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

    Research activity per year

    Search results

    • 2017

      The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: Summary and innovation in genomics

      Zhao, Z., Liu, Z., Chen, K., Guo, Y., Allen, G. I., Zhang, J., Jim Zheng, W. & Ruan, J., Oct 3 2017, In: BMC genomics. 18, 703.

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

      Open Access
      4 Scopus citations
    • 2016

      Divergent viral presentation among human tumors and adjacent normal tissues

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

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

      Open Access
      53 Scopus citations

    • Erratum: Ability to generate patient-derived breast cancer xenografts is enhanced in chemoresistant disease and predicts poor patient outcomes (PLoS ONE (2015) 10:9 (e0136851) DOI: 10.1371/journal.pone.0136851)

      McAuliffe, P. F., Evans, K. W., Akcakanat, A., Chen, K., Zheng, X., Zhao, H., Eterovic, A. K. B., 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., Mar 2016, In: PloS one. 11, 3, e0151121.

      Research output: Contribution to journal › Comment/debate › peer-review

      Open Access
      1 Scopus citations

    • Functional annotation of rare gene aberration drivers of pancreatic cancer

      Tsang, Y. H., Dogruluk, T., Tedeschi, P. M., Wardwell-Ozgo, J., Lu, H., Espitia, M., Nair, N., Minelli, R., Chong, Z., Chen, F., Chang, Q. E., Dennison, J. B., Dogruluk, A., Li, M., Ying, H., Bertino, J. R., Gingras, M. C., Ittmann, M., Kerrigan, J., Chen, K., & 4 othersCreighton, C. J., Eterovic, K., Mills, G. B. & Scott, K. L., Jan 25 2016, In: Nature communications. 7, 10500.

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

      Open Access
      53 Scopus citations

    • Genotyping tumor clones from single-cell data

      Navin, N. E. & Chen, K., Jun 29 2016, In: Nature Methods. 13, 7, p. 555-556 2 p.

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

      8 Scopus citations

    • Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types

      Chen, T., Wang, Z., Zhou, W., Chong, Z., Meric-Bernstam, F., Mills, G. B. & Chen, K., Jun 23 2016, In: BMC genomics. 17, 394.

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

      Open Access
      25 Scopus citations

    • Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol

      Meric-Bernstam, F., Brusco, L., Daniels, M., Wathoo, C., Bailey, A. M., Strong, L., Shaw, K., Lu, K., Qi, Y., Zhao, H., Lara-Guerra, H., Litton, J., Arun, B., Eterovic, A. K., Aytac, U., Routbort, M., Subbiah, V., Janku, F., Davies, M. A., Kopetz, S., & 3 othersMendelsohn, J., Mills, G. B. & Chen, K., May 1 2016, In: Annals of Oncology. 27, 5, p. 795-800 6 p.

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

      Open Access
      128 Scopus citations

    • MET amplification in metastatic colorectal cancer: An acquired response to EGFR inhibition, not a de novo phenomenon

      Raghav, K., Morris, V., Tang, C., Morelli, P., Amin, H. M., Chen, K., Manyam, G. C., Broom, B., Overman, M. J., Shaw, K., Meric-Bernstam, F., Maru, D., Menter, D., Ellis, L. M., Eng, C., Hong, D. & Kopetz, S., 2016, In: Oncotarget. 7, 34, p. 54627-54631 5 p.

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

      Open Access
      48 Scopus citations

    • Monovar: Single-nucleotide variant detection in single cells

      Zafar, H., Wang, Y., Nakhleh, L., Navin, N. & Chen, K., Jun 1 2016, In: Nature Methods. 13, 6, p. 505-507 3 p.

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

      Open Access
      107 Scopus citations

    • Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set

      Roszik, J., Haydu, L. E., Hess, K. R., Oba, J., Joon, A. Y., Siroy, A. E., Karpinets, T. V., Stingo, F. C., Baladandayuthapani, V., Tetzlaff, M. T., Wargo, J. A., Chen, K., Forget, M. A., Haymaker, C. L., Chen, J. Q., Meric-Bernstam, F., Eterovic, A. K., Shaw, K. R., Mills, G. B., Gershenwald, J. E., & 8 othersRadvanyi, L. G., Hwu, P., Futreal, P. A., Gibbons, D. L., Lazar, A. J., Bernatchez, C., Davies, M. A. & Woodman, S. E., Oct 25 2016, In: BMC medicine. 14, 1, 168.

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

      Open Access
      93 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

      Open Access
      67 Scopus citations

    • The degree of intratumor mutational heterogeneity varies by primary tumor sub-site

      Ledgerwood, L. G., Kumar, D., Eterovic, A. K., Wick, J., Chen, K., Zhao, H., Tazi, L., Manna, P., Kerley, S., Joshi, R., Wang, L., Chiosea, S. I., Garnett, J. D., Tsue, T. T., Chien, J., Mills, G. B., Grandis, J. R. & Thomas, S. M., May 10 2016, In: Oncotarget. 7, 19, p. 27185-27198 14 p.

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

      Open Access
      36 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

    • A Decision Support Framework for Genomically Informed Investigational Cancer Therapy

      Meric-Bernstam, F., Johnson, A., Holla, V., Bailey, A. M., Brusco, L., Chen, K., Routbort, M., Patel, K. P., Zeng, J., Kopetz, S., Davies, M. A., Piha-Paul, S. A., Hong, D. S., Eterovic, A. K., Tsimberidou, A. M., Broaddus, R., Bernstam, E. V., Shaw, K. R., Mendelsohn, J. & Mills, G. B., Jul 1 2015, In: Journal of the National Cancer Institute. 107, 7

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

      Open Access
      162 Scopus citations

    • A global reference for human genetic variation

      Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., & 457 othersMarth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Boerwinkle, E., Doddapaneni, H., Han, Y., Korchina, V., Kovar, C., Lee, S., Muzny, D., Reid, J. G., Zhu, Y., Chang, Y., Feng, Q., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Lan, T., Li, G., Li, J., Li, Y., Liu, S., Liu, X., Lu, Y., Ma, X., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Xu, X., Yin, Y., Zhang, D., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Gupta, N., Gharani, N., Toji, L. H., Gerry, N. P., Resch, A. M., Barker, J., Clarke, L., Gil, L., Hunt, S. E., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Thormann, A., Toneva, I., Vaughan, B., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Fulton, L., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Church, D., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'Sullivan, C., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Campbell, C. L., Kong, Y., Marcketta, A., Yu, F., Antunes, L., Bainbridge, M., Sabo, A., Huang, Z., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Alkan, C., Dal, E., Kahveci, F., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Stromberg, M., Ward, A. N., Wu, J., Zhang, M., Daly, M. J., DePristo, M. A., Handsaker, R. E., Banks, E., Bhatia, G., Del Angel, G., Genovese, G., Li, H., Kashin, S., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Yoon, S. C., Lihm, J., Makarov, V., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Rausch, T., Fritz, M. H., Stütz, A. M., Beal, K., Datta, A., Herrero, J., Ritchie, G. R. S., Zerbino, D., Sabeti, P. C., Shlyakhter, I., Schaffner, S. F., Vitti, J., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Cheetham, R. K., Cox, A., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Kenny, E. E., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Ding, L., Koboldt, D. C., Larson, D., Ye, K., Gravel, S., Swaroop, A., Chew, E., Lappalainen, T., Erlich, Y., Gymrek, M., Willems, T. F., Simpson, J. T., Shriver, M. D., Rosenfeld, J. A., Bustamante, C. D., Montgomery, S. B., De La Vega, F. M., Byrnes, J. K., Carroll, A. W., DeGorter, M. K., Lacroute, P., Maples, B. K., Martin, A. R., Moreno-Estrada, A., Shringarpure, S. S., Zakharia, F., Halperin, E., Baran, Y., Cerveira, E., Hwang, J., Malhotra, A., Plewczynski, D., Radew, K., Romanovitch, M., Zhang, C., Hyland, F. C. L., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Antaki, D., Gujral, M., Noor, A., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Devine, S. E., Kang, H. M., Kidd, J. M., Blackwell, T., Caron, S., Chen, W., Emery, S., Fritsche, L., Fuchsberger, C., Jun, G., Li, B., Lyons, R., Scheller, C., Sidore, C., Song, S., Sliwerska, E., Taliun, D., Tan, A., Welch, R., Wing, M. K., Zhan, X., Awadalla, P., Hodgkinson, A., Li, Y., Shi, X., Quitadamo, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Kretzschmar, W., Iqbal, Z., Mathieson, I., Menelaou, A., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Browning, S. R., Hormozdiari, F., Sudmant, P. H., Khurana, E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Colonna, V., Jostins, L., Walter, K., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Lee, D., Liu, J., Mu, X. J., Zhang, J., Zhang, Y., Hartl, C., Shakir, K., Degenhardt, J., Meiers, S., Raeder, B., Casale, F. P., Stegle, O., Lameijer, E. W., Hall, I., Bafna, V., Michaelson, J., Gardner, E. J., Mills, R. E., Dayama, G., Chen, K., Fan, X., Chong, Z., Chen, T., Chaisson, M. J., Huddleston, J., Malig, M., Nelson, B. J., Parrish, N. F., Blackburne, B., Lindsay, S. J., Ning, Z., Zhang, Y., Lam, H., Sisu, C., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Yu, J., Li, W., Habegger, L., Yu, H., Cunningham, F., Dunham, I., Lage, K., Jespersen, J. B., Horn, H., Kim, D., Desalle, R., Narechania, A., Sayres, M. A. W., Mendez, F. L., Poznik, G. D., Underhill, P. A., Mittelman, D., Banerjee, R., Cerezo, M., Fitzgerald, T. W., Louzada, S., Massaia, A., Yang, F., Kalra, D., Hale, W., Dan, X., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Cai, Z., Gao, Y., Chu, J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Mathias, R. A., Hennis, A., Watson, H., McKenzie, C., Qadri, F., LaRocque, R., Deng, X., Asogun, D., Folarin, O., Happi, C., Omoniwa, O., Stremlau, M., Tariyal, R., Jallow, M., Joof, F. S., Corrah, T., Rockett, K., Kwiatkowski, D., Kooner, J., Hien, T. T., Dunstan, S. J., ThuyHang, N., Fonnie, R., Garry, R., Kanneh, L., Moses, L., Schieffelin, J., Grant, D. S., Gallo, C., Poletti, G., Saleheen, D., Rasheed, A., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Vaydylevich, Y., Duncanson, A., Dunn, M. & Schloss, J. A., Sep 30 2015, In: Nature. 526, 7571, p. 68-74 7 p.

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

      Open Access
      10166 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
      1443 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

      136 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

      11 Scopus citations

    • Erratum: 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., Sep 8 2015, In: Nature communications. 6, 8389.

      Research output: Contribution to journal › Comment/debate › peer-review

      Open Access
      2 Scopus citations

    • Functional consequence of the MET-T1010I polymorphism in breast cancer

      Liu, S., Meric-Bernstam, F., Parinyanitikul, N., Wang, B., Eterovic, A. K., Zheng, X., Gagea, M., Chavez-MacGregor, M., Ueno, N. T., Lei, X., Zhou, W., Nair, L., Tripathy, D., Brown, P. H., Hortobagyi, G. N., Chen, K., Mendelsohn, J., Mills, G. B. & Gonzalez-Angulo, A. M., 2015, In: Oncotarget. 6, 5, p. 2604-2614 11 p.

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

      Open Access
      33 Scopus citations

    • Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer

      Hao, C., Wang, L., Peng, S., Cao, M., Li, H., Hu, J., Huang, X., Liu, W., Zhang, H., Wu, S., Pataer, A., Heymach, J. V., Eterovic, A. K., Zhang, Q., Shaw, K. R., Chen, K., Futreal, A., Wang, M., Hofstetter, W., Mehran, R., & 8 othersRice, D., Roth, J. A., Sepesi, B., Swisher, S. G., Vaporciyan, A., Walsh, G. L., Johnson, F. M. & Fang, B., Feb 1 2015, In: Cancer Letters. 357, 1, p. 179-185 7 p.

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

      Open Access
      76 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 othersWeible, 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
      62 Scopus citations

    • Identification of variant-specific functions of PIK3CA by rapid phenotyping of rare mutations

      Dogruluk, T., Tsang, Y. H., Espitia, M., Chen, F., Chen, T., Chong, Z., Appadurai, V., Dogruluk, A., Eterovic, A. K., Bonnen, P. E., Creighton, C. J., Chen, K., Mills, G. B. & Scott, K. L., Dec 15 2015, In: Cancer Research. 75, 24, p. 5341-5354 14 p.

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

      Open Access
      117 Scopus citations

    • Ploidy-Seq: Inferring mutational chronology by sequencing polyploid tumor subpopulations

      Malhotra, A., Wang, Y., Waters, J., Chen, K., Meric-Bernstam, F., Hall, I. M. & Navin, N. E., Jan 28 2015, In: Genome medicine. 7, 1, 6.

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

      5 Scopus citations

    • RET fusion as a novel driver of medullary thyroid carcinoma

      Grubbs, E. G., Ng, P. K. S., Bui, J., Busaidy, N. L., Chen, K., Lee, J. E., Lu, X., Lu, H., Meric-Bernstam, F., Mills, G. B., Palmer, G., Perrier, N. D., Scott, K. L., Shaw, K. R., Waguespack, S. G., Williams, M. D., Yelensky, R. & Cote, G. J., Mar 1 2015, In: Journal of Clinical Endocrinology and Metabolism. 100, 3, p. 788-793 6 p.

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

      60 Scopus citations

    • TransVar: A multilevel variant annotator for precision genomics

      Zhou, W., Chen, T., Chong, Z., Rohrdanz, M. A., Melott, J. M., Wakefield, C., Zeng, J., Weinstein, J. N., Meric-Bernstam, F., Mills, G. B. & Chen, K., Nov 1 2015, In: Nature Methods. 12, 11, p. 1002-1003 2 p.

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

      Open Access
      48 Scopus citations

    • Whole Genome Sequencing in Cancer Clinics

      Chen, K. & Meric-Bernstam, F., 2015, In: EBioMedicine. 2, 1, p. 15-16 2 p.

      Research output: Contribution to journal › Comment/debate › peer-review

      4 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
      28 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
      775 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

      61 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
    • 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
      3705 Scopus citations

    • Integrated genotyping of structural variation

      Fan, X., Nakhleh, L. & Chen, K., 2013, 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings. p. 47-48 2 p. 6736808. (2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

      1 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

      3476 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. M., Ritchie, G. R. S., 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., Barnes, B., Bauer, M., Keira Cheetham, R., Cox, T., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., 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., Xiao, C., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., James Kent, W., 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., Min Kang, H., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Jun, G., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Kate Trost, M., Awadalla, P., Hodgkinson, A., Lunter, G., 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., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Li, H., Scally, A., 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., Jasmine Mu, X., Sisu, C., Degenhardt, J., Stütz, A. M., Keira Cheetham, R., Church, D., Michaelson, J. J., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Mu, X. J., Fowler, G., Hale, W., Kalra, D., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Vaughan, B., 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., O'Sullivan, C., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Gharani, N., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Toji, L. H., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ming, C. 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
      5950 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

      1629 Scopus citations

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

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      Research output: Chapter in Book/Report/Conference proceeding › Chapter

      41 Scopus citations