Section of Computational Biology

Search results

  • 2017

    Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

    CONSORTIA, Mar 14 2017, In: Cell Reports. 18, 11, p. 2780-2794 15 p.

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

    Open Access
    370 Scopus citations

  • MIRMMR: Binary classification of microsatellite instability using methylation and mutations

    Foltz, S. M., Liang, W. W., Xie, M. & Ding, L., Dec 1 2017, In: Bioinformatics. 33, 23, p. 3799-3801 3 p.

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

    Open Access
    18 Scopus citations

  • Precancerous clonal expansion: A new therapeutic target?

    Ding, L. & Chen, F., May 10 2017, In: Journal of Clinical Oncology. 35, 14, p. 1503-1505 3 p.

    Research output: Contribution to journal › Editorial

  • Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

    Huang, K. L., Li, S., Mertins, P., Cao, S., Gunawardena, H. P., Ruggles, K. V., Mani, D. R., Clauser, K. R., Tanioka, M., Usary, J., Kavuri, S. M., Xie, L., Yoon, C., Qiao, J. W., Wrobel, J., Wyczalkowski, M. A., Erdmann-Gilmore, P., Snider, J. E., Hoog, J. & Singh, P. & 25 others, Niu, B., Guo, Z., Sun, S. Q., Sanati, S., Kawaler, E., Wang, X., Scott, A., Ye, K., McLellan, M. D., Wendl, M. C., Malovannaya, A., Held, J. M., Gillette, M. A., Fenyö, D., Kinsinger, C. R., Mesri, M., Rodriguez, H., Davies, S. R., Perou, C. M., Ma, C., Reid Townsend, R., Chen, X., Carr, S. A., Ellis, M. J. & Ding, L., Mar 28 2017, In: Nature communications. 8, 14864.

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

    Open Access
    104 Scopus citations
  • 2016

    An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer

    Ruggles, K. V., Tang, Z., Wang, X., Grover, H., Askenazi, M., Teubl, J., Cao, S., McLellan, M. D., Clauser, K. R., Tabb, D. L., Mertins, P., Slebos, R., Erdmann-Gilmore, P., Li, S., Gunawardena, H. P., Xie, L., Liu, T., Zhou, J. Y., Sun, S. & Hoadley, K. A. & 18 others, Perou, C. M., Chen, X., Davies, S. R., Maher, C. A., Kinsinger, C. R., Rodland, K. D., Zhang, H., Zhang, Z., Ding, L., Townsend, R. R., Rodriguez, H., Chan, D., Smith, R. D., Liebler, D. C., Carr, S. A., Payne, S., Ellis, M. J. & Fenyo, D., Mar 2016, In: Molecular and Cellular Proteomics. 15, 3, p. 1060-1071 12 p.

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

    Open Access
    92 Scopus citations

  • Deregulation of DUX4 and ERG in acute lymphoblastic leukemia

    for the St. Jude Children's Research Hospital?Washington University Pediatric Cancer Genome Project, Dec 1 2016, In: Nature Genetics. 48, 12, p. 1481-1489 9 p.

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

    Open Access
    228 Scopus citations

  • Divergent viral presentation among human tumors and adjacent normal tissues

    Cao, S., Wendl, M. C., Wyczalkowski, M. A., Wylie, K., Ye, K., Jayasinghe, R., Xie, M., Wu, S., Niu, B., Grubb, R., Johnson, K. J., Gay, H., Chen, K., Rader, J. S., Dipersio, J. F., Chen, F. & Ding, L., Jun 24 2016, In: Scientific reports. 6, 28294.

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

    Open Access
    56 Scopus citations

  • DNA defects, epigenetics, and gene expression in cancer-adjacent breast: A study from the cancer genome atlas

    Troester, M. A., Hoadley, K. A., D’arcy, M., Cherniack, A. D., Stewart, C., Koboldt, D. C., Robertson, A. G., Mahurkar, S., Shen, H., Wilkerson, M. D., Sandhu, R., Johnson, N. B., Allison, K. H., Beck, A. H., Yau, C., Bowen, J., Sheth, M., Hwang, E. S., Perou, C. M. & Laird, P. W. & 2 others, Ding, L. & Benz, C. C., Dec 14 2016, In: npj Breast Cancer. 2, 1, 16007.

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

    Open Access
    29 Scopus citations

  • Inactivation of RASA1 promotes melanoma tumorigenesis via R-Ras activation

    Sung, H., Kanchi, K. L., Wang, X., Hill, K. S., Messina, J. L., Lee, J. H., Kim, Y., Dees, N. D., Ding, L., Teer, J. K., Yang, S., Sarnaik, A. A., Sondak, V. K., Mulé, J. J., Wilson, R. K., Weber, J. S. & Kim, M., Apr 26 2016, In: Oncotarget. 7, 17, p. 23885-23896 12 p.

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

    Open Access
    21 Scopus citations

  • Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

    the CPTAC Investigators, Jul 28 2016, In: Cell. 166, 3, p. 755-765 11 p.

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

    Open Access
    702 Scopus citations

  • 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
    1488 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
    37 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

    68 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
    104 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
    1170 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

    3 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

    31 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
    206 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
    35 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
    81 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
    121 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
    10769 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
    1500 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
    95 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
    1334 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
    13 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

    Open Access
    63 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
    874 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
    220 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
    143 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
    649 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
    218 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
    647 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
    7 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
    52 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
    140 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
    380 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
    94 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
    29 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
    1408 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
    514 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
    21 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
    172 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
    102 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
    62 Scopus citations