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Ken Chen, Ph.D.

Present Title & Affiliation

Primary Appointment

Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX

Dual/Joint/Adjunct Appointment

Regular Member, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX
Assistant Professor, Computer Science, Rice University, Houston, TX

Bio Statement

Dr. Chen received his B.E. from Tsinghua University (Beijing), Ph.D. from University of Illinois at Urbana-Champaign, and postdoctoral training from University of California at San Diego. From 2005 to 2011, he worked for Washington University School of Medicine in St. Louis as a senior scientist and a research faculty. Having a background in machine learning, statistical signal processing, and cancer genomics, his primary goal is to develop computational tools to analyze and interpret human genomics and clinical data towards the realization of genomic medicine. Dr. Chen has designed, developed, and co-developed a set of computational tools such as BreakDancer, TIGRA, CREST, BreakTrans, BreakFusion, PolyScan, SomaticSniper, and VarScan that have been widely applied to characterize individual and population genomics in various large-scale next-generation sequencing projects such as those in the Cancer Genome Atlas (TCGA) and the 1000 Genomes Project.  He is particularly interested in comprehensively and accurately constructing the genomes and the transcriptomes of various cancer cell populations towards understanding the heterogeneity and the evolution of cancer as a consequence of genetics and environment.  He is also interested in developing integrative approaches to identify biomarkers that are useful for diagnosis and prognosis.  More information about his research group is available here.

Education & Training

Degree-Granting Education

2004 University of Illinois, Urbana-Champaign, IL, PHD, Electrical and Computer Engineering
1996 Tsinghua University, Beijing, China, BE, Precision Instruments

Postgraduate Training

2004-2005 Research Fellowship, Biochemistry and Biophysics, University of California, San Diego, CA

Experience/Service

Academic Appointments

Research Instructor, Department of Genetics, Washington University, St. Louis, MO, 2009-2011

Other Appointments/Responsibilities

Senior Scientist, The Genome Institute at Washington University School of Medicine, St. Louis, MO, 2005-2011
Intern, Microsoft Research Asia, Beijing, China, 5/2001-8/2001

Professional Memberships

American Association for Cancer Research
Active Member, 2/2012-present
Institute of Electrical and Electronics Engineers
Senior Member, 2009
International Society for Computational Biology
Member, 9/2011-present

Selected Publications

Peer-Reviewed Original Research Articles

1. Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics. e-Pub 1/2014. PMID: 24389657.
2. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: A Targeted Iterative Graph Routing Assembler for breakpoint assembly. Genome Res. e-Pub 12/2013. PMID: 24307552.
3. 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 14(8). e-Pub 8/2013. PMID: 23972288.
4. 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 8(10):e77945, 2013. e-Pub 10/2013. PMID: 24205039.
5. 1000 Genomes Project Consortium, 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 491(7422):56-65, 11/2012. PMCID: PMC3498066.
6. 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 150(6):1121-34, 9/2012. PMCID: PMC3656590.
7. 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 150(2):264-78, 7/2012. PMCID: PMC3407563.
8. 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 486(7403):353-60, 6/2012. e-Pub 6/2012. PMCID: PMC3383766.
9. 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 10(5):570-82, 5/2012. e-Pub 4/2012. PMCID: PMC3348423.
10. 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. e-Pub 5/2012. PMCID: PMC3389765.
11. 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 and Graubert TA. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med 366(12):1090-1098, 2012 Mar 22;366(12):1090-8. Epub 2012 Mar 14., 3/2012. PMCID: PMC3320218.
12. Ding L, Ley T, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis J, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini V, Cook L, McGrath SD, Vickery TL, Wendi MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis E, Wilson R and Dipersio JF. Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing. Nature 481, 1/2012. e-Pub 1/2012. PMCID: PMC3267864.
13. 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. e-Pub 12/2011. PMCID: PMC3268238.
14. 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 305(15):1577-84, 4/2011. PMCID: PMC3156695.
15. 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, Stütz 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, 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65, 2/2011. PMCID: PMC3077050.
16. 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 8(8):652-4, 2011. e-Pub 6/2011. PMCID: PMC3527068.
17. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73, 10/2010. PMCID: PMC3042601.
18. 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 6(9):677-81, 9/2009. e-Pub 8/2009. PMCID: PMC3661775.
19. 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 25(17):2283-5, 9/2009. e-Pub 6/2009. PMCID: PMC2734323.
20. 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 456(7218):66-72, 11/2008. PMCID: PMC2603574.
21. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 10/2008. e-Pub 9/2008. PMCID: PMC2671642.
22. 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 17(5):659-66, 5/2007. e-Pub 4/2007. PMCID: PMC1855178.
23. 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 2(1):e1, 1/2006. e-Pub 1/2006. PMCID: PMC1356089.
24. Chen K, Hasegawa-Johnson M, Cohen A, Borys S, Kim S, Cole J, Choi JY. Prosody dependent speech recognition on radio news corpus of American English. IEEE Transactions on Speech and Audio Processing 14(1):232-245, 2006.

Invited Articles

1. Fan X, Abbott TE, Larson D, Chen K. BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping. In Current Protocols in Bioinformatics (2002), doi:10.1002/0471250953.bi1506s45 Key: citeulike:13116291, 3/2014.

Grant & Contract Support

Title: An Intergrative Analysis of Structural Variation for the 1000 Genomes Project (U41)
Funding Source: NIH/NCI
Role: Principal Investigator-MDACC
Principal Investigator: Charles Lee
Duration: 7/1/2013 - 6/30/2017
 
Title: Delineating Heterogeneous Structural Complexity in Cancer Genomes (R01)
Funding Source: NIH/NCI
Role: Principal Investigator
Duration: 4/1/2013 - 3/31/2017
 
Title: Center for Clinical and Translational Research (PP-2)
Funding Source: NIH/NCI Subcontract from the University of Texas Health Science Center-Houston
Role: Collaborator
Principal Investigator: David McPherson
Duration: 7/1/2012 - 6/30/2017

Last updated: 2/18/2014