Section of Computational Biology

Search results

  • 2014

    Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

    Hughes, A. E. O., Magrini, V., Demeter, R., Miller, C. A., Fulton, R., Fulton, L. L., Eades, W. C., Elliott, K., Heath, S., Westervelt, P., Ding, L., Conrad, D. F., White, B. S., Shao, J., Link, D. C., DiPersio, J. F., Mardis, E. R., Wilson, R. K., Ley, T. J. & Walter, M. J. & 1 others, Graubert, T. A., Jul 2014, In: PLoS genetics. 10, 7, e1004462.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    110 Scopus citations

  • Clonal architectures and driver mutations in metastatic melanomas

    Ding, L., Kim, M., Kanchi, K. L., Dees, N. D., Lu, C., Griffith, M., Fenstermacher, D., Sung, H., Miller, C. A., Goetz, B., Wendl, M. C., Griffith, O., Cornelius, L. A., Linette, G. P., McMichael, J. F., Sondak, V. K., Fields, R. C., Ley, T. J., Mulé, J. J. & Wilson, R. K. & 1 others, Weber, J. S., Nov 13 2014, In: PloS one. 9, 11, e111153.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    66 Scopus citations

  • Comprehensive molecular characterization of gastric adenocarcinoma

    Cancer Genome Atlas Research Network, Sep 11 2014, In: Nature. 513, 7517, p. 202-209 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    5126 Scopus citations

  • Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

    Collisson, E. A., Campbell, J. D., Brooks, A. N., Berger, A. H., Lee, W., Chmielecki, J., Beer, D. G., Cope, L., Creighton, C. J., Danilova, L., Ding, L., Getz, G., Hammerman, P. S., Hayes, D. N., Hernandez, B., Herman, J. G., Heymach, J. V., Jurisica, I., Kucherlapati, R. & Kwiatkowski, D. & 290 others, Ladanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M. S., Travis, W. D., Weinstein, J. N., Wigle, D. A., Wilkerson, M. D., Chu, A., Cherniack, A. D., Hadjipanayis, A., Rosenberg, M., Weisenberger, D. J., Laird, P. W., Radenbaugh, A., Ma, S., Stuart, J. M., Byers, L. A., Baylin, S. B., Govindan, R., Meyerson, M., Gabriel, S. B., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E. S., Lawrence, M. S., Getz, E., Fulton, R., Fulton, L. L., McLellan, M. D., Wilson, R. K., Ye, K., Fronick, C. C., Maher, C. A., Miller, C. A., Wendl, M. C., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R., Robertson, A. G., Wye, N., Thiessen, N., Holt, R. A., Jones, S. J. M., Marra, M. A., Imielinski, M., Onofrio, R. C., Hodis, E., Zack, T., Helman, E., Pedamallu, C. S., Mesirov, J., Saksena, G., Schumacher, S. E., Carter, S. L., Garraway, L., Beroukhim, R., Lee, S., Mahadeshwar, H. S., Pantazi, A., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Yang, L., Zhang, J., Chen, P. C., Parfenov, M., Xu, A. W., Santoso, N., Chin, L., Park, P. J., Hoadley, K. A., Auman, J. T., Meng, S., Shi, Y., Buda, E., Waring, S., Veluvolu, U., Tan, D., Mieczkowski, P. A., Jones, C. D., Simons, J. V., Soloway, M. G., Bodenheimer, T., Jefferys, S. R., Roach, J., Hoyle, A. P., Wu, J., Balu, S., Singh, D., Prins, J. F., Marron, J. S., Parker, J. S., Perou, C. M., Liu, J., Maglinte, D. T., Lai, P. H., Bootwalla, M. S., Van Den Berg, D. J., Triche, T., Cho, J., DiCara, D., Heiman, D., Lin, P., Mallard, W., Voet, D., Zhang, H., Zou, L., Noble, M. S., Gehlenborg, N., Thorvaldsdottir, H., Nazaire, M. D., Robinson, J., Aksoy, B. A., Ciriello, G., Taylor, B. S., Dresdner, G., Gao, J., Gross, B., Seshan, V. E., Reva, B., Sumer, S. O., Weinhold, N., Sander, C., Ng, S., Zhu, J., Benz, C. C., Yau, C., Haussler, D., Spellman, P. T., Kimes, P. K., Broom, B. M., Wang, J., Lu, Y., Ng, P. K. S., Diao, L., Liu, W., Amos, C. I., Akbani, R., Mills, G. B., Curley, E., Paulauskis, J., Lau, K., Morris, S., Shelton, T., Mallery, D., Gardner, J., Penny, R., Saller, C., Tarvin, K., Richards, W. G., Cerfolio, R., Bryant, A., Raymond, D. P., Pennell, N. A., Farver, C., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Brown, J., Bauer, T., Dolzhanskiy, C. O., Potapova, O., Rotin, D., Voronina, O., Nemirovich-Danchenko, E., Fedosenko, K. V., Gal, A., Behera, M., Ramalingam, S. S., Sica, G., Flieder, D., Boyd, J., Weaver, J. E., Kohl, B., Thinh, D. H. Q., Sandusky, G., Juhl, H., Duhig, E., Illei, P., Gabrielson, E., Shin, J., Lee, B., Rogers, K., Trusty, D., Brock, M. V., Williamson, C., Burks, E., Rieger-Christ, K., Holway, A., Sullivan, T., Asiedu, M. K., Kosari, F., Rekhtman, N., Zakowski, M., Rusch, V. W., Zippile, P., Suh, J., Pass, H., Goparaju, C., Owusu-Sarpong, Y., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Sekhon, H., Albert, M., Eckman, J., Myers, J. B., Morrison, C., Gaudioso, C., Borgia, J. A., Bonomi, P., Pool, M., Liptay, M. J., Moiseenko, F., Zaytseva, I., Dienemann, H., Meister, M., Schnabel, P. A., Muley, T. R., Peifer, M., Gomez-Fernandez, C., Herbert, L., Egea, S., Huang, M., Thorne, L. B., Boice, L., Salazar, A. H., Funkhouser, W. K., Rathmell, W. K., Dhir, R., Yousem, S. A., Dacic, S., Schneider, F., Siegfried, J. M., Hajek, R., Watson, M. A., McDonald, S., Meyers, B., Clarke, B., Yang, I. A., Fong, K. M., Hunter, L., Windsor, M., Bowman, R. V., Peters, S., Letovanec, I., Khan, K. Z., Jensen, M. A., Snyder, E. E., Srinivasan, D., Kahn, A. B., Baboud, J., Pot, D. A., Shaw, K. R. M., Sheth, M., Davidsen, T., Demchok, J. A., Yang, L., Wang, Z., Tarnuzzer, R., Zenklusen, J. C., Ozenberger, B. A., Sofia, H. J. & Cheney, R., 2014, In: Nature. 511, 7511, p. 543-550 8 p.

    Research output: Contribution to journal › Article › peer-review

    4421 Scopus citations

  • Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia

    Lim, E. S., Cao, S., Holtz, L. R., Antonio, M., Stine, O. C. & Wang, D., Apr 2014, In: Virology. 454-455, 1, p. 25-33 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    17 Scopus citations

  • Expanding the computational toolbox for mining cancer genomes

    Ding, L., Wendl, M. C., McMichael, J. F. & Raphael, B. J., Aug 2014, In: Nature Reviews Genetics. 15, 8, p. 556-570 15 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    147 Scopus citations

  • Genomic landscape of ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations

    St. Jude Children’s Research Hospital-Washington University Pediatric Cancer Genome Project and the International Cancer Genome Consortium, Nov 1 2014, In: Cancer discovery. 4, 11, p. 1342-1353 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    411 Scopus citations

  • Geographic variation in the eukaryotic virome of human diarrhea

    Holtz, L. R., Cao, S., Zhao, G., Bauer, I. K., Denno, D. M., Klein, E. J., Antonio, M., Stine, O. C., Snelling, T. L., Kirkwood, C. D. & Wang, D., Nov 1 2014, In: Virology. 468, p. 556-564 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    66 Scopus citations

  • High Frequency Strand Slippage Mutations in CTCF in MSI-Positive Endometrial Cancers

    Zighelboim, I., Mutch, D. G., Knapp, A., Ding, L., Xie, M., Cohn, D. E. & Goodfellow, P. J., Jan 2014, In: Human mutation. 35, 1, p. 63-65 3 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    25 Scopus citations

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

    Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., Abecasis, G. R., Auton, A., Brooks, L. D., Depristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., McVean, G., Altshuler, D. M. & Durbin, R. M. & 685 others, Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., Marth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Lander, E. S., Altshuler, D. M., Gabriel, S. B., Gupta, N., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Lehrach, H., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Sherry, S. T., McVean, G. A., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Durbin, R. M., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Auton, A., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Wang, Y., Yu, J., Wang, J., Coin, L. J., Fang, L., Guo, X., Jin, X., Li, G., Li, Q., Li, Y., Li, Z., Lin, H., Liu, B., Luo, R., Qin, N., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., Altshuler, D. M., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Gabriel, S. B., Genovese, G., Gupta, N., Handsaker, R. E., Hartl, C., Lander, E. S., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Korbel, J. O., Rausch, T., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Smith, R. E., Zheng-Bradley, X., Clark, A. G., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Cooper, D. N., Ball, E. V., Stenson, P. D., Bentley, D. R., Barnes, B., Bauer, M., Cheetham, R., Cox, T., Eberle, M., Humphray, S., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Macarthur, D. G., Lek, M., Sudbrak, R., Amstislavskiy, V. S., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Sherry, S. T., Xiao, C., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Trost, M. K., Awadalla, P., Hodgkinson, A., Lunter, G., McVean, G. A., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Mardis, E. R., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Durbin, R. M., Hurles, M. E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Balasubramaniam, S., Chen, Y., Coffey, A. J., Colonna, V., Danecek, P., Huang, N., Jostins, L., Keane, T. M., Li, H., McCarthy, S., Scally, A., Stalker, J., Walter, K., Xue, Y., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Habegger, L., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Li, Y., Luo, R., Zhu, H., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Ward, A. N., Wu, J., Zhang, M., McCarroll, S. A., Altshuler, D. M., Banks, E., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., Nemesh, J. C., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Degenhardt, J., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Korbel, J. O., Rausch, T., Stütz, A. M., Bentley, D. R., Barnes, B., Cheetham, R., Eberle, M., Humphray, S., Kahn, S., Murray, L., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Lacroute, P., Craig, D. W., Homer, N., Church, D., Xiao, C., Sebat, J., Bafna, V., Michaelson, J. J., Ye, K., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Lunter, G., McVean, G. A., Iqbal, Z., Witherspoon, D., Xing, J., Eichler, E. E., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., McLellan, M. D., Wallis, J. W., Hurles, M. E., Blackburne, B., Li, H., Lindsay, S. J., Ning, Z., Scally, A., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Chen, J., Clarke, D., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Kovar, C., Lewis, L., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Yu, J., Guo, X., Li, Y., Wu, R., Marth, G. T., Garrison, E. P., Leong, W. F., Ward, A. N., Del Angel, G., Depristo, M. A., Gabriel, S. B., Gupta, N., Hartl, C., Poplin, R. E., Clark, A. G., Rodriguez-Flores, J. L., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Macarthur, D. G., Bustamante, C. D., Gravel, S., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Sherry, S. T., Xiao, C., Dermitzakis, E., Abecasis, G. R., Kang, H. M., McVean, G. A., Mardis, E. R., Dooling, D., Fulton, L., Fulton, R., Koboldt, D. C., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Gerstein, M. B., Balasubramanian, S., Habegger, L., Garrison, E. P., Gibbs, R. A., Bainbridge, M., Muzny, D., Yu, F., Yu, J., Del Angel, G., Handsaker, R. E., Makarov, V., Rodriguez-Flores, J. L., Jin, H., Kim, W., Kim, K. C., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Zheng-Bradley, X., Tabrizi, S., Macarthur, D. G., Lek, M., Bustamante, C. D., De La Vega, F. M., Craig, D. W., Kurdoglu, A. A., Lappalainen, T., Rosenfeld, J. A., Michelson, L. P., Awadalla, P., Hodgkinson, A., McVean, G. A., Chen, K., Tyler-Smith, C., Chen, Y., Colonna, V., Frankish, A., Harrow, J., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Kovar, C., Kalra, D., Hale, W., Fowler, G., Muzny, D., Reid, J., Wang, J., Guo, X., Li, G., Li, Y., Zheng, X., Altshuler, D. M., Flicek, P., Clarke, L., Barker, J., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Toneva, I., Vaughan, B., Zheng-Bradley, X., Bentley, D. R., Cox, T., Humphray, S., Kahn, S., Sudbrak, R., Albrecht, M. W., Lienhard, M., Craig, D. W., Izatt, T., Kurdoglu, A. A., Sherry, S. T., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Church, D., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'sullivan, C., Ostapchuk, Y., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Xiao, C., Zhang, H., Haussler, D., Abecasis, G. R., McVean, G. A., Alkan, C., Ko, A., Dooling, D., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Chakravarti, A., Abecasis, G. R., Barnes, K. C., Beiswanger, C., Burchard, E., Bustamante, C. D., Cai, H., Cao, H., Durbin, R. M., Gharani, N., Gibbs, R. A., Gignoux, C. R., Gravel, S., Henn, B., Jones, D., Jorde, L., Kaye, J. S., Keinan, A., Kent, A., Kerasidou, A., Li, Y., Mathias, R., McVean, G., Moreno-Estrada, A., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Sudbrak, R., Tian, Z., Timmermann, B., Tishkoff, S., Toji, L. H., Tyler-Smith, C., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ruiz-Linares, A., Ming, C. Z., Yang, G., You, C. J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Oleksyk, T. K., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Green, E. D., Guyer, M. S. & Peterson, J. L., Jun 30 2014, In: Genome biology. 15, 6, R88.

    Research output: Contribution to journal › Article › peer-review

    60 Scopus citations

  • Integrated analysis of germline and somatic variants in ovarian cancer

    Kanchi, K. L., Johnson, K. J., Lu, C., McLellan, M. D., Leiserson, M. D. M., Wendl, M. C., Zhang, Q., Koboldt, D. C., Xie, M., Kandoth, C., McMichael, J. F., Wyczalkowski, M. A., Larson, D. E., Schmidt, H. K., Miller, C. A., Fulton, R. S., Spellman, P. T., Mardis, E. R., Druley, T. E. & Graubert, T. A. & 4 others, Goodfellow, P. J., Raphael, B. J., Wilson, R. K. & Ding, L., Jan 22 2014, In: Nature communications. 5, 3156.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    248 Scopus citations

  • Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

    Delaneau, O., Marchini, J., McVeanh, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Altshuler, D. M., Gabriel, S. B., Lander, E. S., Gupta, N., Daly, M. J. & DePristo, M. A. & 363 others, Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Chris, T. S., Abecasis, G. R., Kang, H. M., Anderson, P., Blackwell, T., Busonero, F., Fuchsberger, C., Jun, G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M. K., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., Murray, L., Shaw, R., Chakravarti, A., Clark, A. G., Keinan, A., Rodriguez-Flores, J. L., De LaVega, F. M., Degenhardt, J., Eichler, E. E., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Fowler, G., Hale, W., Kalra, D., Green, E. D., Knoppers, B. M., Korbel, J. O., Rausch, T., Sttz, A. M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Von Grotthuss, M., Zhang, C., Shi, X., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Herwig, S. R., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Nickerson, D. A., Alkan, C., Hormozdiari, F., Ko, A., Sudmant, P. H., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Sherry, S. T., Xiao, C., Church, D., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Liu, X., Lu, Y., Ma, X., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Lachlan, H., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zheng, H., Zhu, H., Cai, H., Cao, H., Su, Y., Tian, Z., Yang, H., Yang, L., Zhu, J., Cai, Z., Wang, J., Albrecht, M. W., Borodina, T. A., Auton, A., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Gottipati, S., Jones, D., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Kahn, S., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Shriver, M. D., Bustamante, C. D., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Henn, B., Sandoval, K., Byrnes, J. K., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Homer, N., Squire, K., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Angius, A., Cucca, F., Sanna, S., Bigham, A., Jones, C., Reinier, F., Li, Y., Lyons, R., Schlessinger, D., Awadalla, P., Hodgkinson, A., Oleksyk, T. K., Martinez-Cruzado, J. C., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Hajirasouliha, I., Chen, K., Albers, C. A., Gerstein, M. B., Abyzov, A., Chen, J., Fu, Y., Habegger, L., Harmanci, A. O., Mu, X. J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson, J. J., OSullivan, C., Barnes, K. C., Gharani, N., Toji, L. H., Gerry, N., Kaye, J. S., Kent, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Tishkoff, S., Via, M., Bodmer, W., Bedoya, G., Yang, G., You, C. J., Garcia-Montero, A., Orfao, A., Dutil, J., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Guyer, M. S., Peterson, J. L., Duncanson, A., Dunn, M. & Peltonen, L., Jun 13 2014, In: Nature communications. 5, 3934.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    308 Scopus citations

  • MSIsensor: Microsatellite instability detection using paired tumor-normal sequence data

    Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., Wendl, M. C. & Ding, L., Apr 1 2014, In: Bioinformatics. 30, 7, p. 1015-1016 2 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    610 Scopus citations

  • Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

    The Cancer Genome Atlas Research Network, Aug 14 2014, In: Cell. 158, 4, p. 929-944 16 p.

    Research output: Contribution to journal › Article › peer-review

    1187 Scopus citations

  • Predicting structure and stability for RNA complexes with intermolecular loop - Loop base-pairing

    Cao, S., Xu, X. & Chen, S. J., Jun 2014, In: RNA. 20, 6, p. 835-845 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    19 Scopus citations

  • Proteogenomic characterization of human colon and rectal cancer

    Zhang, B., Wang, J., Wang, X., Zhu, J., Liu, Q., Shi, Z., Chambers, M. C., Zimmerman, L. J., Shaddox, K. F., Kim, S., Davies, S. R., Wang, S., Wang, P., Kinsinger, C. R., Rivers, R. C., Rodriguez, H., Townsend, R. R., Ellis, M. J. C., Carr, S. A. & Tabb, D. L. & 44 others, Coffey, R. J., Slebos, R. J. C., Liebler, D. C., Gillette, M. A., Klauser, K. R., Kuhn, E., Mani, D. R., Mertins, P., Ketchum, K. A., Paulovich, A. G., Whiteaker, J. R., Edwards, N. J., McGarvey, P. B., Madhavan, S., Chan, D., Pandey, A., Shih, I. M., Zhang, H., Zhang, Z., Zhu, H., Whiteley, G. A., Skates, S. J., White, F. M., Levine, D. A., Boja, E. S., Hiltke, T., Mesri, M., Shaw, K. M., Stein, S. E., Fenyo, D., Liu, T., McDermott, J. E., Payne, S. H., Rodland, K. D., Smith, R. D., Rudnick, P., Snyder, M., Zhao, Y., Chen, X., Ransohoff, D. F., Hoofnagle, A. N., Sanders, M. E., Wang, Y. & Ding, L., Sep 18 2014, In: Nature. 513, 7518, p. 382-387 6 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1137 Scopus citations

  • Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma

    Chen, X., Bahrami, A., Pappo, A., Easton, J., Dalton, J., Hedlund, E., Ellison, D., Shurtleff, S., Wu, G., Wei, L., Parker, M., Rusch, M., Nagahawatte, P., Wu, J., Mao, S., Boggs, K., Mulder, H., Yergeau, D., Lu, C. & Ding, L. & 11 others, Edmonson, M., Qu, C., Wang, J., Li, Y., Navid, F., Daw, N. C., Mardis, E. R., Wilson, R. K., Downing, J. R., Zhang, J. & Dyer, M. A., Oct 4 2014, In: Cell Reports. 7, 1, p. 104-112 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    588 Scopus citations

  • Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci

    Service, S. K., Teslovich, T. M., Fuchsberger, C., Ramensky, V., Yajnik, P., Koboldt, D. C., Larson, D. E., Zhang, Q., Lin, L., Welch, R., Ding, L., McLellan, M. D., O'Laughlin, M., Fronick, C., Fulton, L. L., Magrini, V., Swift, A., Elliott, P., Jarvelin, M. R. & Kaakinen, M. & 14 others, McCarthy, M. I., Peltonen, L., Pouta, A., Bonnycastle, L. L., Collins, F. S., Narisu, N., Stringham, H. M., Tuomilehto, J., Ripatti, S., Fulton, R. S., Sabatti, C., Wilson, R. K., Boehnke, M. & Freimer, N. B., Jan 2014, In: PLoS genetics. 10, 1, e1004147.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    46 Scopus citations

  • SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

    Miller, C. A., White, B. S., Dees, N. D., Griffith, M., Welch, J. S., Griffith, O. L., Vij, R., Tomasson, M. H., Graubert, T. A., Walter, M. J., Ellis, M. J., Schierding, W., DiPersio, J. F., Ley, T. J., Mardis, E. R., Wilson, R. K. & Ding, L., Aug 7 2014, In: PLoS computational biology. 10, 8, e1003665.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    354 Scopus citations

  • Simple and accurate methods for quantifying deformation, disruption, and development in biological tissues

    Boyle, J. J., Kume, M., Wyczalkowski, M. A., Taber, L. A., Pless, R. B., Xia, Y., Genin, G. M. & Thomopoulos, S., Nov 6 2014, In: Journal of the Royal Society Interface. 11, 100, 0685.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    31 Scopus citations

  • Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia

    Roberts, K. G., Li, Y., Payne-Turner, D., Harvey, R. C., Yang, Y. L., Pei, D., McCastlain, K., Ding, L., Lu, C., Song, G., Ma, J., Becksfort, J., Rusch, M., Chen, S. C., Easton, J., Cheng, J., Boggs, K., Santiago-Morales, N., Iacobucci, I. & Fulton, R. S. & 54 others, Wen, J., Valentine, M., Cheng, C., Paugh, S. W., Devidas, M., Chen, I. M., Reshmi, S., Smith, A., Hedlund, E., Gupta, P., Nagahawatte, P., Wu, G., Chen, X., Yergeau, D., Vadodaria, B., Mulder, H., Winick, N. J., Larsen, E. C., Carroll, W. L., Heerema, N. A., Carroll, A. J., Grayson, G., Tasian, S. K., Moore, A. S., Keller, F., Frei-Jones, M., Whitlock, J. A., Raetz, E. A., White, D. L., Hughes, T. P., Guidry Auvil, J. M., Smith, M. A., Marcucci, G., Bloomfield, C. D., Mrózek, K., Kohlschmidt, J., Stock, W., Kornblau, S. M., Konopleva, M., Paietta, E., Pui, C. H., Jeha, S., Relling, M. V., Evans, W. E., Gerhard, D. S., Gastier-Foster, J. M., Mardis, E., Wilson, R. K., Loh, M. L., Downing, J. R., Hunger, S. P., Willman, C. L., Zhang, J. & Mullighan, C. G., Sep 11 2014, In: New England Journal of Medicine. 371, 11, p. 1005-1015 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    1171 Scopus citations

  • The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma

    Wu, G., Diaz, A. K., Paugh, B. S., Rankin, S. L., Ju, B., Li, Y., Zhu, X., Qu, C., Chen, X., Zhang, J., Easton, J., Edmonson, M., Ma, X., Lu, C., Nagahawatte, P., Hedlund, E., Rusch, M., Pounds, S., Lin, T. & Onar-Thomas, A. & 27 others, Huether, R., Kriwacki, R., Parker, M., Gupta, P., Becksfort, J., Wei, L., Mulder, H. L., Boggs, K., Vadodaria, B., Yergeau, D., Russell, J. C., Ochoa, K., Fulton, R. S., Fulton, L. L., Jones, C., Boop, F. A., Broniscer, A., Wetmore, C., Gajjar, A., Ding, L., Mardis, E. R., Wilson, R. K., Taylor, M. R., Downing, J. R., Ellison, D. W., Zhang, J. & Baker, S. J., May 2014, In: Nature Genetics. 46, 5, p. 444-450 7 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    838 Scopus citations

  • The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

    Huether, R., Dong, L., Chen, X., Wu, G., Parker, M., Wei, L., Ma, J., Edmonson, M. N., Hedlund, E. K., Rusch, M. C., Shurtleff, S. A., Mulder, H. L., Boggs, K., Vadordaria, B., Cheng, J., Yergeau, D., Song, G., Becksfort, J., Lemmon, G. & Weber, C. & 19 others, Cai, Z., Dang, J., Walsh, M., Gedman, A. L., Faber, Z., Easton, J., Gruber, T., Kriwacki, R. W., Partridge, J. F., Ding, L., Wilson, R. K., Mardis, E. R., Mullighan, C. G., Gilbertson, R. J., Baker, S. J., Zambetti, G., Ellison, D. W., Zhang, J. & Downing, J. R., Apr 8 2014, In: Nature communications. 5, 3630.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    322 Scopus citations

  • TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

    Chen, K., Chen, L., Fan, X., Wallis, J., Ding, L. & Weinstock, G., Feb 2014, In: Genome research. 24, 2, p. 310-317 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    67 Scopus citations
  • 2013

    Activating HER2 mutations in HER2 gene amplification negative breast cancer

    Bose, R., Kavuri, S. M., Searleman, A. C., Shen, W., Shen, D., Koboldt, D. C., Monsey, J., Goel, N., Aronson, A. B., Li, S., Ma, C. X., Ding, L., Mardis, E. R. & Ellis, M. J., 2013, In: Cancer discovery. 3, 2, p. 224-237 14 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    707 Scopus citations

  • Advances for studying clonal evolution in cancer

    Ding, L., Raphael, B. J., Chen, F. & Wendl, M. C., Nov 1 2013, In: Cancer Letters. 340, 2, p. 212-219 8 p.

    Research output: Contribution to journal › Review article › peer-review

    Open Access
    59 Scopus citations

  • BreakTrans: Uncovering the genomic architecture of gene fusions

    Chen, K., Navin, N. E., Wang, Y., Schmidt, H. K., Wallis, J. W., Niu, B., Fan, X., Zhao, H., McLellan, M. D., Hoadley, K. A., Mardis, E. R., Ley, T. J., Perou, C. M., Wilson, R. K. & Ding, L., Aug 23 2013, In: Genome biology. 14, 8, R87.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    20 Scopus citations

  • Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

    Walter, M. J., Shen, D., Shao, J., Ding, L., White, B., Kandoth, C., Miller, C. A., Niu, B., McLellan, M. D., Dees, N. D., Fulton, R., Elliot, K., Heath, S., Grillot, M., Westervelt, P., Link, D. C., DiPersio, J. F., Mardis, E., Ley, T. J. & Wilson, R. K. & 1 others, Graubert, T. A., Jun 2013, In: Leukemia. 27, 6, p. 1275-1282 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    247 Scopus citations

  • Comprehensive identification of mutational cancer driver genes across 12 tumor types

    Tamborero, D., Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J., Kandoth, C., Reimand, J., Lawrence, M. S., Getz, G., Bader, G. D., Ding, L. & Lopez-Bigas, N., 2013, In: Scientific reports. 3, 2650.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    405 Scopus citations

  • Computational and experimental study of the mechanics of embryonic wound healing

    Wyczalkowski, M. A., Varner, V. D. & Taber, L. A., Dec 2013, In: Journal of the Mechanical Behavior of Biomedical Materials. 28, p. 125-146 22 p.

    Research output: Contribution to journal › Article › peer-review

    14 Scopus citations

  • Computational approaches to identify functional genetic variants in cancer genomes

    Gonzalez-Perez, A., Mustonen, V., Reva, B., Ritchie, G. R. S., Creixell, P., Karchin, R., Vazquez, M., Fink, J. L., Kassahn, K. S., Pearson, J. V., Bader, G. D., Boutros, P. C., Muthuswamy, L., Ouellette, B. F. F., Reimand, J., Linding, R., Shibata, T., Valencia, A., Butler, A. & Dronov, S. & 8 others, Flicek, P., Shannon, N. B., Carter, H., Li, D., Sander, C., Stuart, J. M., Stein, L. D. & Lopez-Bigas, N., Aug 2013, In: Nature Methods. 10, 8, p. 723-729 7 p.

    Research output: Contribution to journal › Review article › peer-review

    134 Scopus citations

  • Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem

    Wendl, M. C., Kota, K., Weinstock, G. M. & Mitreva, M., Nov 2013, In: Journal of Mathematical Biology. 67, 5, p. 1141-1161 21 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    22 Scopus citations

  • DGIdb: Mining the druggable genome

    Griffith, M., Griffith, O. L., Coffman, A. C., Weible, J. V., Mcmichael, J. F., Spies, N. C., Koval, J., Das, I., Callaway, M. B., Eldred, J. M., Miller, C. A., Subramanian, J., Govindan, R., Kumar, R. D., Bose, R., Ding, L., Walker, J. R., Larson, D. E., Dooling, D. J. & Smith, S. M. & 3 others, Ley, T. J., Mardis, E. R. & Wilson, R. K., Dec 2013, In: Nature Methods. 10, 12, p. 1209-1210 2 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    416 Scopus citations

  • Differences that matter in cancer genomics

    Ding, L. & Wendl, M. C., Oct 2013, In: Nature Biotechnology. 31, 10, p. 892-893 2 p.

    Research output: Contribution to journal › Comment/debate

    3 Scopus citations

  • Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts

    Li, S., Shen, D., Shao, J., Crowder, R., Liu, W., Prat, A., He, X., Liu, S., Hoog, J., Lu, C., Ding, L., Griffith, O. L., Miller, C., Larson, D., Fulton, R. S., Harrison, M., Mooney, T., McMichael, J. F., Luo, J. & Tao, Y. & 35 others, Goncalves, R., Schlosberg, C., Hiken, J. F., Saied, L., Sanchez, C., Giuntoli, T., Bumb, C., Cooper, C., Kitchens, R. T., Lin, A., Phommaly, C., Davies, S. R., Zhang, J., Kavuri, M. S., McEachern, D., Dong, Y. Y., Ma, C., Pluard, T., Naughton, M., Bose, R., Suresh, R., McDowell, R., Michel, L., Aft, R., Gillanders, W., DeSchryver, K., Wilson, R. K., Wang, S., Mills, G. B., Gonzalez-Angulo, A., Edwards, J. R., Maher, C., Perou, C. M., Mardis, E. R. & Ellis, M. J., Sep 26 2013, In: Cell Reports. 4, 6, p. 1116-1130 15 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    527 Scopus citations

  • Erratum: Differences that matter in cancer genomics (Nature Biotechnology (2013) 31 (892-893) DOI:10.1038/nbt.2715)

    Ding, L. & Wendl, M. C., Dec 1 2013, In: Nature Biotechnology. 31, 12, 1 p.

    Research output: Contribution to journal › Comment/debate

  • ERRATUM: Comprehensive identification of mutational cancer driver genes across 12 tumor types (Scientific Reports (2013) 3:2650 doi: 10.1038/srep02650)

    Tamborero, D., Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J., Kandoth, C., Reimand, J., Lawrence, M. S., Getz, G., Bader, G. D., Ding, L. & Lopez-Bigas, N., Oct 11 2013, In: Scientific reports. 3, 2952.

    Research output: Contribution to journal › Comment/debate

    Open Access
    3 Scopus citations

  • Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

    Ley, T. J., Miller, C., Ding, L., Raphael, B. J., Mungall, A. J., Robertson, G., Hoadley, K., Triche, T. J., Laird, P. W., Baty, J. D., Fulton, L. L., Fulton, R., Heath, S. E., Kalicki-Veizer, J., Kandoth, C., Klco, J. M., Koboldt, D. C., Kanchi, K. L., Kulkarni, S. & Lamprecht, T. L. & 119 others, Larson, D. E., Lin, G., Lu, C., McLellan, M. D., McMichael, J. F., Payton, J., Schmidt, H., Spencer, D. H., Tomasson, M. H., Wallis, J. W., Wartman, L. D., Watson, M. A., Welch, J., Wendl, M. C., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H. J., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Jones, S., Karsan, A., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, K., Parker, J., Pleasance, E., Plettner, P., Schein, J., Stoll, D., Swanson, L., Tam, A., Thiessen, N., Varhol, R., Wye, N., Zhao, Y., Gabriel, S., Getz, G., Sougnez, C., Zou, L., Leiserson, M. D. M., Vandin, F., Wu, H. T., Applebaum, F., Baylin, S. B., Akbani, R., Broom, B. M., Chen, K., Motter, T. C., Nguyen, K., Weinstein, J. N., Zhang, N., Ferguson, M. L., Adams, C., Black, A., Bowen, J., Gastier-Foster, J., Grossman, T., Lichtenberg, T., Wise, L., Davidsen, T., Demchok, J. A., Mills Shaw, K. R., Sheth, M., Sofia, H. J., Yang, L., Downing, J. R., Eley, G., Alonso, S., Ayala, B., Baboud, J., Backus, M., Barletta, S. P., Berton, D. L., Chu, A. L., Girshik, S., Jensen, M. A., Kahn, A., Kothiyal, P., Nicholls, M. C., Pihl, T. D., Pot, D. A., Raman, R., Sanbhadti, R. N., Snyder, E. E., Srinivasan, D., Walton, J., Wan, Y., Wang, Z., Issa, J. P. J., Beau, M. L., Carroll, M., Kantarjian, H., Kornblau, S., Bootwalla, M. S., Lai, P. H., Shen, H., Van Den Berg, D. J., Weisenberger, D. J., Link, D. C., Walter, M. J., Ozenberger, B. A., Mardis, E. R., Westervelt, P., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., May 30 2013, In: New England Journal of Medicine. 368, 22, p. 2059-2074 16 p.

    Research output: Contribution to journal › Article › peer-review

    4067 Scopus citations

  • Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif

    Hamilton, M. P., Rajapakshe, K., Hartig, S. M., Reva, B., McLellan, M. D., Kandoth, C., Ding, L., Zack, T. I., Gunaratne, P. H., Wheeler, D. A., Coarfa, C. & McGuire, S. E., 2013, In: Nature communications. 4, 2730.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    100 Scopus citations

  • Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

    Zhao, G., Krishnamurthy, S., Cai, Z., Popov, V. L., Travassos da Rosa, A. P., Guzman, H., Cao, S., Virgin, H. W., Tesh, R. B. & Wang, D., Oct 22 2013, In: PloS one. 8, 10, e78470.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    64 Scopus citations

  • Integrated genomic characterization of endometrial carcinoma

    Getz, G., Gabriel, S. B., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., Lawrence, M., Kandoth, C., Dooling, D., Fulton, R., Fulton, L., Kalicki-Veizer, J., McLellan, M. D., O'Laughlin, M., Schmidt, H., Wilson, R. K., Ye, K., Li, D., Ally, A. & Balasundaram, M. & 256 others, Birol, I., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H. J. E., Dhalla, N., Guin, R., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Plettner, P., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R. J., Gordon Robertson, A., Cherniack, A. D., Pashtan, I., Saksena, G., Onofrio, R. C., Schumacher, S. E., Tabak, B., Carter, S. L., Hernandez, B., Gentry, J., Salvesen, H. B., Ardlie, K., Winckler, W., Beroukhim, R., Meyerson, M., Hadjipanayis, A., Lee, S., Mahadeshwar, H. S., 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. P., Jefferys, S. R., Jones, C. D., Meng, S., Mieczkowski, P. A., Mose, L. E., Parker, J. S., Perou, C. M., Roach, J., Yan, S., Simons, J. V., Soloway, M. G., Tan, D., Topal, M. D., Waring, S., Wu, J., Hoadley, K. A., Baylin, S. B., Bootwalla, M. S., Lai, P. H., Triche, T. J., Van Den Berg, D. J., Weisenberger, D. J., Laird, P. W., Shen, H., Cho, J., Dicara, D., Frazer, S., Heiman, D., Jing, R., Lin, P., Mallard, W., Stojanov, P., Voet, D., Zhang, H., Zou, L., Noble, M., Reynolds, S. M., Shmulevich, I., Arman Aksoy, B., Antipin, Y., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Ladanyi, M., Reva, B., Sander, C., Sinha, R., Onur Sumer, S., Taylor, B. S., Cerami, E., Weinhold, N., Schultz, N., Shen, R., Benz, S., Goldstein, T., Haussler, D., Ng, S., Szeto, C., Stuart, J., Benz, C. C., Yau, C., Zhang, W., Annala, M., Broom, B. M., Casasent, T. D., Ju, Z., Liang, H., Liu, G., Lu, Y., Unruh, A. K., Wakefield, C., Weinstein, J. N., Zhang, N., Liu, Y., Broaddus, R., Akbani, R., Mills, G. B., Adams, C., Barr, T., Black, A. D., Bowen, J., Deardurff, J., Frick, J., Gastier-Foster, J. M., Grossman, T., Harper, H. A., Hart-Kothari, M., Helsel, C., Hobensack, A., Kuck, H., Kneile, K., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Pyatt, R. E., Ramirez, N. C., Tabler, T. R., Vanhoose, N., White, P., Wise, L., Zmuda, E., Barnabas, N., Berry-Green, C., Blanc, V., Boice, L., Button, M., Farkas, A., Green, A., MacKenzie, J., Nicholson, D., Kalloger, S. E., Blake Gilks, C., Karlan, B. Y., Lester, J., Orsulic, S., Borowsky, M., Cadungog, M., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Witkin, G., Nemirovich-Danchenko, E., Potapova, O., Rotin, D., Berchuck, A., Birrer, M., Disaia, P., Monovich, L., Curley, E., Gardner, J., Mallery, D., Penny, R., Dowdy, S. C., Winterhoff, B., Dao, L., Gostout, B., Meuter, A., Teoman, A., Dao, F., Olvera, N., Bogomolniy, F., Garg, K., Soslow, R. A., Abramov, M., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Moiseenko, F., Clarke, B. A., Goodman, M. T., Carney, M. E., Matsuno, R. K., Fisher, J., Huang, M., Kimryn Rathmell, W., Thorne, L., Van Le, L., Dhir, R., Edwards, R., Elishaev, E., Zorn, K., Goodfellow, P. J., Mutch, D., Kahn, A. B., Bell, D. W., Pollock, P. M., Wang, C., Wheeler, D., Shinbrot, E., Gordon Robertson, A., Ding, L., Blake Gilks, C., Mardis, E. R., Ayala, B., Chu, A. L., Jensen, M. A., Kothiyal, P., Pihl, T. D., Pontius, J., Pot, D. A., Snyder, E. E., Srinivasan, D., Mills Shaw, K. R., Sheth, M., Davidsen, T., Eley, G., Ferguson, M. L., Yang, L., Guyer, M. S., Ozenberger, B. A., Sofia, H. J., Gordon Robertson, A. & Levine, D. A., 2013, In: Nature. 497, 7447, p. 67-73 7 p.

    Research output: Contribution to journal › Article › peer-review

    4268 Scopus citations

  • Integrative annotation of variants from 1092 humans: Application to cancer genomics

    1000 Genomes Project Consortium, Oct 4 2013, In: Science. 342, 6154, 1235587.

    Research output: Contribution to journal › Article › peer-review

    296 Scopus citations

  • Mutational landscape and significance across 12 major cancer types

    Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., Leiserson, M. D. M., Miller, C. A., Welch, J. S., Walter, M. J., Wendl, M. C., Ley, T. J., Wilson, R. K., Raphael, B. J. & Ding, L., 2013, In: Nature. 502, 7471, p. 333-339 7 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    3560 Scopus citations

  • Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

    Ewing, A. D., Ballinger, T. J., Earl, D., Harris, C. C., Ding, L., Wilson, R. K. & Haussler, D., Mar 13 2013, In: Genome biology. 14, 3, R22.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    91 Scopus citations

  • Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma

    Gutmann, D. H., McLellan, M. D., Hussain, I., Wallis, J. W., Fulton, L. L., Fulton, R. S., Magrini, V., Demeter, R., Wylie, T., Kandoth, C., Leonard, J. R., Guha, A., Miller, C. A., Ding, L. & Mardis, E. R., Mar 2013, In: Genome research. 23, 3, p. 431-439 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    110 Scopus citations

  • Targeting Oxidative Stress in Embryonal Rhabdomyosarcoma

    Chen, X., Stewart, E., Shelat, A. A., Qu, C., Bahrami, A., Hatley, M., Wu, G., Bradley, C., McEvoy, J., Pappo, A., Spunt, S., Valentine, M. B., Valentine, V., Krafcik, F., Lang, W. H., Wierdl, M., Tsurkan, L., Tolleman, V., Federico, S. M. & Morton, C. & 26 others, Lu, C., Ding, L., Easton, J., Rusch, M., Nagahawatte, P., Wang, J., Parker, M., Wei, L., Hedlund, E., Finkelstein, D., Edmonson, M., Shurtleff, S., Boggs, K., Mulder, H., Yergeau, D., Skapek, S., Hawkins, D. S., Ramirez, N., Potter, P. M., Sandoval, J. A., Davidoff, A. M., Mardis, E. R., Wilson, R. K., Zhang, J., Downing, J. R. & Dyer, M. A., Dec 9 2013, In: Cancer Cell. 24, 6, p. 710-724 15 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    247 Scopus citations

  • The cancer genome atlas pan-cancer analysis project

    Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A. & Chuah, E. & 316 others, Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 1 2013, In: Nature Genetics. 45, 10, p. 1113-1120 8 p.

    Research output: Contribution to journal › Article › peer-review

    6092 Scopus citations

  • The genomic landscape of hypodiploid acute lymphoblastic leukemia

    Holmfeldt, L., Wei, L., Diaz-Flores, E., Walsh, M., Zhang, J., Ding, L., Payne-Turner, D., Churchman, M., Andersson, A., Chen, S. C., Mccastlain, K., Becksfort, J., Ma, J., Wu, G., Patel, S. N., Heatley, S. L., Phillips, L. A., Song, G., Easton, J. & Parker, M. & 43 others, Chen, X., Rusch, M., Boggs, K., Vadodaria, B., Hedlund, E., Drenberg, C., Baker, S., Pei, D., Cheng, C., Huether, R., Lu, C., Fulton, R. S., Fulton, L. L., Tabib, Y., Dooling, D. J., Ochoa, K., Minden, M., Lewis, I. D., To, L. B., Marlton, P., Roberts, A. W., Raca, G., Stock, W., Neale, G., Drexler, H. G., Dickins, R. A., Ellison, D. W., Shurtleff, S. A., Pui, C. H., Ribeiro, R. C., Devidas, M., Carroll, A. J., Heerema, N. A., Wood, B., Borowitz, M. J., Gastier-Foster, J. M., Raimondi, S. C., Mardis, E. R., Wilson, R. K., Downing, J. R., Hunger, S. P., Loh, M. L. & Mullighan, C. G., Mar 2013, In: Nature Genetics. 45, 3, p. 242-252 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    571 Scopus citations

  • The somatic genomic landscape of glioblastoma

    TCGA Research Network, Oct 10 2013, In: Cell. 155, 2, p. 462 1 p.

    Research output: Contribution to journal › Article › peer-review

    3876 Scopus citations

  • Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

    Zhang, J., Wu, G., Miller, C. P., Tatevossian, R. G., Dalton, J. D., Tang, B., Orisme, W., Punchihewa, C., Parker, M., Qaddoumi, I., Boop, F. A., Lu, C., Kandoth, C., Ding, L., Lee, R., Huether, R., Chen, X., Hedlund, E., Nagahawatte, P. & Rusch, M. & 28 others, Boggs, K., Cheng, J., Becksfort, J., Ma, J., Song, G., Li, Y., Wei, L., Wang, J., Shurtleff, S., Easton, J., Zhao, D., Fulton, R. S., Fulton, L. L., Dooling, D. J., Vadodaria, B., Mulder, H. L., Tang, C., Ochoa, K., Mullighan, C. G., Gajjar, A., Kriwacki, R., Sheer, D., Gilbertson, R. J., Mardis, E. R., Wilson, R. K., Downing, J. R., Baker, S. J. & Ellison, D. W., Jun 2013, In: Nature Genetics. 45, 6, p. 602-612 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    708 Scopus citations