Li Ding

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Li Ding

David English Smith Professorship in Medicine #3, Professor of Medicine, Professor of Genetics

 https://orcid.org/0000-0003-1517-2975

    Willing to Mentor

    Available to Mentor:

    PhD/MSTP Students

    • 183524
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    1996 …2024

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    • 2016

      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
      709 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
      1504 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

      69 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
      105 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
      1182 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

    • 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
      209 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

      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
      1513 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

    • 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
      1341 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
      890 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
      652 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
      219 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
      651 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
      141 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
      382 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
      95 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
      1419 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
      518 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
      104 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

    • 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
      4774 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
      4134 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
      379 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

      Open Access
      59 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
      234 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
      288 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
      537 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

      Open Access
      1127 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
      1077 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
      543 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
      337 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
      1099 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
      798 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
      311 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
      65 Scopus citations