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KEN CHEN

TitleAssociate Professor
InstitutionMD Anderson
DepartmentBioinformatics & Computational Biology
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Meric-Bernstam F, Johnson A, Holla V, Bailey AM, Brusco L, Chen K, Routbort M, Patel KP, Zeng J, Kopetz S, Davies MA, Piha-Paul SA, Hong DS, Eterovic AK, Tsimberidou AM, Broaddus R, Bernstam EV, Shaw KR, Mendelsohn J, Mills GB. A decision support framework for genomically informed investigational cancer therapy. J Natl Cancer Inst. 2015 Jul; 107(7). PMID: 25863335.
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    2. Liu S, Meric-Bernstam F, Parinyanitikul N, Wang B, Eterovic AK, Zheng X, Gagea M, Chavez-MacGregor M, Ueno NT, Lei X, Zhou W, Nair L, Tripathy D, Brown PH, Hortobagyi GN, Chen K, Mendelsohn J, Mills GB, Gonzalez-Angulo AM. Functional consequence of the MET-T1010I polymorphism in breast cancer. Oncotarget. 2015 Feb 20; 6(5):2604-14. PMID: 25605252.
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    3. Chen K, Meric-Bernstam F, Zhao H, Zhang Q, Ezzeddine N, Tang LY, Qi Y, Mao Y, Chen T, Chong Z, Zhou W, Zheng X, Johnson A, Aldape KD, Routbort MJ, Luthra R, Kopetz S, Davies MA, de Groot J, Moulder S, Vinod R, Farhangfar CJ, Shaw KM, Mendelsohn J, Mills GB, Eterovic AK. Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clin Chem. 2015 Mar; 61(3):544-53. PMID: 25626406.
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    4. Hao C, Wang L, Peng S, Cao M, Li H, Hu J, Huang X, Liu W, Zhang H, Wu S, Pataer A, Heymach JV, Eterovic AK, Zhang Q, Shaw KR, Chen K, Futreal A, Wang M, Hofstetter W, Mehran R, Rice D, Roth JA, Sepesi B, Swisher SG, Vaporciyan A, Walsh GL, Johnson FM, Fang B. Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer. Cancer Lett. 2015 Feb 01; 357(1):179-185. PMID: 25444907.
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    5. Fan X, Zhou W, Chong Z, Nakhleh L, Chen K. Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinformatics. 2014 Sep 08; 15:299. PMID: 25201439.
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    6. Wang Y, Waters J, Leung ML, 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 NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014 Aug 14; 512(7513):155-60. PMID: 25079324.
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    7. Bailey AM, Mao Y, Zeng J, Holla V, Johnson A, Brusco L, Chen K, Mendelsohn J, Routbort MJ, Mills GB, Meric-Bernstam F. Implementation of biomarker-driven cancer therapy: existing tools and remaining gaps. Discov Med. 2014 Feb; 17(92):101-14. PMID: 24534473.
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    8. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 2014 Feb; 24(2):310-7. PMID: 24307552.
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    9. Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K. CanDrA: cancer-specific driver missense mutation annotation with optimized features. PLoS One. 2013; 8(10):e77945. PMID: 24205039.
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    10. Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol. 2013 Aug 23; 14(8):R87. PMID: 23972288.
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    11. Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RG. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev. 2013 Jul 01; 27(13):1462-72. PMID: 23796897.
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    12. Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, 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 MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013 05 30; 368(22):2059-74. PMID: 23634996.
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    13. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 01; 491(7422):56-65. PMID: 23128226.
      View in: PubMed
    14. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell. 2012 Sep 14; 150(6):1121-34. PMID: 22980976.
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    15. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK. The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20; 150(2):264-78. PMID: 22817890.
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    16. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10; 486(7403):353-60. PMID: 22722193.
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    17. Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics. 2012 Jul 15; 28(14):1923-4. PMID: 22563071.
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    18. Young MA, Larson DE, Sun CW, George DR, Ding L, Miller CA, Lin L, Pawlik KM, Chen K, Fan X, Schmidt H, Kalicki-Veizer J, Cook LL, Swift GW, Demeter RT, Wendl MC, Sands MS, Mardis ER, Wilson RK, Townes TM, Ley TJ. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell. 2012 May 04; 10(5):570-82. PMID: 22542160.
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    19. Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan MD, 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 JL, Eades W, Tomasson M, Westervelt P, DiPersio JF, Link DC, Mardis ER, Ley TJ, Wilson RK, Graubert TA. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med. 2012 Mar 22; 366(12):1090-8. PMID: 22417201.
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    20. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11; 481(7382):506-10. PMID: 22237025.
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    21. Koboldt DC, Larson DE, Chen K, Ding L, Wilson RK. Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol. 2012; 838:369-84. PMID: 22228022.
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    22. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012 Feb 01; 28(3):311-7. PMID: 22155872.
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    23. Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011 Jun 12; 8(8):652-4. PMID: 21666668.
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    24. Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender RH, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Abbott R, O'Laughlin M, Chen K, McLellan MD, Varghese N, Nagarajan R, Heath S, Graubert TA, Ding L, Ley TJ, Zambetti GP, Wilson RK, Mardis ER. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA. 2011 Apr 20; 305(15):1568-76. PMID: 21505135.
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    25. Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen K, Payton JE, Fulton RS, Veizer J, Schmidt H, Vickery TL, Heath S, Watson MA, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Ley TJ, Wilson RK. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA. 2011 Apr 20; 305(15):1577-84. PMID: 21505136.
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    26. Wartman LD, Larson DE, Xiang Z, Ding L, Chen K, Lin L, Cahan P, Klco JM, Welch JS, Li C, Payton JE, Uy GL, Varghese N, Ries RE, Hoock M, Koboldt DC, McLellan MD, Schmidt H, Fulton RS, Abbott RM, Cook L, McGrath SD, Fan X, Dukes AF, Vickery T, Kalicki J, Lamprecht TL, Graubert TA, Tomasson MH, Mardis ER, Wilson RK, Ley TJ. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest. 2011 Apr; 121(4):1445-55. PMID: 21436584.
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    27. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, St├╝tz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 03; 470(7332):59-65. PMID: 21293372.
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    28. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28; 467(7319):1061-73. PMID: 20981092.
      View in: PubMed
    29. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010 Apr 15; 464(7291):999-1005. PMID: 20393555.
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    30. Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK, Borecki IB, Province MA. CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics. 2010 Feb 15; 26(4):464-9. PMID: 20031968.
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    31. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009 Sep; 6(9):677-81. PMID: 19668202.
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    32. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009 Sep 10; 361(11):1058-66. PMID: 19657110.
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    33. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 01; 25(17):2283-5. PMID: 19542151.
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    34. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008 Nov 06; 456(7218):66-72. PMID: 18987736.
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    35. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23; 455(7216):1069-75. PMID: 18948947.
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    36. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23; 455(7216):1061-8. PMID: 18772890.
      View in: PubMed
    37. McLaughlin WA, Chen K, Hou T, Wang W. On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics. 2007 Oct 16; 8:390. PMID: 17937820.
      View in: PubMed
    38. Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 2007 May; 17(5):659-66. PMID: 17416743.
      View in: PubMed
    39. Hou T, Chen K, McLaughlin WA, Lu B, Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol. 2006 Jan; 2(1):e1. PMID: 16446784.
      View in: PubMed
    40. Hou T, McLaughlin W, Lu B, Chen K, Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res. 2006 Jan; 5(1):32-43. PMID: 16396493.
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    41. Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics. 30:1073-1080.
    42. Genome Modeling System. PLoS Computational Biology. 11.
    43. A map of human genome variation from population-scale sequencing. Nature. 467:1061-1073.
    44. Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours. Nature Communications. 6.
    45. The degree of intratumor mutational heterogeneity varies by primary tumor sub-site. Oncotarget. 7:27185-27198.
    46. Prosody dependent speech recognition with explicit duration modelling at intonational phrase boundaries. 393-396.
    47. NovoBreak. Nature Methods. 14:65-67.
    48. ClinSeK. Genome Medicine. 7.
    49. An automatic prosody labeling system using ANN-based syntactic-prosodic model and GMM-based acoustic-prosodic model.
    50. MET amplification in metastatic colorectal cancer. Oncotarget. 7:54627-54631.
    51. Modeling pronunciation variation using artificial neural networks for English spontaneous speech. 1461-1464.
    52. Genotyping tumor clones from single-cell data. Nature Methods. 13:555-556.
    53. Divergent viral presentation among human tumors and adjacent normal tissues. Scientific Reports. 6.
    54. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nature Communications. 7.
    55. Erratum. Nature Communications. 6.
    56. Automatic recognition of pitch movements using multilayer perception and time-delay recursive neural network. IEEE Signal Processing Letters. 11:645-648.
    57. An evaluation of using mutual information for selection of acoustic-features representation of phonemes for speech recognition. 2129-2132.
    58. Landmark-based speech recognition.
    59. TransVar. Nature Methods. 12:1002-1003.
    60. Prosody dependent speech recognition on radio news corpus of American English. IEEE Transactions on Audio, Speech and Language Processing. 14:232-244.
    61. Improving the robustness of prosody dependent language modeling based on prosody syntax dependence. 435-440.
    62. BreakDancer. Current Protocols in Bioinformatics.
    63. Ability to generate patient-derived Breast cancer xenografts is enhanced in chemoresistant disease and predicts poor patient outcomes. PLoS One. 10.
    64. Monovar. Nature Methods.
    65. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6.
    66. CMDS. Bioinformatics. 26:464-469.
    67. Integrated genotyping of structural variation. 47-48.
    68. Simultaneous recognition of words and prosody in the Boston University Radio Speech Corpus. Speech Communication. 46:418-439.
    69. Mapping copy number variation by population-scale genome sequencing. Nature. 470:59-65.
    70. Identification of variant-specific functions of PIK3CA by rapid phenotyping of rare mutations. Cancer Research. 75:5341-5354.
    71. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics. 17.
    72. Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Annals of Oncology. 27:795-800.
    73. Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set. BMC Medicine. 14.
    74. Ploidy-Seq. Genome Medicine. 7.
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