Lab Members
Ken Chen, Ph.D.
Principal Investigator
Scopus profile
Elsevier Pure profile
My Bibliography at My NCBI
Google Scholar profile
Dr. Ken Chen is currently a tenured professor of Bioinformatics and Computational Biology at UT MD Anderson in Houston, Texas. He is a fellow of the American Institute of Medical and Biological Engineering (AIMBE) and a fellow of the Asia-Pacific Artificial Intelligence Association (AAIA). He received a B.Eng. degree from Tsinghua University, China (Precision Instruments, 1996), a Ph.D. from University of Illinois at Urbana-Champaign (Electrical and Computer Engineering, 2004, mentor: Mark Hasegawa-Johnson) and postdoctoral training from University of California, San Diego (Biophysics and Biochemistry, 2005). He also worked as a visiting researcher in Microsoft Research Asia (2001) and in Johns Hopkins University (Center for Language and Speech Processing, 2004). From 2005 to 2011, he worked for the Genome Institute at Washington University in St. Louis as a senior scientist and a research faculty (mentor: Elaine Mardis). Having a background in machine learning, statistical signal processing, bioinformatics, and genomics, his primary interest 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, novoBreak, monoVar, SiFit, TransVar, BreakTrans, BreakFusion, TIGRA, CREST, PolyScan, SomaticSniper, and VarScan, which have been widely applied to characterize individual and population genomics in various large-scale sequencing projects such as those in The Cancer Genome Atlas (TCGA), the 1000 Genomes Project and Human Cell Atlas. He is particularly interested in comprehensively and accurately constructing the genomes and the transcriptomes of various cancer and immune cell populations with a focus on structural variants, towards understanding the heterogeneity and the evolution of cancer and tumor microenvironment as a consequence of genetics and treatment. He is also interested in correlating genomics with diseases towards identifying biomarkers that are useful for personalized diagnosis and prognosis.
Vakul Mohanty
Research instructor, bioinformatics
Research interests: Systems biology, omics-driven cancer target discovery for targeted/immuno-therapy
Xianli Jiang
Postdoc, biology/bioinformatics
Research interests: Protein structural modeling, tumor microenvironment in immunotherapy
Merve Dede
Postdoc, bioinformatics, M.D./Ph.D.
Research interests: systems biology, functional genomics
Yukun Tan
Postdoc, electrical engineering
Research interests: cancer genomics, applications of artificial intelligence in molecular medicine
Nejla Ozirmak Lermi
Data scientist
Role: Bioinformatics/spatial omics analytics for the TMP-IL platform
Qing Ye
Postdoc, AI molecular medicine
Research interest: AI/ML Methods development for cancer molecular medicine
Meher Niger
Postdoc, co-mentored with Ziyi Li
Research interest: 3D pathology, large-scale computation
Kun Hee Kim
Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences
Research interests: single-cell immunology, TCR structural modeling and T cell fate
Yuchen Pan
Ph.D. student, UT School of Public Health
Research interests: Single-cell immunology, spatial transcriptomics
Yujia Wang
Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, Biostat track
Research interest: Tumor cellular ecosystem modeling, agent-based modeling
Ziyi Wang
Ph.D. student, Baylor College of Medicine, Quantitative & Computational Bioscience
Research interest: Cancer evolution, multiomics
Taylor Schababerle
Graduate Student, UT MD Anderson School of Health Professions, Diagnostic Genetics and Genomics
Research Interest: Malignant Pleural Mesothelioma
Co-mentors: Nejla Lermi Ozirmak, Cara Haymaker, et al.
- Reem Ali A Elghaish, UT MD Anderson UT Health Houston Graduate School of Biomedical Sciences QS Ph.D., with Nicholas Navin
- Songyun Li, UT MD Anderson UT Health Houston Graduate School of Biomedical Sciences QS Ph.D., with Nicholas Navin
- Yoonkyu (Ryan) Lee, CPRIT TRIUMPH fellowship, with Michael Andreeff
- Margaret He
Undergraduate neuroscience major at Rice University
Research interests: Protein structural modeling, artificial intelligence and pMHC-TCR interaction - Jasnoor Singh Aulakh
Undergraduate math and biology major at University of Houston
CATALYST summer intern - Ivor Ho
Undergraduate computer science and biology major at Florida State University
CATALYST summer intern
Postdoctoral and graduate research assistant positions are often available
We always welcome inquiries from trainees interested in our research and collaboration.
Former Members
Qingnan Liang, Postdoc, human genetics, Research interest: Methods development for Spatial Omics data analysis. now Assistant Professor at OUHSC | Computational Biology | Genomics
Qi Miao, Ph.D. student, UT School of Public Health, Research interests: Single-cell CyTOF data analysis; PhD defended in Apr. 2026
Shan (Chloe) He, Ph.D., defended May 2025 from UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, Biostat track, Research interest: Data-driven immunological state characterization , now Senior Scientist (Computational) at Genentech, San Francisco, CA.
Jinzhuang Dou, Associate data scientist, applied math/bioinformatics, Research interests: Math/computational methods for single-cell, population multiomics, now tenure-track Assistant Professor at University of Alabama Birmingham, June, 2025.
Shengbin Ye, Ph.D., from Rice Statistics, co-supervised with Prof. Meng Li at Rice, Research interests: symbolic regression, now teaching assistant professor at Northwestern University, 2025.
Yuanxin Wang, Ph.D., defended March 2025 from UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences; Research interests: cellular transitions, cell expression/communication, now application scientist at Amazon, San Diego, CA, May. 2025.
Ramiz Iqbal, Bioinformatics Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, Research interests: Cancer knowledge representation, literature mining
Fanwei Ruan, BCM, QCB, rotation student, cancer genomic rearrangement, 2025 spring
Yuanyuan Zhu, Rice Bioengineering, rotation student, AI education, 2025 spring
Catherine Zhou, CPRIT summer intern, Rice Computer Science, 2024
Jae Jun Ku, summer intern from Rice University, Computer Science, 2024
David Guan, summer intern from UT Austin, 2024
Satvik Elayavalli, CPRIT CURE/UPWARDS summer intern from Emory University, Georgia, 2023
Yuefan Huang, Ph.D. obtained in May 2023 from Biostats at UT School of Public Health, single-cell metabolism, cancer genomics, immunotherapy, now Translational Medical Scientist at Natera.
Holly Hill, Ph.D. obtained May 2023 from Epidemiology at UT School of Public Health, cancer genomics, personalized medicine, now Senior Scientist at Danaher Corporation, Clinical Science and Evidence Generation, Diagnostics.
Yang Zhang, Baylor College of Medicine Ph.D. student, 3rd rotation, 2023 Spring, cancer clonal-spatial evolution
Samhita Vinay, Undergraduate student from CS at Rice University, cancer/clinical genomics, supervised by Holly Hill
Sahil Chowdhury, Remote Intern from Junior high, Dulles High school, Sugar Land, Texas
Shaoheng Liang, Ph.D. obtained December 2022 in Rice CS, Research interests: single-cell statistics/machine-learning, now a postdoctoral fellow at CMU.
Haonan Feng, Rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, 2021-2022
Alice Feng, Intern high-school student, 2021-2022 from the Harker's School, CA, now undergraduate at Harvard University.
Richel Wang, Undergraduate student from CS at Rice University, TX, 2021-2022
Kyle Tsai, 2022 UT MD Anderson Summer Undergraduate Research Program (SURP) Intern, Freshman from CS at Princeton University, NJ. Supervised by Yuefan Huang
Sahil Chowdhury, 2022 Summer Intern, Junior high, Dulles High school, Sugar Land, TX
Siqi Lai (2021 Fall rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), Bioinformatics
Haodong Xu (postdoc, proteomics/machine-learning), now assistant professor at UTHealth
Chenjie Lyu (M.S. student from UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, 2019-2021), machine learning
Junke Wang (2021 Spring rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), Bioinformatics
Yupei Lin (2020 fall rotation Ph.D. student, BCM), Computational Biology
Fang Wang (Postdoctoral fellow, math/bioinformatics), math/statistics issues in tumor heterogeneity/single-cell data, integrated approaches for functional variant discovery, now principal investigator at Sun Yat-sen University, Guangzhou, China
Yifei Shen (Postdoc, bioinformatics), RNA analysis, personalized cancer therapy, now principal investigator at the 1st hospital of Zhejiang University, Zhejiang, China
Zhen Zuo (2019 fall rotation Ph.D. student, BCM), Statistics
Qihan (Chuck) Wang (Undergraduate student at Rice CS), Math, machine learning for tumor classification/diagnosis, now Software Engineer at Microsoft in Cambridge, Massachusetts.
Jincheng Han (2019 spring rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), Cancer Biology
Yu-yu (Fish) Lin (visiting Bioinformatics Ph.D. student from Taiwan), genome assembly, variant detection, high performance computing
Xiaofei Song (visiting Genetics Ph.D. student from BCM), structural variation mechanism and disease association, now assistant professor at Moffitt Cancer Center.
Albert Oh (summer intern from Univ. of Notre Dame), 2018, now in medical school
Xian Fan (Ph.D. Rice University Computer Science), structural variation characterization, 3rd generation sequencing, now assistant professor at Florida State University
Hamim Zafar (Ph.D. Rice University Computer Science), variant detection and tumor phylogeny from single-cell sequencing data; now an assistant professor at IIT Kanpur, India.
Nam Sy Vo (Postdoctoral fellow), immunoinformatics; now director, Center for Biomedical Informatics, Vin Big Data Affiliate Faculty, College of Engineering and Computer Science, Vin University, Hanoi, Vietnam
Zixing Wang (Postdoctoral fellow), statistical cancer genomics, integrative omics, unusual responders; now senior biostatistician at Seattle Genetics
Lucy Fox (rotation Rice CS undergraduate), dMMR prediction from patient mutation data/patterns using AI; software engineer at Google Brain
Zechen Chong (Postdoctoral fellow), structural variation detection and characterization, DREAM 8.5 Challenge winner, awarded the highly competitive Keck Computational Cancer Biology Training Program (CCBTP) fellowship in 2016, started as a tenured associate professor at University of Alabama Birmingham in March 2017.
Mike Spurgat (summer intern from University of Houston), 2016, now Ph.D. student at UT Medical Branch at Galveston (UTMB)
Jack Leighton (rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), neoantigen prediction
Tenghui Chen (Ph.D. 5/2016 from UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), recipients of the graduate school Deans Gee Family Legacy award for 2015-2016 and the 2015 Presidents' Research Scholarships for academic achievements, now Senior Investigator, Data Science at H3 Biomedicine
Jie Yang (rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences)
Naveen Ramesh (rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), double-hit mutations
Smruthy Sivakumar (rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), impact of tumor heterogeneity
Haijing Jin (rotation student, Baylor College of Medicine), gene annotation
Daniel Konecki (rotation student, Baylor College of Medicine), cancer driver gene identification
Wanding Zhou (Postdoctoral fellow), Genomic Bioinformatics, Odyssey postdoctoral fellowship, now a tenure-track assistant professor at Children's Hospital of Philadelphia (CHOP)
Yong Mao (Postdoctoral fellow), cancer driver prediction, clinical sequencing, now Vice President, Quartz Core Developer at Bank of America, Merrill Lynch
Kevin Zhu (rotation Ph.D. student, UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), quantification of experimental assays
Han Chen (M.S. student from UT MD Anderson UTHealth Houston Graduate School of Biomedical Sciences), cancer pathway/module identification
Rajendra Bahadur Shahi (visiting graduate student from Vrije University Brussel), genomics of non-small cell lung cancer