De novo transcriptome assembly with ABySS

by Birol, I., Jackman, S., Nielsen, C., Qian, J., Varhol, Richard, Stazyk, G., Morin, R., Zhao, Y., Hirst, M., Schein, J., Horsman, D., Connors, J., Gascoyne, R., Marra, M., Jones, S.
Published 2009

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak

by Gardy, J., Johnston, J., Ho Sui, S., Cook, V., Shah, L., Brodkin, E., Rempel, S., Moore, R., Zhao, Y., Holt, R., Varhol, Richard, Birol, I., Lem, M., Sharma, M., Elwood, K., Jones, S., Brinkman, F., Brunham, R., Tang, P.
Published 2011

De novo assembly and analysis of RNA-seq data

by Robertson, G., Schein, J., Chiu, R., Corbett, R., Field, M., Jackman, S., Mungall, K., Lee, S., Okada, H., Qian, J., Griffith, M., Raymond, A., Thiessen, N., Cezard, T., Butterfield, Y., Newsome, R., Chan, S., She, R., Varhol, Richard, Kamoh, B., Prabhu, A., Tam, A., Zhao, Y., Moore, R., Hirst, M., Marra, M., Jones, S., Hoodless, P., Birol, I.
Published 2010

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

by Swanson, L., Robertson, G., Mungall, K., Butterfield, Y., Chiu, R., Corbett, R., Docking, T., Hogge, D., Jackman, S., Moore, R., Mungall, A., Nip, K., Parker, J., Qian, J., Raymond, A., Sung, S., Tam, A., Thiessen, N., Varhol, Richard, Wang, S., Yorukoglu, D., Zhao, Y., Hoodless, P., Sahinalp, S., Karsan, A., Birol, I.
Published 2013

Complete genomic landscape of a recurring sporadic parathyroid carcinoma

by Kasaian, K., Wiseman, S., Thiessen, N., Mungall, K., Corbett, R., Qian, J., Nip, K., He, A., Tse, K., Chuah, E., Varhol, Richard, Pandoh, P., McDonald, H., Zeng, T., Tam, A., Schein, J., Birol, I., Mungall, A., Moore, R., Zhao, Y., Hirst, M., Marra, M., Walker, B., Jones, S.
Published 2013

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers

by Yip, S., Butterfield, Y., Morozova, O., Chittaranjan, S., Blough, M., An, J., Birol, I., Chesnelong, C., Chiu, R., Chuah, E., Corbett, R., Docking, R., Firme, M., Hirst, M., Jackman, S., Karsan, A., Li, H., Louis, D., Maslova, A., Moore, R., Moradian, A., Mungall, K., Perizzolo, M., Qian, J., Roldan, G., Smith, E., Tamura-Wells, J., Thiessen, N., Varhol, Richard, Weiss, S., Wu, W., Young, S., Zhao, Y., Mungall, A., Jones, S., Morin, G., Chan, J., Cairncross, J., Marra, M.
Published 2012

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

by Morin, R., Johnson, N., Severson, T., Mungall, A., An, J., Goya, R., Paul, J., Boyle, M., Woolcock, B., Kuchenbauer, F., Yap, D., Humphries, R., Griffith, O., Shah, S., Zhu, H., Kimbara, M., Shashkin, P., Charlot, J., Tcherpakov, M., Corbett, R., Tam, A., Varhol, Richard, Smailus, D., Moksa, M., Zhao, Y., Delaney, A., Qian, H., Birol, I., Schein, J., Moore, R., Holt, R., Horsman, D., Connors, J., Jones, S., Aparicio, S., Hirst, M., Gascoyne, R., Marra, M.
Published 2010

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

by Shah, S., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., Bashashati, A., Prentice, L., Khattra, J., Burleigh, A., Yap, D., Bernard, V., McPherson, A., Shumansky, K., Crisan, A., Giuliany, R., Heravi-Moussavi, A., Rosner, J., Lai, D., Birol, I., Varhol, Richard, Tam, A., Dhalla, N., Zeng, T., Ma, K., Chan, S., Griffith, M., Moradian, A., Cheng, S., Morin, G., Watson, P., Gelmon, K., Chia, S., Chin, S., Curtis, C., Rueda, O., Pharoah, P., Damaraju, S., MacKey, J., Hoon, K., Harkins, T., Tadigotla, V., Sigaroudinia, M., Gascard, P., Tlsty, T., Costello, J., Meyer, I., Eaves, C., Wasserman, W., Jones, S., Huntsman, D., Hirst, M., Caldas, C., Marra, M., Aparicio, S.
Published 2012

The cancer genome atlas pan-cancer analysis project

by Weinstein, J., Collisson, E., Mills, G., Shaw, K., Ozenberger, B., Ellrott, K., Sander, C., Stuart, J., Chang, K., Creighton, C., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chu, A., Chuah, E., Chun, H., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R., Jones, S., Lee, D., Li, H., Marra, M., Mayo, M., Moore, R., Mungall, A., Robertson, A., Schein, J., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, Richard, Beroukhim, R., Bhatt, A., Brooks, A., Cherniack, A., Freeman, S., Gabriel, S., Helman, E., Jung, J., Meyerson, M., Ojesina, A., Pedamallu, C., Saksena, G., Schumacher, S., Tabak, B., Zack, T., Lander, E., Bristow, C., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L., Mahadeshwar, H., Pantazi, A., Parfenov, M., Park, P., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A., Yang, L., Zeng, D., Auman, J., Balu, S., Buda, E.
Published 2013

Comprehensive genomic characterization of squamous cell lung cancers

by Hammerman, P., Voet, D., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N., Meyerson, M., Chu, A., Hye-Chun, J., Mungall, A., Pleasance, E., Robertson, A., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, K., Nip, K., Olshen, A., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P., Haseley, P., Lee, E., Chin, L.
Published 2012

Comprehensive molecular characterization of human colon and rectal cancer

by Muzny, D., Bainbridge, M., Chang, K., Dinh, H., Drummond, J., Fowler, G., Kovar, C., Lewis, L., Morgan, M., Newsham, I., Reid, J., Santibanez, J., Shinbrot, E., Trevino, L., Wu, Y., Wang, M., Gunaratne, P., Donehower, L., Creighton, C., Wheeler, D., Gibbs, R., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Ding, L., Fulton, R., Koboldt, D., Wylie, T., Walker, J., Dooling, D., Fulton, L., Delehaunty, K., Fronick, C., Demeter, R., Mardis, E., Wilson, R., Chu, A., Chun, H., Mungall, A., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Bass, A., Ramos, A., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Pho, N., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K.
Published 2012

Comprehensive molecular portraits of human breast tumours

by Koboldt, D., Fulton, R., McLellan, M., Schmidt, H., Kalicki-Veizer, J., McMichael, J., Fulton, L., Dooling, D., Ding, L., Mardis, E., Wilson, R., Ally, A., Balasundaram, M., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Mungall, A., Pleasance, E., Robertson, A., Schein, J., Shafiei, A., Sipahimalani, P., Slobodan, J., Stoll, D., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S., Marra, M., Cherniack, A., Saksena, G., Onofrio, R., Pho, N., Carter, S., Schumacher, S., Tabak, B., Hernandez, B., Gentry, J., Nguyen, H., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Getz, G., Gabriel, S., Meyerson, M., Chin, L., Kucherlapati, R., Hoadley, K., Auman, J., Fan, C., Turman, Y., Shi, Y., Li, L., Topal, M., He, X., Chao, H., Prat, A., Silva, G., Iglesia, M.
Published 2012

Integrated genomic characterization of endometrial carcinoma

by Getz, G., Gabriel, S., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., Lawrence, M., Kandoth, C., Dooling, D., Fulton, R., Fulton, L., Kalicki-Veizer, J., McLellan, M., O'Laughlin, M., Schmidt, H., Wilson, R., Ye, K., Li, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H., Dhalla, N., Guin, R., Hirst, C., Holt, R., Jones, S., Lee, D., Li, H., Marra, M., Mayo, M., Moore, R., Mungall, A., Plettner, P., Schein, J., Sipahimalani, P., Tam, A., Varhol, Richard, Gordon Robertson, A., Cherniack, A., Pashtan, I., Saksena, G., Onofrio, R., Schumacher, S., Tabak, B., Carter, S., Hernandez, B., Gentry, J., Salvesen, H., Ardlie, K., Winckler, W., Beroukhim, R., Meyerson, M., Hadjipanayis, A., Lee, S., Mahadeshwar, H., Park, P., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Xi, R., Yang, L., Dong, Z., Kucherlapati, R., Chin, L., Zhang, J., Todd Auman, J., Balu, S., Bodenheimer, T., Buda, E., Neil Hayes, D., Hoyle, A., Jefferys, S., Jones, C., Meng, S., Mieczkowski, P., Mose, L., Parker, J., Perou, C.
Published 2013

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

by Northcott, P., Shih, D., Peacock, J., Garzia, L., Sorana Morrissy, A., Zichner, T., Stútz, A., Korshunov, A., Reimand, J., Schumacher, S., Beroukhim, R., Ellison, D., Marshall, C., Lionel, A., MacK, S., Dubuc, A., Yao, Y., Ramaswamy, V., Luu, B., Rolider, A., Cavalli, F., Wang, X., Remke, M., Wu, X., Chiu, R., Chu, A., Chuah, E., Corbett, R., Hoad, G., Jackman, S., Li, Y., Lo, A., Mungall, K., Ming Nip, K., Qian, J., Raymond, A., Thiessen, N., Varhol, Richard, Birol, I., Moore, R., Mungall, A., Holt, R., Kawauchi, D., Roussel, M., Kool, M., Jones, D., Witt, H., Fernandez-L, A., Kenney, A., Wechsler-Reya, R., Dirks, P., Aviv, T., Grajkowska, W., Perek-Polnik, M., Haberler, C., Delattre, O., Reynaud, S., Doz, F., Pernet-Fattet, S., Cho, B., Kim, S., Wang, K., Scheurlen, W., Eberhart, C., Fèvre-Montange, M., Jouvet, A., Pollack, I., Fan, X., Muraszko, K., Yancey Gillespie, G., Di Rocco, C., Massimi, L., Michiels, E., Kloosterhof, N., French, P., Kros, J., Olson, J., Ellenbogen, R., Zitterbart, K., Kren, L., Thompson, R., Cooper, M.
Published 2012

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

by Ley, T., Miller, C., Ding, L., Raphael, B., Mungall, A., Robertson, G., Hoadley, K., Triche, T., Laird, P., Baty, J., Fulton, L., Fulton, R., Heath, S., Kalicki-Veizer, J., Kandoth, C., Klco, J., Koboldt, D., Kanchi, K., Kulkarni, S., Lamprecht, T., Larson, D., Lin, G., Lu, C., McLellan, M., McMichael, J., Payton, J., Schmidt, H., Spencer, D., Tomasson, M., Wallis, J., Wartman, L., Watson, M., Welch, J., Wendl, M., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R., Jones, S., Karsan, A., Lee, D., Li, H., Marra, M., Mayo, M., Moore, R., Mungall, K., Parker, J., Pleasance, E., Plettner, P., Schein, J., Stoll, D., Swanson, L., Tam, A., Thiessen, N., Varhol, Richard, Wye, N., Zhao, Y., Gabriel, S., Getz, G., Sougnez, C., Zou, L., Leiserson, M., Vandin, F., Wu, H., Applebaum, F., Baylin, S., Akbani, R., Broom, B., Chen, K., Motter, T., Nguyen, K., Weinstein, J., Zhang, N., Ferguson, M., Adams, C., Black, A., Bowen, J., Gastier-Foster, J., Grossman, T., Lichtenberg, T., Wise, L., Davidsen, T., Demchok, J., Mills Shaw, K., Sheth, M., Sofia, H., Yang, L., Downing, J., Eley, G.
Published 2013