Section of Computational Biology

Search results

  • 2016

    Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

    Ceccarelli, M., Barthel, F. P., Malta, T. M., Sabedot, T. S., Salama, S. R., Murray, B. A., Morozova, O., Newton, Y., Radenbaugh, A., Pagnotta, S. M., Anjum, S., Wang, J., Manyam, G., Zoppoli, P., Ling, S., Rao, A. A., Grifford, M., Cherniack, A. D., Zhang, H. & Poisson, L. & 188 others, Carlotti, C. G., Tirapelli, D. P. D. C., Rao, A., Mikkelsen, T., Lau, C. C., Yung, W. K. A., Rabadan, R., Huse, J., Brat, D. J., Lehman, N. L., Barnholtz-Sloan, J. S., Zheng, S., Hess, K., Rao, G., Meyerson, M., Beroukhim, R., Cooper, L., Akbani, R., Wrensch, M., Haussler, D., Aldape, K. D., Laird, P. W., Gutmann, D. H., Noushmehr, H., Arachchi, H., Auman, J. T., Balasundaram, M., Balu, S., Barnett, G., Baylin, S., Bell, S., Benz, C., Bir, N., Black, K. L., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Bristow, C. A., Butterfield, Y. S. N., Chen, Q. R., Chin, L., Cho, J., Chuah, E., Chudamani, S., Coetzee, S. G., Cohen, M. L., Colman, H., Couce, M., D'Angelo, F., Davidsen, T., Davis, A., Demchok, J. A., Devine, K., Ding, L., Duell, R., Elder, J. B., Eschbacher, J. M., Fehrenbach, A., Ferguson, M., Frazer, S., Fuller, G., Fulop, J., Gabriel, S. B., Garofano, L., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Getz, G., Giannini, C., Gibson, W. J., Hadjipanayis, A., Hayes, D. N., Heiman, D. I., Hermes, B., Hilty, J., Hoadley, K. A., Hoyle, A. P., Huang, M., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Ju, Z., Kastl, A., Kendler, A., Kim, J., Kucherlapati, R., Lai, P. H., Lawrence, M. S., Lee, S., Leraas, K. M., Lichtenberg, T. M., Lin, P., Liu, Y., Liu, J., Ljubimova, J. Y., Lu, Y., Ma, Y., Maglinte, D. T., Mahadeshwar, H. S., Marra, M. A., McGraw, M., McPherson, C., Meng, S., Mieczkowski, P. A., Miller, C. R., Mills, G. B., Moore, R. A., Mose, L. E., Mungall, A. J., Naresh, R., Naska, T., Neder, L., Noble, M. S., Noss, A., O'Neill, B. P., Ostrom, Q. T., Palmer, C., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Pierson, C. R., Pihl, T., Protopopov, A., Radenbaugh, A., Ramirez, N. C., Rathmell, W. K., Ren, X., Roach, J., Robertson, A. G., Saksena, G., Schein, J. E., Schumacher, S. E., Seidman, J., Senecal, K., Seth, S., Shen, H., Shi, Y., Shih, J., Shimmel, K., Sicotte, H., Sifri, S., Silva, T., Simons, J. V., Singh, R., Skelly, T., Sloan, A. E., Sofia, H. J., Soloway, M. G., Song, X., Sougnez, C., Souza, C., Staugaitis, S. M., Sun, H., Sun, C., Tan, D., Tang, J., Tang, Y., Thorne, L., Trevisan, F. A., Triche, T., Van Den Berg, D. J., Veluvolu, U., Voet, D., Wan, Y., Wang, Z., Warnick, R., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Williams, F., Wise, L., Wolinsky, Y., Wu, J., Xu, A. W., Yang, L., Yang, L., Zack, T. I., Zenklusen, J. C., Zhang, J., Zhang, W., Zhang, J., Zmuda, E., Noushmehr, H., Iavarone, A. & Verhaak, R. G. W., Jan 28 2016, In: Cell. 164, 3, p. 550-563 14 p.

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

    Open Access
    1579 Scopus citations

  • NCR1 expression identifies canine natural killer cell subsets with phenotypic similarity to human natural killer cells

    Foltz, J. A., Somanchi, S. S., Yang, Y., Aquino-Lopez, A., Bishop, E. E. & Lee, D. A., Nov 23 2016, In: Frontiers in immunology. 7, NOV, 521.

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

    Open Access
    41 Scopus citations

  • NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence

    Manda, K. R., Tripathi, P., Hsi, A. C., Ning, J., Ruzinova, M. B., Liapis, H., Bailey, M., Zhang, H., Maher, C. A., Humphrey, P. A., Andriole, G. L., Ding, L., You, Z. & Chen, F., Jun 23 2016, In: Oncogene. 35, 25, p. 3282-3292 11 p.

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

    Open Access
    38 Scopus citations

  • NovoBreak: Local assembly for breakpoint detection in cancer genomes

    Chong, Z., Ruan, J., Gao, M., Zhou, W., Chen, T., Fan, X., Ding, L., Lee, A. Y., Boutros, P., Chen, J. & Chen, K., Dec 29 2016, In: Nature Methods. 14, 1, p. 65-67 3 p.

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

    71 Scopus citations

  • Protein-structure-guided discovery of functional mutations across 19 cancer types

    Niu, B., Scott, A. D., Sengupta, S., Bailey, M. H., Batra, P., Ning, J., Wyczalkowski, M. A., Liang, W. W., Zhang, Q., McLellan, M. D., Sun, S. Q., Tripathi, P., Lou, C., Ye, K., Jay Mashl, R., Wallis, J., Wendl, M. C., Chen, F. & Ding, L., Aug 1 2016, In: Nature Genetics. 48, 8, p. 827-837 11 p.

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

    Open Access
    109 Scopus citations

  • Proteogenomics connects somatic mutations to signalling in breast cancer

    Mertins, P., Mani, D. R., Ruggles, K. V., Gillette, M. A., Clauser, K. R., Wang, P., Wang, X., Qiao, J. W., Cao, S., Petralia, F., Kawaler, E., Mundt, F., Krug, K., Tu, Z., Lei, J. T., Gatza, M. L., Wilkerson, M., Perou, C. M., Yellapantula, V. & Huang, K. L. & 16 others, Lin, C., McLellan, M. D., Yan, P., Davies, S. R., Townsend, R. R., Skates, S. J., Wang, J., Zhang, B., Kinsinger, C. R., Mesri, M., Rodriguez, H., Ding, L., Paulovich, A. G., Fenyö, D., Ellis, M. J. & Carr, S. A., May 25 2016, In: Nature. 534, 7605, p. 55-62 8 p.

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

    Open Access
    1232 Scopus citations

  • Pseudonymous fame

    Wendl, M. C., Mar 25 2016, In: Science. 351, 6280, p. 1406 1 p.

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

    4 Scopus citations

  • Systematic discovery of complex insertions and deletions in human cancers

    Ye, K., Wang, J., Jayasinghe, R., Lameijer, E. W., McMichael, J. F., Ning, J., McLellan, M. D., Xie, M., Cao, S., Yellapantula, V., Huang, K. L., Scott, A., Foltz, S., Niu, B., Johnson, K. J., Moed, M., Slagboom, P. E., Chen, F., Wendl, M. C. & Ding, L., Jan 1 2016, In: Nature medicine. 22, 1, p. 97-104 8 p.

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

    Open Access
    83 Scopus citations

  • Targeted Next-Generation Sequencing Successfully Detects Causative Genes in Chinese Patients with Hereditary Hearing Loss

    Chen, S., Dong, C., Wang, Q., Zhong, Z., Qi, Y., Ke, X. & Liu, Y., Nov 2016, In: Genetic Testing and Molecular Biomarkers. 20, 11, p. 660-665 6 p.

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

    35 Scopus citations

  • The genomic landscape of core-binding factor acute myeloid leukemias

    Faber, Z. J., Chen, X., Gedman, A. L., Boggs, K., Cheng, J., Ma, J., Radtke, I., Chao, J. R., Walsh, M. P., Song, G., Andersson, A. K., Dang, J., Dong, L., Liu, Y., Huether, R., Cai, Z., Mulder, H., Wu, G., Edmonson, M. & Rusch, M. & 29 others, Qu, C., Li, Y., Vadodaria, B., Wang, J., Hedlund, E., Cao, X., Yergeau, D., Nakitandwe, J., Pounds, S. B., Shurtleff, S., Fulton, R. S., Fulton, L. L., Easton, J., Parganas, E., Pui, C. H., Rubnitz, J. E., Ding, L., Mardis, E. R., Wilson, R. K., Gruber, T. A., Mullighan, C. G., Schlenk, R. F., Paschka, P., Döhner, K., Döhner, H., Bullinger, L., Zhang, J., Klco, J. M. & Downing, J. R., Dec 1 2016, In: Nature Genetics. 48, 12, p. 1551-1556 6 p.

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

    Open Access
    222 Scopus citations

  • The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis

    Jones, K. B., Barrott, J. J., Xie, M., Haldar, M., Jin, H., Zhu, J. F., Monument, M. J., Mosbruger, T. L., Langer, E. M., Randall, R. L., Wilson, R. K., Cairns, B. R., Ding, L. & Capecchi, M. R., Sep 22 2016, In: Oncogene. 35, 38, p. 5021-5032 12 p.

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

    Open Access
    37 Scopus citations

  • Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

    Hoadley, K. A., Siegel, M. B., Kanchi, K. L., Miller, C. A., Ding, L., Zhao, W., He, X., Parker, J. S., Wendl, M. C., Fulton, R. S., Demeter, R. T., Wilson, R. K., Carey, L. A., Perou, C. M. & Mardis, E. R., Dec 2016, In: PLoS medicine. 13, 12, e1002174.

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

    Open Access
    85 Scopus citations

  • Visualizing tumor evolution with the fishplot package for R

    Miller, C. A., McMichael, J., Dang, H. X., Maher, C. A., Ding, L., Ley, T. J., Mardis, E. R. & Wilson, R. K., Nov 7 2016, In: BMC genomics. 17, 1, 880.

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

    Open Access
    129 Scopus citations
  • 2015

    A global reference for human genetic variation

    Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., 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. & 457 others, Marth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Boerwinkle, E., Doddapaneni, H., Han, Y., Korchina, V., Kovar, C., Lee, S., Muzny, D., Reid, J. G., Zhu, Y., Chang, Y., Feng, Q., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Lan, T., Li, G., Li, J., Li, Y., Liu, S., Liu, X., Lu, Y., Ma, X., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Xu, X., Yin, Y., Zhang, D., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Gupta, N., Gharani, N., Toji, L. H., Gerry, N. P., Resch, A. M., Barker, J., Clarke, L., Gil, L., Hunt, S. E., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Thormann, A., Toneva, I., Vaughan, B., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Fulton, L., 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., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Campbell, C. L., Kong, Y., Marcketta, A., Yu, F., Antunes, L., Bainbridge, M., Sabo, A., Huang, Z., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Alkan, C., Dal, E., Kahveci, F., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Stromberg, M., Ward, A. N., Wu, J., Zhang, M., Daly, M. J., DePristo, M. A., Handsaker, R. E., Banks, E., Bhatia, G., Del Angel, G., Genovese, G., Li, H., Kashin, S., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Yoon, S. C., Lihm, J., Makarov, V., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Rausch, T., Fritz, M. H., Stütz, A. M., Beal, K., Datta, A., Herrero, J., Ritchie, G. R. S., Zerbino, D., Sabeti, P. C., Shlyakhter, I., Schaffner, S. F., Vitti, J., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Cheetham, R. K., Cox, A., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Kenny, E. E., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Ding, L., Koboldt, D. C., Larson, D., Ye, K., Gravel, S., Swaroop, A., Chew, E., Lappalainen, T., Erlich, Y., Gymrek, M., Willems, T. F., Simpson, J. T., Shriver, M. D., Rosenfeld, J. A., Bustamante, C. D., Montgomery, S. B., De La Vega, F. M., Byrnes, J. K., Carroll, A. W., DeGorter, M. K., Lacroute, P., Maples, B. K., Martin, A. R., Moreno-Estrada, A., Shringarpure, S. S., Zakharia, F., Halperin, E., Baran, Y., Cerveira, E., Hwang, J., Malhotra, A., Plewczynski, D., Radew, K., Romanovitch, M., Zhang, C., Hyland, F. C. L., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Antaki, D., Gujral, M., Noor, A., 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., Devine, S. E., Kang, H. M., Kidd, J. M., Blackwell, T., Caron, S., Chen, W., Emery, S., Fritsche, L., Fuchsberger, C., Jun, G., Li, B., Lyons, R., Scheller, C., Sidore, C., Song, S., Sliwerska, E., Taliun, D., Tan, A., Welch, R., Wing, M. K., Zhan, X., Awadalla, P., Hodgkinson, A., Li, Y., Shi, X., Quitadamo, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Kretzschmar, W., Iqbal, Z., Mathieson, I., Menelaou, A., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Browning, S. R., Hormozdiari, F., Sudmant, P. H., Khurana, E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Colonna, V., Jostins, L., Walter, K., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Lee, D., Liu, J., Mu, X. J., Zhang, J., Zhang, Y., Hartl, C., Shakir, K., Degenhardt, J., Meiers, S., Raeder, B., Casale, F. P., Stegle, O., Lameijer, E. W., Hall, I., Bafna, V., Michaelson, J., Gardner, E. J., Mills, R. E., Dayama, G., Chen, K., Fan, X., Chong, Z., Chen, T., Chaisson, M. J., Huddleston, J., Malig, M., Nelson, B. J., Parrish, N. F., Blackburne, B., Lindsay, S. J., Ning, Z., Zhang, Y., Lam, H., Sisu, C., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Yu, J., Li, W., Habegger, L., Yu, H., Cunningham, F., Dunham, I., Lage, K., Jespersen, J. B., Horn, H., Kim, D., Desalle, R., Narechania, A., Sayres, M. A. W., Mendez, F. L., Poznik, G. D., Underhill, P. A., Mittelman, D., Banerjee, R., Cerezo, M., Fitzgerald, T. W., Louzada, S., Massaia, A., Yang, F., Kalra, D., Hale, W., Dan, X., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Cai, Z., Gao, Y., Chu, J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Mathias, R. A., Hennis, A., Watson, H., McKenzie, C., Qadri, F., LaRocque, R., Deng, X., Asogun, D., Folarin, O., Happi, C., Omoniwa, O., Stremlau, M., Tariyal, R., Jallow, M., Joof, F. S., Corrah, T., Rockett, K., Kwiatkowski, D., Kooner, J., Hien, T. T., Dunstan, S. J., ThuyHang, N., Fonnie, R., Garry, R., Kanneh, L., Moses, L., Schieffelin, J., Grant, D. S., Gallo, C., Poletti, G., Saleheen, D., Rasheed, A., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Vaydylevich, Y., Duncanson, A., Dunn, M. & Schloss, J. A., Sep 30 2015, In: Nature. 526, 7571, p. 68-74 7 p.

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

    Open Access
    11584 Scopus citations

  • An integrated map of structural variation in 2,504 human genomes

    Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M. H. Y., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Casale, F. P., Chen, J., Hormozdiari, F., Dayama, G., Chen, K. & Malig, M. & 62 others, Chaisson, M. J. P., Walter, K., Meiers, S., Kashin, S., Garrison, E., Auton, A., Lam, H. Y. K., Mu, X. J., Alkan, C., Antaki, D., Bae, T., Cerveira, E., Chines, P., Chong, Z., Clarke, L., Dal, E., Ding, L., Emery, S., Fan, X., Gujral, M., Kahveci, F., Kidd, J. M., Kong, Y., Lameijer, E. W., McCarthy, S., Flicek, P., Gibbs, R. A., Marth, G., Mason, C. E., Menelaou, A., Muzny, D. M., Nelson, B. J., Noor, A., Parrish, N. F., Pendleton, M., Quitadamo, A., Raeder, B., Schadt, E. E., Romanovitch, M., Schlattl, A., Sebra, R., Shabalin, A. A., Untergasser, A., Walker, J. A., Wang, M., Yu, F., Zhang, C., Zhang, J., Zheng-Bradley, X., Zhou, W., Zichner, T., Sebat, J., Batzer, M. A., McCarroll, S. A., Mills, R. E., Gerstein, M. B., Bashir, A., Stegle, O., Devine, S. E., Lee, C., Eichler, E. E. & Korbel, J. O., Sep 30 2015, In: Nature. 526, 7571, p. 75-81 7 p.

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

    Open Access
    1588 Scopus citations

  • Association of somatic mutations of ADAMTS genes with chemotherapy sensitivity and survival in high-grade serous ovarian carcinoma

    Liu, Y., Yasukawa, M., Chen, K., Hu, L., Broaddus, R. R., Ding, L., Mardis, E. R., Spellman, P., Levine, D. A., Mills, G. B., Shmulevich, I., Sood, A. K. & Zhang, W., Jul 1 2015, In: JAMA oncology. 1, 4, p. 486-494 9 p.

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

    Open Access
    36 Scopus citations

  • Characteristics of de novo structural changes in the human genome

    Genome of the Netherlands Consortium, Jun 1 2015, In: Genome research. 25, 6, p. 792-801 10 p.

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

    Open Access
    100 Scopus citations

  • Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

    Ciriello, G., Gatza, M. L., Beck, A. H., Wilkerson, M. D., Rhie, S. K., Pastore, A., Zhang, H., McLellan, M., Yau, C., Kandoth, C., Bowlby, R., Shen, H., Hayat, S., Fieldhouse, R., Lester, S. C., Tse, G. M. K., Factor, R. E., Collins, L. C., Allison, K. H. & Chen, Y. Y. & 119 others, Jensen, K., Johnson, N. B., Oesterreich, S., Mills, G. B., Cherniack, A. D., Robertson, G., Benz, C., Sander, C., Laird, P. W., Hoadley, K. A., King, T. A., Akbani, R., Auman, J. T., Balasundaram, M., Balu, S., Barr, T., Benz, S., Berrios, M., Beroukhim, R., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Brooks, D., Chin, L., Cho, J., Chudamani, S., Davidsen, T., Demchok, J. A., Dennison, J. B., Ding, L., Felau, I., Ferguson, M. L., Frazer, S., Gabriel, S. B., Gao, J. J., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Getz, G., Gibson, W. J., Hayes, D. N., Heiman, D. I., Holbrook, A., Holt, R. A., Hoyle, A. P., Hu, H., Huang, M., Hutter, C. M., Hwang, E. S., Jefferys, S. R., Jones, S. J. M., Ju, Z., Kim, J., Lai, P. H., Lawrence, M. S., Leraas, K. M., Lichtenberg, T. M., Lin, P., Ling, S., Liu, J., Liu, W., Lolla, L., Lu, Y., Ma, Y., Maglinte, D. T., Mardis, E., Marks, J., Marra, M. A., McAllister, C., Meng, S., Meyerson, M., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Naresh, R., Noble, M. S., Olopade, O., Parker, J. S., Pihl, T., Saksena, G., Schumacher, S. E., Shaw, K. R. M., Ramirez, N. C., Rathmell, W. K., Roach, J., Robertson, A. G., Schein, J. E., Schultz, N., Sheth, M., Shi, Y., Shih, J., Shelley, C. S., Shriver, C., Simons, J. V., Sofia, H. J., Soloway, M. G., Sougnez, C., Sun, C., Tarnuzzer, R., Tiezzi, D. G., Van Den Berg, D. J., Voet, D., Wan, Y., Wang, Z., Weinstein, J. N., Weisenberger, D. J., Wilson, R., Wise, L., Wiznerowicz, M., Wu, J., Wu, Y., Yang, L., Zack, T. I., Zenklusen, J. C., Zhang, J., Zmuda, E. & Perou, C. M., Oct 8 2015, In: Cell. 163, 2, p. 506-519 14 p.

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

    Open Access
    1415 Scopus citations

  • Current theoretical models fail to predict the topological complexity of the human genome

    Arsuaga, J., Jayasinghe, R. G., Scharein, R. G., Segal, M. R., Stolz, R. H. & Vazquez, M., Aug 21 2015, In: Frontiers in Molecular Biosciences. 2, AUG, 48.

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

    Open Access
    14 Scopus citations

  • Genome Modeling System: A Knowledge Management Platform for Genomics

    Griffith, M., Griffith, O. L., Smith, S. M., Ramu, A., Callaway, M. B., Brummett, A. M., Kiwala, M. J., Coffman, A. C., Regier, A. A., Oberkfell, B. J., Sanderson, G. E., Mooney, T. P., Nutter, N. G., Belter, E. A., Du, F., Long, R. L., Abbott, T. E., Ferguson, I. T., Morton, D. L. & Burnett, M. M. & 44 others, Weible, J. V., Peck, J. B., Dukes, A., McMichael, J. F., Lolofie, J. T., Derickson, B. R., Hundal, J., Skidmore, Z. L., Ainscough, B. J., Dees, N. D., Schierding, W. S., Kandoth, C., Kim, K. H., Lu, C., Harris, C. C., Maher, N., Maher, C. A., Magrini, V. J., Abbott, B. S., Chen, K., Clark, E., Das, I., Fan, X., Hawkins, A. E., Hepler, T. G., Wylie, T. N., Leonard, S. M., Schroeder, W. E., Shi, X., Carmichael, L. K., Weil, M. R., Wohlstadter, R. W., Stiehr, G., McLellan, M. D., Pohl, C. S., Miller, C. A., Koboldt, D. C., Walker, J. R., Eldred, J. M., Larson, D. E., Dooling, D. J., Ding, L., Mardis, E. R. & Wilson, R. K., Jul 1 2015, In: PLoS computational biology. 11, 7, e1004274.

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

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    65 Scopus citations

  • Germline mutations in predisposition genes in pediatric cancer

    Zhang, J., Walsh, M. F., Wu, G., Edmonson, M. N., Gruber, T. A., Easton, J., Hedges, D., Ma, X., Zhou, X., Yergeau, D. A., Wilkinson, M. R., Vadodaria, B., Chen, X., McGee, R. B., Dowell, S. H., Nuccio, R., Quinn, E., Shurtleff, S. A., Rusch, M. & Patel, A. & 12 others, Becksfort, J. B., Wang, S., Weaver, M. S., Ding, L., Mardis, E. R., Wilson, R. K., Gajjar, A., Ellison, D. W., Pappo, A. S., Pui, C. H., Nichols, K. E. & Downing, J. R., Dec 10 2015, In: New England Journal of Medicine. 373, 24, p. 2336-2346 11 p.

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

    Open Access
    945 Scopus citations

  • Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

    Reyes, A., Blanton, L. V., Cao, S., Zhao, G., Manary, M., Trehan, I., Smith, M. I., Wang, D., Virgin, S., Rohwer, F. & Gordon, J. I., Sep 22 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 38, p. 11941-11946 6 p.

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

    Open Access
    231 Scopus citations

  • Optimizing Cancer Genome Sequencing and Analysis

    Griffith, M., Miller, C. A., Griffith, O. L., Krysiak, K., Skidmore, Z. L., Ramu, A., Walker, J. R., Dang, H. X., Trani, L., Larson, D. E., Demeter, R. T., Wendl, M. C., McMichael, J. F., Austin, R. E., Magrini, V., McGrath, S. D., Ly, A., Kulkarni, S., Cordes, M. G. & Fronick, C. C. & 7 others, Fulton, R. S., Maher, C. A., Ding, L., Klco, J. M., Mardis, E. R., Ley, T. J. & Wilson, R. K., Sep 23 2015, In: Cell Systems. 1, 3, p. 210-223 14 p., 35.

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

    Open Access
    145 Scopus citations

  • Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

    Leiserson, M. D. M., Vandin, F., Wu, H. T., Dobson, J. R., Eldridge, J. V., Thomas, J. L., Papoutsaki, A., Kim, Y., Niu, B., McLellan, M., Lawrence, M. S., Gonzalez-Perez, A., Tamborero, D., Cheng, Y., Ryslik, G. A., Lopez-Bigas, N., Getz, G., Ding, L. & Raphael, B. J., Jan 1 2015, In: Nature Genetics. 47, 2, p. 106-114 9 p.

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

    Open Access
    670 Scopus citations

  • Patterns and functional implications of rare germline variants across 12 cancer types

    Lu, C., Xie, M., Wendl, M. C., Wang, J., McLellan, M. D., Leiserson, M. D. M., Huang, K. L., Wyczalkowski, M. A., Jayasinghe, R., Banerjee, T., Ning, J., Tripathi, P., Zhang, Q., Niu, B., Ye, K., Schmidt, H. K., Fulton, R. S., McMichael, J. F., Batra, P. & Kandoth, C. & 23 others, Bharadwaj, M., Koboldt, D. C., Miller, C. A., Kanchi, K. L., Eldred, J. M., Larson, D. E., Welch, J. S., You, M., Ozenberger, B. A., Govindan, R., Walter, M. J., Ellis, M. J., Mardis, E. R., Graubert, T. A., Dipersio, J. F., Ley, T. J., Wilson, R. K., Goodfellow, P. J., Raphael, B. J., Chen, F., Johnson, K. J., Parvin, J. D. & Ding, L., Dec 22 2015, In: Nature communications. 6, 10086.

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

    Open Access
    231 Scopus citations

  • Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia

    Wong, T. N., Ramsingh, G., Young, A. L., Miller, C. A., Touma, W., Welch, J. S., Lamprecht, T. L., Shen, D., Hundal, J., Fulton, R. S., Heath, S., Baty, J. D., Klco, J. M., Ding, L., Mardis, E. R., Westervelt, P., Dipersio, J. F., Walter, M. J., Graubert, T. A. & Ley, T. J. & 3 others, Druley, T. E., Link, D. C. & Wilson, R. K., Feb 26 2015, In: Nature. 518, 7540, p. 552-555 4 p.

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

    Open Access
    689 Scopus citations

  • Species-specific transmission of novel picornaviruses in lemurs

    Lim, E. S., Deem, S. L., Porton, I. J., Cao, S. & Wang, D., 2015, In: Journal of virology. 89, 7, p. 4002-4010 9 p.

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

    Open Access
    8 Scopus citations

  • The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

    Muñoz, J. F., Gauthier, G. M., Desjardins, C. A., Gallo, J. E., Holder, J., Sullivan, T. D., Marty, A. J., Carmen, J. C., Chen, Z., Ding, L., Gujja, S., Magrini, V., Misas, E., Mitreva, M., Priest, M., Saif, S., Whiston, E. A., Young, S., Zeng, Q. & Goldman, W. E. & 6 others, Mardis, E. R., Taylor, J. W., McEwen, J. G., Clay, O. K., Klein, B. S. & Cuomo, C. A., 2015, In: PLoS genetics. 11, 10, e1005493.

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

    Open Access
    56 Scopus citations

  • The genomic landscape of childhood and adolescent melanoma

    Lu, C., Zhang, J., Nagahawatte, P., Easton, J., Lee, S., Liu, Z., Ding, L., Wyczalkowski, M. A., Valentine, M., Navid, F., Mulder, H., Tatevossian, R. G., Dalton, J., Davenport, J., Yin, Z., Edmonson, M., Rusch, M., Wu, G., Li, Y. & Parker, M. & 14 others, Hedlund, E., Shurtleff, S., Raimondi, S., Bhavin, V., Donald, Y., Mardis, E. R., Wilson, R. K., Evans, W. E., Ellison, D. W., Pounds, S., Dyer, M., Downing, J. R., Pappo, A. & Bahrami, A., Mar 12 2015, In: Journal of Investigative Dermatology. 135, 3, p. 816-823 8 p.

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

    Open Access
    149 Scopus citations

  • The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias

    Andersson, A. K., Ma, J., Wang, J., Chen, X., Gedman, A. L., Dang, J., Nakitandwe, J., Holmfeldt, L., Parker, M., Easton, J., Huether, R., Kriwacki, R., Rusch, M., Wu, G., Li, Y., Mulder, H., Raimondi, S., Pounds, S., Kang, G. & Shi, L. & 30 others, Becksfort, J., Gupta, P., Payne-Turner, D., Vadodaria, B., Boggs, K., Yergeau, D., Manne, J., Song, G., Edmonson, M., Nagahawatte, P., Wei, L., Cheng, C., Pei, D., Sutton, R., Venn, N. C., Chetcuti, A., Rush, A., Catchpoole, D., Heldrup, J., Fioretos, T., Lu, C., Ding, L., Pui, C. H., Shurtleff, S., Mullighan, C. G., Mardis, E. R., Wilson, R. K., Gruber, T. A., Zhang, J. & Downing, J. R., Apr 28 2015, In: Nature Genetics. 47, 4, p. 330-337 8 p.

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

    Open Access
    397 Scopus citations

  • U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing

    Okeyo-Owuor, T., White, B. S., Chatrikhi, R., Mohan, D. R., Kim, S., Griffith, M., Ding, L., Ketkar-Kulkarni, S., Hundal, J., Laird, K. M., Kielkopf, C. L., Ley, T. J., Walter, M. J. & Graubert, T. A., Apr 15 2015, In: Leukemia. 29, 4, p. 909-917 9 p.

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

    Open Access
    99 Scopus citations

  • Whole exome sequencing identified MCM2 as a novel causative gene for autosomal dominant nonsyndromic deafness in a Chinese family

    Gao, J., Wang, Q., Dong, C., Chen, S., Qi, Y. & Liu, Y., Jul 21 2015, In: PloS one. 10, 7, e0133522.

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

    Open Access
    32 Scopus citations
  • 2014

    Activation of NFAT signaling establishes a tumorigenic microenvironment through cell autonomous and non-cell autonomous mechanisms

    Tripathi, P., Wang, Y., Coussens, M., Manda, K. R., Casey, A. M., Lin, C., Poyo, E., Pfeifer, J. D., Basappa, N., Bates, C. M., Ma, L., Zhang, H., Pan, M., Ding, L. & Chen, F., Apr 3 2014, In: Oncogene. 33, 14, p. 1840-1849 10 p.

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

    Open Access
    29 Scopus citations

  • Age-related mutations associated with clonal hematopoietic expansion and malignancies

    Xie, M., Lu, C., Wang, J., McLellan, M. D., Johnson, K. J., Wendl, M. C., McMichael, J. F., Schmidt, H. K., Yellapantula, V., Miller, C. A., Ozenberger, B. A., Welch, J. S., Link, D. C., Walter, M. J., Mardis, E. R., Dipersio, J. F., Chen, F., Wilson, R. K., Ley, T. J. & Ding, L., Dec 1 2014, In: Nature medicine. 20, 12, p. 1472-1478 7 p.

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

    Open Access
    1479 Scopus citations

  • Analysis of the clinical audiological characteristics in 92 Chinese Alport syndrome cases

    Chen, L., Xue, J., Zhang, Y., Wang, F., Chen, S., Duan, J., Liu, Y. & Ding, J., Nov 1 2014, In: Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery. 49, 11, p. 902-907 6 p.

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

    3 Scopus citations

  • An outbreak of acute febrile illness caused by sandfly fever sicilian virus in the Afar Region of Ethiopia, 2011

    Woyessa, A. B., Omballa, V., Wang, D., Lambert, A., Waiboci, L., Ayele, W., Ahmed, A., Abera, N. A., Cao, S., Ochieng, M., Montgomery, J. M., Jima, D. & Fields, B., Dec 1 2014, In: American Journal of Tropical Medicine and Hygiene. 91, 6, p. 1250-1253 4 p.

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

    Open Access
    20 Scopus citations

  • C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma

    Parker, M., Mohankumar, K. M., Punchihewa, C., Weinlich, R., Dalton, J. D., Li, Y., Lee, R., Tatevossian, R. G., Phoenix, T. N., Thiruvenkatam, R., White, E., Tang, B., Orisme, W., Gupta, K., Rusch, M., Chen, X., Li, Y., Nagahawhatte, P., Hedlund, E. & Finkelstein, D. & 29 others, Wu, G., Shurtleff, S., Easton, J., Boggs, K., Yergeau, D., Vadodaria, B., Mulder, H. L., Becksford, J., Gupta, P., Huether, R., Ma, J., Song, G., Gajjar, A., Merchant, T., Boop, F., Smith, A. A., Ding, L., Lu, C., Ochoa, K., Zhao, D., Fulton, R. S., Fulton, L. L., Mardis, E. R., Wilson, R. K., Downing, J. R., Green, D. R., Zhang, J., Ellison, D. W. & Gilbertson, R. J., 2014, In: Nature. 506, 7489, p. 451-455 5 p.

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

    Open Access
    548 Scopus citations

  • Caspase-9 is required for normal hematopoietic development and protection from alkylator-induced DNA damage in mice

    Lu, E. P., McLellan, M., Ding, L., Fulton, R., Mardis, E. R., Wilson, R. K., Miller, C. A., Westervelt, P., DiPersio, J. F., Link, D. C., Walter, M. J., Ley, T. J. & Graubert, T. A., Dec 18 2014, In: Blood. 124, 26, p. 3887-3895 9 p.

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

    Open Access
    22 Scopus citations

  • Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma

    Liu, Y., Patel, L., Mills, G. B., Lu, K. H., Sood, A. K., Ding, L., Kucherlapati, R., Mardis, E. R., Levine, D. A., Shmulevich, I., Broaddus, R. R. & Zhang, W., Sep 1 2014, In: Journal of the National Cancer Institute. 106, 9

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

    Open Access
    178 Scopus citations

  • 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
    108 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
    4984 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

    Open Access
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  • 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
    16 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
    146 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
    397 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. 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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. 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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. 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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

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    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
    242 Scopus citations