JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

gan Butterfield, Yaron S., Kreitzman, Maayan, Thiessen, Nina, Corbett, Richard D., Li, Yisu, Pang, Johnson, Ma, Yussanne P., Jones, Steven J. M., Birol, İnanç
Cyhoeddwyd 2014

Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA

gan Haile, Simon, Corbett, Richard D., Bilobram, Steve, Mungall, Karen, Grande, Bruno M., Kirk, Heather, Pandoh, Pawan, MacLeod, Tina, McDonald, Helen, Bala, Miruna, Coope, Robin J., Moore, Richard A., Mungall, Andrew J., Zhao, Yongjun, Morin, Ryan D., Jones, Steven J., Marra, Marco A.
Cyhoeddwyd yn PLoS One (2019)

Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing

gan Haile, Simon, Corbett, Richard D., MacLeod, Tina, Bilobram, Steve, Smailus, Duane, Tsao, Philip, Kirk, Heather, McDonald, Helen, Pandoh, Pawan, Bala, Miruna, Hirst, Martin, Miller, Diane, Moore, Richard A., Mungall, Andrew J., Schein, Jacquie, Coope, Robin J., Ma, Yussanne, Zhao, Yongjun, Holt, Rob A., Jones, Steven J., Marra, Marco A.
Cyhoeddwyd yn BMC Genomics (2017)

Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples

gan Haile, Simon, Corbett, Richard D, Bilobram, Steve, Bye, Morgan H, Kirk, Heather, Pandoh, Pawan, Trinh, Eva, MacLeod, Tina, McDonald, Helen, Bala, Miruna, Miller, Diane, Novik, Karen, Coope, Robin J, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Ma, Yussanne, Holt, Rob A, Jones, Steven J, Marra, Marco A
Cyhoeddwyd yn Nucleic Acids Res (2019)

Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis

gan Haile, Simon, Pandoh, Pawan, McDonald, Helen, Corbett, Richard D., Tsao, Philip, Kirk, Heather, MacLeod, Tina, Jones, Martin, Bilobram, Steve, Brooks, Denise, Smailus, Duane, Steidl, Christian, Scott, David W., Bala, Miruna, Hirst, Martin, Miller, Diane, Moore, Richard A., Mungall, Andrew J., Coope, Robin J., Ma, Yussanne, Zhao, Yongjun, Holt, Rob A., Jones, Steven J., Marra, Marco A.
Cyhoeddwyd yn PLoS One (2017)

A Distributed Whole Genome Sequencing Benchmark Study

gan Corbett, Richard D., Eveleigh, Robert, Whitney, Joe, Barai, Namrata, Bourgey, Mathieu, Chuah, Eric, Johnson, Joanne, Moore, Richard A., Moradin, Neda, Mungall, Karen L., Pereira, Sergio, Reuter, Miriam S., Thiruvahindrapuram, Bhooma, Wintle, Richard F., Ragoussis, Jiannis, Strug, Lisa J., Herbrick, Jo-Anne, Aziz, Naveed, Jones, Steven J. M., Lathrop, Mark, Scherer, Stephen W., Staffa, Alfredo, Mungall, Andrew J.
Cyhoeddwyd yn Front Genet (2020)

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells

gan Haile, Simon, Corbett, Richard D., LeBlanc, Veronique G., Wei, Lisa, Pleasance, Stephen, Bilobram, Steve, Nip, Ka Ming, Brown, Kirstin, Trinh, Eva, Smith, Jillian, Trinh, Diane L., Bala, Miruna, Chuah, Eric, Coope, Robin J. N., Moore, Richard A., Mungall, Andrew J., Mungall, Karen L., Zhao, Yongjun, Hirst, Martin, Aparicio, Samuel, Birol, Inanc, Jones, Steven J. M., Marra, Marco A.
Cyhoeddwyd yn Front Genet (2021)

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

gan 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
Cyhoeddwyd 2013

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing

gan Morin, Ryan D., Mungall, Karen, Pleasance, Erin, Mungall, Andrew J., Goya, Rodrigo, Huff, Ryan D., Scott, David W., Ding, Jiarui, Roth, Andrew, Chiu, Readman, Corbett, Richard D., Chan, Fong Chun, Mendez-Lago, Maria, Trinh, Diane L., Bolger-Munro, Madison, Taylor, Greg, Hadj Khodabakhshi, Alireza, Ben-Neriah, Susana, Pon, Julia, Meissner, Barbara, Woolcock, Bruce, Farnoud, Noushin, Rogic, Sanja, Lim, Emilia L., Johnson, Nathalie A., Shah, Sohrab, Jones, Steven, Steidl, Christian, Holt, Robert, Birol, Inanc, Moore, Richard, Connors, Joseph M., Gascoyne, Randy D., Marra, Marco A.
Cyhoeddwyd 2013

The genetic landscape of high-risk neuroblastoma

gan 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.
Cyhoeddwyd 2013

Spatial heterogeneity in medulloblastoma

gan Morrissy, A Sorana, Cavalli, Florence MG, Remke, Marc, Ramaswamy, Vijay, Shih, David JH, Holgado, Borja L, Farooq, Hamza, Donovan, Laura K, Garzia, Livia, Agnihotri, Sameer, Kiehna, Erin N, Mercier, Eloi, Mayoh, Chelsea, Papillon-Cavanagh, Simon, Nikbakht, Hamid, Gayden, Tenzin, Torchia, Jonathon, Picard, Daniel, Merino, Diana M, Luu, Betty, Wu, Xiaochong, Horswell, Stuart, Thompson, Yuan Yao, Hovestadt, Volker, Northcott, Paul A, Jones, David TW, Peacock, John, Wang, Xin, Mack, Stephen C, Reimand, Juri, Albrecht, Steffen, Fontebasso, Adam M, Thiessen, Nina, Li, Yisu, Schein, Jacqueline E, Lee, Darlene, Carlsen, Rebecca, Mayo, Michael, Tse, Kane, Tam, Angela, Dhalla, Noreen, Ally, Adrian, Chuah, Eric, Cheng, Young, Plettner, Patrick, Li, Haiyan I, Corbett, Richard D, Wong, Tina, Long, William, Loukides, James, Buczkowicz, Pawel, Hawkins, Cynthia E, Tabori, Uri, Rood, Brian R, Myseros, John S, Packer, Roger J, Korshunov, Andrey, Lichter, Peter, Kool, Marcel, Pfister, Stefan M, Schüller, Ulrich, Dirks, Peter, Huang, Annie, Bouffet, Eric, Rutka, James T, Bader, Gary D, Swanton, Charles, Ma, Yusanne, Moore, Richard A, Mungall, Andrew J, Majewski, Jacek, Jones, Steven JM, Das, Sunit, Malkin, David, Jabado, Nada, Marra, Marco A, Taylor, Michael D
Cyhoeddwyd yn Nat Genet (2017)

Subgroup specific structural variation across 1,000 medulloblastoma genomes

gan 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
Cyhoeddwyd 2012

Divergent clonal selection dominates medulloblastoma at recurrence

gan Morrissy, A. Sorana, Garzia, Livia, Shih, David J. H., Zuyderduyn, Scott, Huang, Xi, Skowron, Patryk, Remke, Marc, Cavalli, Florence M. G., Ramaswamy, Vijay, Lindsay, Patricia E., Jelveh, Salomeh, Donovan, Laura K., Wang, Xin, Luu, Betty, Zayne, Kory, Li, Yisu, Mayoh, Chelsea, Thiessen, Nina, Mercier, Eloi, Mungall, Karen L., Ma, Yusanne, Tse, Kane, Zeng, Thomas, Shumansky, Karey, Roth, Andrew J. L., Shah, Sohrab, Farooq, Hamza, Kijima, Noriyuki, Holgado, Borja L., Lee, John J. Y., Matan-Lithwick, Stuart, Liu, Jessica, Mack, Stephen C., Manno, Alex, Michealraj, K. A., Nor, Carolina, Peacock, John, Qin, Lei, Reimand, Juri, Rolider, Adi, Thompson, Yuan Y., Wu, Xiaochong, Pugh, Trevor, Ally, Adrian, Bilenky, Mikhail, Butterfield, Yaron S. N., Carlsen, Rebecca, Cheng, Young, Chuah, Eric, Corbett, Richard D., Dhalla, Noreen, He, An, Lee, Darlene, Li, Haiyan I., Long, William, Mayo, Michael, Plettner, Patrick, Qian, Jenny Q., Schein, Jacqueline E., Tam, Angela, Wong, Tina, Birol, Inanc, Zhao, Yongjun, Faria, Claudia C., Pimentel, José, Nunes, Sofia, Shalaby, Tarek, Grotzer, Michael, Pollack, Ian F., Hamilton, Ronald L., Li, Xiao-Nan, Bendel, Anne E., Fults, Daniel W., Walter, Andrew W., Kumabe, Toshihiro, Tominaga, Teiji, Collins, V. Peter, Cho, Yoon-Jae, Hoffman, Caitlin, Lyden, David, Wisoff, Jeffrey H., Garvin, James H., Stearns, Duncan S., Massimi, Luca, Schüller, Ulrich, Sterba, Jaroslav, Zitterbart, Karel, Puget, Stephanie, Ayrault, Olivier, Dunn, Sandra E., Tirapelli, Daniela P. C., Carlotti, Carlos G., Wheeler, Helen, Hallahan, Andrew R., Ingram, Wendy, MacDonald, Tobey J., Olson, Jeffrey J., Van Meir, Erwin G., Lee, Ji-Yeoun, Wang, Kyu-Chang, Kim, Seung-Ki, Cho, Byung-Kyu, Pietsch, Torsten, Fleischhack, Gudrun, Tippelt, Stephan, Ra, Young Shin, Bailey, Simon, Lindsey, Janet C., Clifford, Steven C., Eberhart, Charles G., Cooper, Michael K., Packer, Roger J., Massimino, Maura, Garre, Maria Luisa, Bartels, Ute, Tabori, Uri, Hawkins, Cynthia E., Dirks, Peter, Bouffet, Eric, Rutka, James T., Wechsler-Reya, Robert J., Weiss, William A., Collier, Lara S., Dupuy, Adam J., Korshunov, Andrey, Jones, David T. W., Kool, Marcel, Northcott, Paul A., Pfister, Stefan M., Largaespada, David A., Mungall, Andrew J., Moore, Richard A., Jabado, Nada, Bader, Gary D., Jones, Steven J. M., Malkin, David, Marra, Marco A., Taylor, Michael D.
Cyhoeddwyd yn Nature (2016)