Ken Chen

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Ken Chen

Professor

 https://orcid.org/0000-0003-4013-5279

    • 6767 Bertner Ave, Mitchell Basic Science Research Building

      77030 Houston

      United States

    Calculated based on number of publications stored in Pure and citations from Scopus
    20022024

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    • 2004

      Automatic recognition of pitch movements using multilayer perception and time-delay recursive neural network

      Kim, S. S., Hasegawa-Johnson, M. & Chen, K., Jul 2004, In: IEEE Signal Processing Letters. 11, 7, p. 645-648 4 p.

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

      7 Scopus citations
    • 2005

      Simultaneous recognition of words and prosody in the Boston University Radio Speech Corpus

      Hasegawa-Johnson, M., Chen, K., Cole, J., Borys, S., Kim, S. S., Cohen, A., Zhang, T., Choi, J. Y., Kim, H., Yoon, T. & Chavarria, S., Jul 2005, In: Speech Communication. 46, 3-4, p. 418-439 22 p.

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

      40 Scopus citations
    • 2006

      Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain

      Hou, T., Chen, K., McLaughlin, W. A., Lu, B. & Wang, W., Jan 2006, In: PLoS computational biology. 2, 1, p. 46-55 10 p.

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

      146 Scopus citations

    • Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis

      Hou, T., McLaughlin, W., Lu, B., Chen, K. & Wang, W., Jan 2006, In: Journal of Proteome Research. 5, 1, p. 32-43 12 p.

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

      67 Scopus citations

    • Prosody dependent speech recognition on radio news corpus of American English

      Chen, K., Hasegawa-Johnson, M., Cohen, A., Borys, S., Kim, S. S., Cole, J. & Choi, J. Y., Jan 2006, In: IEEE Transactions on Audio, Speech and Language Processing. 14, 1, p. 232-244 13 p.

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

      44 Scopus citations
    • 2007

      On the detection of functionally coherent groups of protein domains with an extension to protein annotation

      McLaughlin, W. A., Chen, K., Hou, T. & Wang, W., Oct 16 2007, In: BMC bioinformatics. 8, 390.

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

      4 Scopus citations

    • PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data

      Chen, K., McLellan, M. D., Ding, L., Wendl, M. C., Kasai, Y., Wilson, R. K. & Mardis, E. R., May 2007, In: Genome research. 17, 5, p. 659-666 8 p.

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

      69 Scopus citations
    • 2008

      Comprehensive genomic characterization defines human glioblastoma genes and core pathways

      McLendon, R., Friedman, A., Bigner, D., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Mikkelsen, T., Lehman, N., Aldape, K., Yung, W. K. A., Bogler, O., Weinstein, J. N., VandenBerg, S., Berger, M., Prados, M., Muzny, D., Morgan, M., Scherer, S., Sabo, A., & 211 othersNazareth, L., Lewis, L., Hall, O., Zhu, Y., Ren, Y., Alvi, O., Yao, J., Hawes, A., Jhangiani, S., Fowler, G., San Lucas, A., Kovar, C., Cree, A., Dinh, H., Santibanez, J., Joshi, V., Gonzalez-Garay, M. L., Miller, C. A., Milosavljevic, A., Donehower, L., Wheeler, D. A., Gibbs, R. A., Cibulskis, K., Sougnez, C., Fennell, T., Mahan, S., Wilkinson, J., Ziaugra, L., Onofrio, R., Bloom, T., Nicol, R., Ardlie, K., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., McLellan, M. D., Wallis, J., Larson, D. E., Shi, X., Abbott, R., Fulton, L., Chen, K., Koboldt, D. C., Wendl, M. C., Meyer, R., Tang, Y., Lin, L., Osborne, J. R., Dunford-Shore, B. H., Miner, T. L., Delehaunty, K., Markovic, C., Swift, G., Courtney, W., Pohl, C., Abbott, S., Hawkins, A., Leong, S., Haipek, C., Schmidt, H., Wiechert, M., Vickery, T., Scott, S., Dooling, D. J., Chinwalla, A., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Getz, G., Winckler, W., Verhaak, R. G. W., Lawrence, M. S., O'Kelly, M., Robinson, J., Alexe, G., Beroukhim, R., Carter, S., Chiang, D., Gould, J., Gupta, S., Korn, J., Mermel, C., Mesirov, J., Monti, S., Nguyen, H., Parkin, M., Reich, M., Stransky, N., Weir, B. A., Garraway, L., Golub, T., Meyerson, M., Chin, L., Protopopov, A., Zhang, J., Perna, I., Aronson, S., Sathiamoorthy, N., Ren, G., Yao, J., Wiedemeyer, W. R., Kim, H., Sek, W. K., Xiao, Y., Kohane, I. S., Seidman, J., Park, P. J., Kucherlapati, R., Laird, P. W., Cope, L., Herman, J. G., Weisenberger, D. J., Pan, F., Van Den Berg, D., Van Neste, L., Joo, M. Y., Schuebel, K. E., Baylin, S. B., Absher, D. M., Li, J. Z., Southwick, A., Brady, S., Aggarwal, A., Chung, T., Sherlock, G., Brooks, J. D., Myers, R. M., Spellman, P. T., Purdom, E., Jakkula, L. R., Lapuk, A. V., Marr, H., Dorton, S., Yoon, G. C., Han, J., Ray, A., Wang, V., Durinck, S., Robinson, M., Wang, N. J., Vranizan, K., Peng, V., Van Name, E., Fontenay, G. V., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Brennan, C., Socci, N. D., Olshen, A., Taylor, B. S., Lash, A., Schultz, N., Reva, B., Antipin, Y., Stukalov, A., Gross, B., Cerami, E., Wei, Q. W., Qin, L. X., Seshan, V. E., Villafania, L., Cavatore, M., Borsu, L., Viale, A., Gerald, W., Sander, C., Ladanyi, M., Perou, C. M., Hayes, D. N., Topal, M. D., Hoadley, K. A., Qi, Y., Balu, S., Shi, Y., Wu, J., Penny, R., Bittner, M., Shelton, T., Lenkiewicz, E., Morris, S., Beasley, D., Sanders, S., Kahn, A., Sfeir, R., Chen, J., Nassau, D., Feng, L., Hickey, E., Barker, A., Gerhard, D. S., Vockley, J., Compton, C., Vaught, J., Fielding, P., Ferguson, M. L., Schaefer, C., Zhang, J., Madhavan, S., Buetow, K. H., Collins, F., Good, P., Guyer, M., Ozenberger, B., Peterson, J. & Thomson, E., Oct 23 2008, In: Nature. 455, 7216, p. 1061-1068 8 p.

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

      6171 Scopus citations

    • DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

      Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D., Dunford-Shore, B. H., McGrath, S., Hickenbotham, M., Cook, L., Abbott, R., Larson, D. E., Koboldt, D. C., Pohl, C., Smith, S., Hawkins, A., Abbott, S., Locke, D., Hillier, L. W., & 28 othersMiner, T., Fulton, L., Magrini, V., Wylie, T., Glasscock, J., Conyers, J., Sander, N., Shi, X., Osborne, J. R., Minx, P., Gordon, D., Chinwalla, A., Zhao, Y., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M., Baty, J., Ivanovich, J., Heath, S., Shannon, W. D., Nagarajan, R., Walter, M. J., Link, D. C., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., Nov 6 2008, In: Nature. 456, 7218, p. 66-72 7 p.

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

      1048 Scopus citations

    • Somatic mutations affect key pathways in lung adenocarcinoma

      Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., Fulton, L., Fulton, R. S., Zhang, Q., Wendl, M. C., Lawrence, M. S., Larson, D. E., Chen, K., Dooling, D. J., Sabo, A., Hawes, A. C., & 70 othersShen, H., Jhangiani, S. N., Lewis, L. R., Hall, O., Zhu, Y., Mathew, T., Ren, Y., Yao, J., Scherer, S. E., Clerc, K., Metcalf, G. A., Ng, B., Milosavljevic, A., Gonzalez-Garay, M. L., Osborne, J. R., Meyer, R., Shi, X., Tang, Y., Koboldt, D. C., Lin, L., Abbott, R., Miner, T. L., Pohl, C., Fewell, G., Haipek, C., Schmidt, H., Dunford-Shore, B. H., Kraja, A., Crosby, S. D., Sawyer, C. S., Vickery, T., Sander, S., Robinson, J., Winckler, W., Baldwin, J., Chirieac, L. R., Dutt, A., Fennell, T., Hanna, M., Johnson, B. E., Onofrio, R. C., Thomas, R. K., Tonon, G., Weir, B. A., Zhao, X., Ziaugra, L., Zody, M. C., Giordano, T., Orringer, M. B., Roth, J. A., Spitz, M. R., Wistuba, I. I., Ozenberger, B., Good, P. J., Chang, A. C., Beer, D. G., Watson, M. A., Ladanyi, M., Broderick, S., Yoshizawa, A., Travis, W. D., Pao, W., Province, M. A., Weinstock, G. M., Varmus, H. E., Gabriel, S. B., Lander, E. S., Gibbs, R. A., Meyerson, M. & Wilson, R. K., Oct 23 2008, In: Nature. 455, 7216, p. 1069-1075 7 p.

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

      2272 Scopus citations
    • 2009

      BreakDancer: An algorithm for high-resolution mapping of genomic structural variation

      Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., Shi, X., Fulton, R. S., Ley, T. J., Wilson, R. K., Ding, L. & Mardis, E. R., 2009, In: Nature Methods. 6, 9, p. 677-681 5 p.

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

      Open Access
      1109 Scopus citations

    • CMDS: A population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

      Zhang, Q., Ding, L., Larson, D. E., Koboldt, D. C., McLellan, M. D., Chen, K., Shi, X., Kraja, A., Mardis, E. R., Wilson, R. K., Borecki, I. B. & Province, M. A., Dec 23 2009, In: Bioinformatics. 26, 4, p. 464-469 6 p.

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

      54 Scopus citations

    • Recurring mutations found by sequencing an acute myeloid leukemia genome

      Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Locke, D. P., Magrini, V. J., Abbott, R. M., Vickery, T. L., Reed, J. S., Robinson, J. S., Wylie, T., Smith, S. M., Carmichael, L., & 38 othersEldred, J. M., Harris, C. C., Walker, J., Peck, J. B., Du, F., Dukes, A. F., Sanderson, G. E., Brummett, A. M., Clark, E., McMichael, J. F., Meyer, R. J., Schindler, J. K., Pohl, C. S., Wallis, J. W., Shi, X., Lin, L., Schmidt, H., Tang, Y., Haipek, C., Wiechert, M. E., Ivy, J. V., Kalicki, J., Elliott, G., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M. A., Baty, J., Heath, S., Shannon, W. D., Nagarajan, R., Link, D. C., Walter, M. J., Graubert, T. A., DiPersio, J. F., Wilson, R. K. & Ley, T. J., Sep 10 2009, In: New England Journal of Medicine. 361, 11, p. 1058-1066 9 p.

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

      Open Access
      1890 Scopus citations

    • VarScan: Variant detection in massively parallel sequencing of individual and pooled samples

      Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K. & Ding, L., 2009, In: Bioinformatics. 25, 17, p. 2283-2285 3 p.

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

      962 Scopus citations
    • 2010

      A map of human genome variation from population-scale sequencing

      Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M., Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L., & 348 othersSchafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Wang, S. J., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, J., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Bentley, I. D. R., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., Mc Kernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, H., Zheng, X., Zhou, Y., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W. P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Korbel, J. O., Stütz, A. M., Humphray, I. S., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Ye, K., Fu, Y., Hyland, F. C. L., Manning, J. M., Stephen, F. M., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Mark, A. B., Konkel, M. K., Walker, J. A., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Gil, A. M., Auton, A., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Li, Y., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Eichler, E. E., Aksay, G., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., CenkSahinalp, S., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Matt, E. H., Jin, H., Jostins, L., Keane, T. M., Quang Le, S., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Chris Tyler-Smith, T-S., Walter, K., Zhang, Y., Gerstein, M. B., Snyder, M., Abyzov, A., Balasubramanian, S., Bjornson, R., Grubert, F., Habegger, L., Haraksingh, R., Khurana, E., Lam, H. Y. K., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., McCarroll, S. A., Zheng-Bradley, X., Batzer, M. A., Hurles, M. E., Du, J., Jee, J., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Coffey, A., Scott, C., Tyler-Smith, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Oct 28 2010, In: Nature. 467, 7319, p. 1061-1073 13 p.

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

      Open Access
      6193 Scopus citations

    • Diversity of human copy number variation and multicopy genes

      Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., Eichler, E. E., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M., & 343 othersFlicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L., Schafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., McKernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, X., Zhou, Y., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W. P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McCarroll, S. A., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Zheng-Bradley, X., Korbel, J. O., Stütz, A. M., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Fu, Y., Hyland, F. C., Manning, J. M., McLaughlin, S. F., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Batzer, M. A., Konkel, M. K., Walker, J. A., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Auton, A., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Aksay, G., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., Sahinalp, S. C., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Hurles, M. E., Jin, H., Jostins, L., Keane, T. M., Le, S. Q., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Tyler-Smith, C., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Bjornson, R., Du, J., Grubert, F., Habegger, L., Haraksingh, R., Jee, J., Khurana, E., Lam, H. Y., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Scott, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Oct 29 2010, In: Science. 330, 6004, p. 641-646 6 p.

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

      Open Access
      525 Scopus citations

    • Genome remodelling in a basal-like breast cancer metastasis and xenograft

      Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., Harris, C. C., McLellan, M. D., Fulton, R. S., Fulton, L. L., Abbott, R. M., Hoog, J., Dooling, D. J., Koboldt, D. C., Schmidt, H., Kalicki, J., Zhang, Q., Chen, L., Lin, L., Wendl, M. C., & 49 othersMcMichael, J. F., Magrini, V. J., Cook, L., McGrath, S. D., Vickery, T. L., Appelbaum, E., Deschryver, K., Davies, S., Guintoli, T., Lim, L., Crowder, R., Tao, Y., Snider, J. E., Smith, S. M., Dukes, A. F., Sanderson, G. E., Pohl, C. S., Delehaunty, K. D., Fronick, C. C., Pape, K. A., Reed, J. S., Robinson, J. S., Hodges, J. S., Schierding, W., Dees, N. D., Shen, D., Locke, D. P., Wiechert, M. E., Eldred, J. M., Peck, J. B., Oberkfell, B. J., Lolofie, J. T., Du, F., Hawkins, A. E., Oĝlaughlin, M. D., Bernard, K. E., Cunningham, M., Elliott, G., Mason, M. D., Thompson, D. M., Ivanovich, J. L., Goodfellow, P. J., Perou, C. M., Weinstock, G. M., Aft, R., Watson, M., Ley, T. J., Wilson, R. K. & Mardis, E. R., Apr 15 2010, In: Nature. 464, 7291, p. 999-1005 7 p.

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

      1012 Scopus citations
    • 2011

      CREST maps somatic structural variation in cancer genomes with base-pair resolution

      Wang, J., Mullighan, C. G., Easton, J., Roberts, S., Heatley, S. L., Ma, J., Rusch, M. C., Chen, K., Harris, C. C., Ding, L., Holmfeldt, L., Payne-Turner, D., Fan, X., Wei, L., Zhao, D., Obenauer, J. C., Naeve, C., Mardis, E. R., Wilson, R. K., Downing, J. R., & 1 othersZhang, J., Aug 2011, In: Nature Methods. 8, 8, p. 652-654 3 p.

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

      Open Access
      393 Scopus citations

    • Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML

      Link, D. C., Schuettpelz, L. G., Shen, D., Wang, J., Walter, M. J., Kulkarni, S., Payton, J. E., Ivanovich, J., Goodfellow, P. J., Le Beau, M., Koboldt, D. C., Dooling, D. J., Fulton, R. S., Bender, R. H. F., Fulton, L. L., Delehaunty, K. D., Fronick, C. C., Appelbaum, E. L., Schmidt, H., Abbott, R., & 12 othersO'Laughlin, M., Chen, K., McLellan, M. D., Varghese, N., Nagarajan, R., Heath, S., Graubert, T. A., Ding, L., Ley, T. J., Zambetti, G. P., Wilson, R. K. & Mardis, E. R., Apr 20 2011, In: JAMA. 305, 15, p. 1568-1576 9 p.

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

      Open Access
      139 Scopus citations

    • Mapping copy number variation by population-scale genome sequencing

      Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M., & 352 othersKonkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y. K., Leng, J., Li, R., Li, Y., Lin, C. Y., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Sütz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A., Korbel, J. O., Collins, F. S., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., De La Vega, F. M., Donnelly, P., Egholm, M., Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., Nickerson, D. A., Peltonen, L., Schafer, A. J., Sherry, S. T., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Li, J., Jian, M., Li, G., Liang, H., Tian, G., Wang, B., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., McKernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Tai, S., Wu, H., Zheng, X., Zhou, Y., Garrison, E. P., Huang, W., Indap, A., Lee, W. P., Leong, W. F., Quinlan, A. R., Ward, A. N., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Makarov, V., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Zheng-Bradley, X., Stütz, A. M., Bauer, M., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Hyland, F. C., Manning, J. M., McLaughlin, S. F., Sakarya, O., Sun, Y. A., Tsung, E. F., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Auton, A., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Aksay, G., Sahinalp, S. C., Sudmant, P. H., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Jin, H., Jostins, L., Keane, T. M., Le, S. Q., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Tyler-Smith, C., Balasubramanian, S., Bjornson, R., Du, J., Habegger, L., Haraksingh, R., Jee, J., Lam, H. Y., Jeng, J., Zhang, Z., Bank, E., Yoon, S., Kidd, J., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Khouri, H. M., Scott, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Feb 3 2011, In: Nature. 470, 7332, p. 59-65 7 p.

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

      Open Access
      858 Scopus citations

    • Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression

      Wartman, L. D., Larson, D. E., Xiang, Z., Ding, L., Chen, K., Lin, L., Cahan, P., Klco, J. M., Welch, J. S., Li, C., Payton, J. E., Uy, G. L., Varghese, N., Ries, R. E., Hoock, M., Koboldt, D. C., McLellan, M. D., Schmidt, H., Fulton, R. S., Abbott, R. M., & 12 othersCook, L., McGrath, S. D., Fan, X., Dukes, A. F., Vickery, T., Kalicki, J., Lamprecht, T. L., Graubert, T. A., Tomasson, M. H., Mardis, E. R., Wilson, R. K. & Ley, T. J., Apr 1 2011, In: Journal of Clinical Investigation. 121, 4, p. 1445-1455 11 p.

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

      86 Scopus citations

    • Use of whole-genome sequencing to diagnose a cryptic fusion oncogene

      Welch, J. S., Westervelt, P., Ding, L., Larson, D. E., Klco, J. M., Kulkarni, S., Wallis, J., Chen, K., Payton, J. E., Fulton, R. S., Veizer, J., Schmidt, H., Vickery, T. L., Heath, S., Watson, M. A., Tomasson, M. H., Link, D. C., Graubert, T. A., DiPersio, J. F., Mardis, E. R., & 2 othersLey, T. J. & Wilson, R. K., Apr 20 2011, In: JAMA. 305, 15, p. 1577-1584 8 p.

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

      Open Access
      220 Scopus citations
    • 2012

      An integrated map of genetic variation from 1,092 human genomes

      Altshuler, D. M., Durbin, R. M., 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., & 371 othersMcVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., 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., Gupta, N., Clarke, L., Leinonen, R., Smith, R. E., 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., Fulton, R., Weinstock, G. M., 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., Auton, A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Coin, L. J. M., Fang, L., Li, Q., 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., Garrison, E. P., Kural, D., Lee, W. P., Fung Leong, W., Ward, A. N., Wu, J., Zhang, M., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., Von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., 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., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Cheol Kim, K., Rausch, T., Beal, K., Cunningham, F., Herrero, J., McLaren, W. 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Z., Yang, G., Jia You, C., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Guyer, M. S., Peterson, J. L. & Lacroute, P., Nov 1 2012, In: Nature. 491, 7422, p. 56-65 10 p.

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

      Open Access
      5956 Scopus citations

    • Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells

      Young, M. A., Larson, D. E., Sun, C. W., George, D. R., Ding, L., Miller, C. A., Lin, L., Pawlik, K. M., Chen, K., Fan, X., Schmidt, H., Kalicki-Veizer, J., Cook, L. L., Swift, G. W., Demeter, R. T., Wendl, M. C., Sands, M. S., Mardis, E. R., Wilson, R. K., Townes, T. M., & 1 othersLey, T. J., May 4 2012, In: Cell Stem Cell. 10, 5, p. 570-582 13 p.

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

      167 Scopus citations

    • Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

      Chen, K., Wallis, J. W., Kandoth, C., Kalicki-veizer, J. M., Mungall, K. L., Mungall, A. J., Jones, S. J., Marra, M. A., Ley, T. J., Mardis, E. R., Wilson, R. K., Weinstein, J. N. & Ding, L., Jul 2012, In: Bioinformatics. 28, 14, p. 1923-1924 2 p., bts272.

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

      46 Scopus citations

    • Clonal Architecture of Secondary Acute Myeloid Leukemia

      Walter, M. J., Shen, D., Ding, L., Shao, J., Koboldt, D. C., Chen, K., Larson, D. E., McLellan, M. D., Dooling, D., Abbott, R., Fulton, R., Magrini, V., Schmidt, H., Kalicki-Veizer, J., O'Laughlin, M., Fan, X., Grillot, M., Witowski, S., Heath, S., Frater, J. L., & 9 othersEades, W., Tomasson, M., Westervelt, P., Dipersio, J. F., Link, D. C., Mardis, E. R., Ley, T. J., Wilson, R. K. & Graubert, T. A., Mar 22 2012, In: New England Journal of Medicine. 366, 12, p. 1090-1098 9 p.

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

      Open Access
      641 Scopus citations

    • Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

      Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., McMichael, J. F., Wallis, J. W., Lu, C., Shen, D., Harris, C. C., Dooling, D. J., Fulton, R. S., Fulton, L. L., Chen, K., Schmidt, H., & 19 othersKalicki-Veizer, J., Magrini, V. J., Cook, L., McGrath, S. D., Vickery, T. L., Wendl, M. C., Heath, S., Watson, M. A., Link, D. C., Tomasson, M. H., Shannon, W. D., Payton, J. E., Kulkarni, S., Westervelt, P., Walter, M. J., Graubert, T. A., Mardis, E. R., Wilson, R. K. & Dipersio, J. F., Jan 26 2012, In: Nature. 481, 7382, p. 506-510 5 p.

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

      1630 Scopus citations

    • Genomic landscape of non-small cell lung cancer in smokers and never-smokers

      Govindan, R., Ding, L., Griffith, M., Subramanian, J., Dees, N. D., Kanchi, K. L., Maher, C. A., Fulton, R., Fulton, L., Wallis, J., Chen, K., Walker, J., McDonald, S., Bose, R., Ornitz, D., Xiong, D., You, M., Dooling, D. J., Watson, M., Mardis, E. R., & 1 othersWilson, R. K., Sep 14 2012, In: Cell. 150, 6, p. 1121-1134 14 p.

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

      975 Scopus citations

    • Somaticsniper: Identification of somatic point mutations in whole genome sequencing data

      Larson, D. E., Harris, C. C., Chen, K., Koboldt, D. C., Abbott, T. E., Dooling, D. J., Ley, T. J., Mardis, E. R., Wilson, R. K. & Ding, L., Feb 2012, In: Bioinformatics. 28, 3, p. 311-317 7 p., btr665.

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

      448 Scopus citations

    • The origin and evolution of mutations in acute myeloid leukemia

      Welch, J. S., Ley, T. J., Link, D. C., Miller, C. A., Larson, D. E., Koboldt, D. C., Wartman, L. D., Lamprecht, T. L., Liu, F., Xia, J., Kandoth, C., Fulton, R. S., McLellan, M. D., Dooling, D. J., Wallis, J. W., Chen, K., Harris, C. C., Schmidt, H. K., Kalicki-Veizer, J. M., Lu, C., & 34 othersZhang, Q., Lin, L., O'Laughlin, M. D., McMichael, J. F., Delehaunty, K. D., Fulton, L. A., Magrini, V. J., McGrath, S. D., Demeter, R. T., Vickery, T. L., Hundal, J., Cook, L. L., Swift, G. W., Reed, J. P., Alldredge, P. A., Wylie, T. N., Walker, J. R., Watson, M. A., Heath, S. E., Shannon, W. D., Varghese, N., Nagarajan, R., Payton, J. E., Baty, J. D., Kulkarni, S., Klco, J. M., Tomasson, M. H., Westervelt, P., Walter, M. J., Graubert, T. A., Dipersio, J. F., Ding, L., Mardis, E. R. & Wilson, R. K., Jul 20 2012, In: Cell. 150, 2, p. 264-278 15 p.

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

      1257 Scopus citations

    • Whole-genome analysis informs breast cancer response to aromatase inhibition

      Ellis, M. J., Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., Van Tine, B. A., Hoog, J., Goiffon, R. J., Goldstein, T. C., Ng, S., Lin, L., Crowder, R., Snider, J., Ballman, K., Weber, J., Chen, K., Koboldt, D. C., Kandoth, C., Schierding, W. S., & 39 othersMcMichael, J. F., Miller, C. A., Lu, C., Harris, C. C., McLellan, M. D., Wendl, M. C., Deschryver, K., Allred, D. C., Esserman, L., Unzeitig, G., Margenthaler, J., Babiera, G. V., Marcom, P. K., Guenther, J. M., Leitch, M., Hunt, K., Olson, J., Tao, Y., Maher, C. A., Fulton, L. L., Fulton, R. S., Harrison, M., Oberkfell, B., Du, F., Demeter, R., Vickery, T. L., Elhammali, A., Piwnica-Worms, H., McDonald, S., Watson, M., Dooling, D. J., Ota, D., Chang, L. W., Bose, R., Ley, T. J., Piwnica-Worms, D., Stuart, J. M., Wilson, R. K. & Mardis, E. R., Jun 21 2012, In: Nature. 486, 7403, p. 353-360 8 p.

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

      858 Scopus citations
    • 2013

      A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival

      Zheng, S., Fu, J., Vegesna, R., Mao, Y., Heathcock, L. E., Torres-Garcia, W., Ezhilarasan, R., Wang, S., McKenna, A., Chin, L., Brennan, C. W., Alfred Yung, W. K., Weinstein, J. N., Aldape, K. D., Sulman, E. P., Chen, K., Koul, D. & Verhaak, R. G. W., Jul 1 2013, In: Genes and Development. 27, 13, p. 1462-1472 11 p.

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

      61 Scopus citations

    • BreakTrans: Uncovering the genomic architecture of gene fusions

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

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

      Open Access
      20 Scopus citations

    • CanDrA: Cancer-specific driver missense mutation annotation with optimized features

      Mao, Y., Chen, H., Liang, H., Meric-Bernstam, F., Mills, G. B. & Chen, K., Oct 30 2013, In: PloS one. 8, 10, e77945.

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

      87 Scopus citations

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

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

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

      Open Access
      3721 Scopus citations

    • The somatic genomic landscape of glioblastoma

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

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

      3492 Scopus citations
    • 2014

      Bias from removing read duplication in ultra-deep sequencing experiments

      Zhou, W., Chen, T., Zhao, H., Eterovic, A. K., Meric-Bernstam, F., Mills, G. B. & Chen, K., 2014, In: Bioinformatics. 30, 8, p. 1073-1080 8 p.

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

      Open Access
      29 Scopus citations

    • BreakDancer: Identification of genomic structural variation from paired-end read mapping

      Fan, X., Abbott, T. E., Larson, D. & Chen, K., 2014, In: Current Protocols in Bioinformatics. SUPPL.45, 15.6.

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

      121 Scopus citations

    • Catalytic mTOR inhibitors can overcome intrinsic and acquired resistance to allosteric mTOR inhibitors

      Hassan, B., Akcakanat, A., Sangai, T., Evans, K. W., Adkins, F., Eterovic, A. K., Zhao, H., Chen, K., Chen, H., Do, K. A., Xie, S. M., Holder, A. M., Naing, A., Mills, G. B. & Meric-Bernstam, F., 2014, In: Oncotarget. 5, 18, p. 8544-8557 14 p.

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

      Open Access
      55 Scopus citations

    • Clonal evolution in breast cancer revealed by single nucleus genome sequencing

      Wang, Y., Waters, J., Leung, M. L., Unruh, A., Roh, W., Shi, X., Chen, K., Scheet, P., Vattathil, S., Liang, H., Multani, A., Zhang, H., Zhao, R., Michor, F., Meric-Bernstam, F. & Navin, N. E., Aug 14 2014, In: Nature. 512, 7513, p. 155-160 6 p.

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

      Open Access
      776 Scopus citations

    • Implementation of biomarker-driven cancer therapy: Existing tools and remaining gaps

      Bailey, A. M., Mao, Y., Zeng, J., Holla, V., Johnson, A., Brusco, L., Chen, K., Mendelsohn, J., Routbort, M. J., Mills, G. B. & Meric-Bernstam, F., Feb 2014, In: Discovery Medicine. 17, 92, p. 101-114 14 p.

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

      52 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., 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., Banks, E., & 362 othersBhatia, 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

      280 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

      62 Scopus citations

    • Towards accurate characterization of clonal heterogeneity based on structural variation

      Fan, X., Zhou, W., Chong, Z., Nakhleh, L. & Chen, K., Sep 8 2014, In: BMC bioinformatics. 15, 1, 299.

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

      9 Scopus citations
    • 2015

      Ability to generate patient-derived Breast cancer xenografts is enhanced in chemoresistant disease and predicts poor patient outcomes

      McAuliffe, P. F., Evans, K. W., Akcakanat, A., Chen, K., Zheng, X., Zhao, H., Eterovic, A. K., Sangai, T., Holder, A. M., Sharma, C., Chen, H., Do, K. A., Tarco, E., Gagea, M., Naff, K. A., Sahin, A., Multani, A. S., Black, D. M., Mittendorf, E. A., Bedrosian, I., & 3 othersMills, G. B., Gonzalez-Angulo, A. M. & Meric-Bernstam, F., Sep 1 2015, In: PloS one. 10, 9, e0136851.

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

      Open Access
      46 Scopus citations

    • Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

      Abyzov, A., Li, S., Kim, D. R., Mohiyuddin, M., Stütz, A. M., Parrish, N. F., Mu, X. J., Clark, W., Chen, K., Hurles, M., Korbel, J. O., Lam, H. Y. K., Lee, C. & Gerstein, M. B., Jun 1 2015, In: Nature communications. 6, 7256.

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

      62 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 othersChaisson, 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
      1446 Scopus citations

    • Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours

      Ince, T. A., Sousa, A. D., Jones, M. A., Harrell, J. C., Agoston, E. S., Krohn, M., Selfors, L. M., Liu, W., Chen, K., Yong, M., Buchwald, P., Wang, B., Hale, K. S., Cohick, E., Sergent, P., Witt, A., Kozhekbaeva, Z., Gao, S., Agoston, A. T., Merritt, M. A., & 5 othersFoster, R., Rueda, B. R., Crum, C. P., Brugge, J. S. & Mills, G. B., Jun 17 2015, In: Nature communications. 6, 7419.

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

      137 Scopus citations

    • Clinical actionability enhanced through deep targeted sequencing of solid tumors

      Chen, K., Meric-Bernstam, F., Zhao, H., Zhang, Q., Ezzeddine, N., Tang, L. Y., Qi, Y., Mao, Y., Chen, T., Chong, Z., Zhou, W., Zheng, X., Johnson, A., Aldape, K. D., Routbort, M. J., Luthra, R., Kopetz, S., Davies, M. A., De Groot, J., Moulder, S., & 6 othersVinod, R., Farhangfar, C. J., Shaw, K. M., Mendelsohn, J., Mills, G. B. & Eterovic, A. K., Mar 1 2015, In: Clinical chemistry. 61, 3, p. 544-553 10 p.

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

      Open Access
      84 Scopus citations

    • ClinSeK: A targeted variant characterization framework for clinical sequencing

      Zhou, W., Zhao, H., Chong, Z., Mark, R. J., Eterovic, A. K., Meric-Bernstam, F. & Chen, K., Mar 31 2015, In: Genome medicine. 7, 1, 34.

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

      12 Scopus citations