein, Lee, McKenna, Aaron, Pedamallu, Chandra Sekhar, Ramos, Alex H., Shefler, Erica, Sivachenko, Andrey, Sougnez, Carrie, Stewart, Chip, Ally, Adrian, Birol, Inanc, Chiu, Readman, Corbett, Richard D., Hirst, Martin, Jackman, Shaun D., Kamoh, Baljit, Khodabakshi, Alireza Hadj, Krzywinski, Martin, Lo, Allan, Moore, Richard A., Mungall, Karen L., Qian, Jenny, Tam, Angela, Thiessen, Nina, Zhao, Yongjun, Cole, Kristina A., Diamond, Maura, Diskin, Sharon J., Mosse, Yael P., Wood, Andrew C., Ji, Lingyun, Sposto, Richard, Badgett, Thomas, London, Wendy B., Moyer, Yvonne, Gastier-Foster, Julie M., Smith, Malcolm A., Auvil, Jaime M. Guidry, Gerhard, Daniela S., Hogarty, Michael D., Jones, Steven J. M., Lander, Eric S., Gabriel, Stacey B., Getz, Gad, Seeger, Robert C., Khan, Javed, Marra, Marco A., Meyerson, Matthew, Maris, John M.
Publicado em 2013

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Por Earl, Dent, Bradnam, Keith, St. John, John, Darling, Aaron, Lin, Dawei, Fass, Joseph, Yu, Hung On Ken, Buffalo, Vince, Zerbino, Daniel R., Diekhans, Mark, Nguyen, Ngan, Ariyaratne, Pramila Nuwantha, Sung, Wing-Kin, Ning, Zemin, Haimel, Matthias, Simpson, Jared T., Fonseca, Nuno A., Birol, İnanç, Docking, T. Roderick, Ho, Isaac Y., Rokhsar, Daniel S., Chikhi, Rayan, Lavenier, Dominique, Chapuis, Guillaume, Naquin, Delphine, Maillet, Nicolas, Schatz, Michael C., Kelley, David R., Phillippy, Adam M., Koren, Sergey, Yang, Shiaw-Pyng, Wu, Wei, Chou, Wen-Chi, Srivastava, Anuj, Shaw, Timothy I., Ruby, J. Graham, Skewes-Cox, Peter, Betegon, Miguel, Dimon, Michelle T., Solovyev, Victor, Seledtsov, Igor, Kosarev, Petr, Vorobyev, Denis, Ramirez-Gonzalez, Ricardo, Leggett, Richard, MacLean, Dan, Xia, Fangfang, Luo, Ruibang, Li, Zhenyu, Xie, Yinlong, Liu, Binghang, Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J., Yin, Shuangye, Sharpe, Ted, Hall, Giles, Kersey, Paul J., Durbin, Richard, Jackman, Shaun D., Chapman, Jarrod A., Huang, Xiaoqiu, DeRisi, Joseph L., Caccamo, Mario, Li, Yingrui, Jaffe, David B., Green, Richard E., Haussler, David, Korf, Ian, Paten, Benedict
Publicado em 2011

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Por 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, Élénie, 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
Publicado em 2013

Subgroup specific structural variation across 1,000 medulloblastoma genomes

Por Northcott, Paul A, Shih, David JH, Peacock, John, Garzia, Livia, Morrissy, Sorana, Zichner, Thomas, Stütz, Adrian M, Korshunov, Andrey, Reimand, Juri, Schumacher, Steven E, Beroukhim, Rameen, Ellison, David W, Marshall, Christian R, Lionel, Anath C, Mack, Stephen, Dubuc, Adrian, Yao, Yuan, Ramaswamy, Vijay, Luu, Betty, Rolider, Adi, Cavalli, Florence, Wang, Xin, Remke, Marc, Wu, Xiaochong, Chiu, Readman YB, Chu, Andy, Chuah, Eric, Corbett, Richard D, Hoad, Gemma R, Jackman, Shaun D, Li, Yisu, Lo, Allan, Mungall, Karen L, Nip, Ka Ming, Qian, Jenny Q, Raymond, Anthony GJ, Thiessen, Nina, Varhol, Richard J, Birol, Inanc, Moore, Richard A, Mungall, Andrew J, Holt, Robert, Kawauchi, Daisuke, Roussel, Martine F, Kool, Marcel, Jones, David TW, Witt, Hendrick, Fernandez-L, Africa, Kenney, Anna M, Wechsler-Reya, Robert J, Dirks, Peter, Aviv, Tzvi, Grajkowska, Wieslawa A, Perek-Polnik, Marta, Haberler, Christine C, Delattre, Olivier, Reynaud, Stéphanie S, Doz, François F, Pernet-Fattet, Sarah S, Cho, Byung-Kyu, Kim, Seung-Ki, Wang, Kyu-Chang, Scheurlen, Wolfram, Eberhart, Charles G, Fèvre-Montange, Michelle, Jouvet, Anne, Pollack, Ian F, Fan, Xing, Muraszko, Karin M, Gillespie, G. Yancey, Di Rocco, Concezio, Massimi, Luca, Michiels, Erna MC, Kloosterhof, Nanne K, French, Pim J, Kros, Johan M, Olson, James M, Ellenbogen, Richard G, Zitterbart, Karel, Kren, Leos, Thompson, Reid C, Cooper, Michael K, Lach, Boleslaw, McLendon, Roger E, Bigner, Darell D, Fontebasso, Adam, Albrecht, Steffen, Jabado, Nada, Lindsey, Janet C, Bailey, Simon, Gupta, Nalin, Weiss, William A, Bognár, László, Klekner, Almos, Van Meter, Timothy E, Kumabe, Toshihiro, Tominaga, Teiji, Elbabaa, Samer K, Leonard, Jeffrey R, Rubin, Joshua B, Liau, Linda M, Van Meir, Erwin G, Fouladi, Maryam, Nakamura, Hideo, Cinalli, Giuseppe, Garami, Miklós, Hauser, Peter, Saad, Ali G, Iolascon, Achille, Jung, Shin, Carlotti, Carlos G, Vibhakar, Rajeev, Ra, Young Shin, Robinson, Shenandoah, Zollo, Massimo, Faria, Claudia C, Chan, Jennifer A, Levy, Michael L, Sorensen, Poul HB, Meyerson, Matthew, Pomeroy, Scott L, Cho, Yoon-Jae, Bader, Gary D, Tabori, Uri, Hawkins, Cynthia E, Bouffet, Eric, Scherer, Stephen W, Rutka, James T, Malkin, David, Clifford, Steven C, Jones, Steven JM, Korbel, Jan O, Pfister, Stefan M, Marra, Marco A, Taylor, Michael D
Publicado em 2012