Lab Members
Ken Chen, Ph.D.
Principal Investigator
Scopus profile
MDA Elseveir Pure
Web of Science
My Bibliography at My NCBI
Google Scholar Profile
Dr. Ken Chen is currently a tenured professor of Bioinformatics and Computational Biology at MD Anderson Cancer Center in Houston, Texas. 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
Jinzhuang Dou
Associate data scientist, applied math/bioinformatics
Research interests: Math/computational methods for single-cell, population multiomics
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
Haijing Jin
CPRIT TRIUMPH postdoctoral fellow
Research interests: Genome clonal evolution in cancer and associated translational impact
Qingnan Liang
Postdoc, human genetics
Research interest: Methods development for Spatial Omics data analysis
Nejla Ozirmak Lermi
Associate data scientist
Role: Bioinformatics/analytics for the TMP-IL platform
Ramiz Iqbal
Bioinformatics Ph.D. student, MD Anderson UTHealth Graduate School
Research interests: Cancer knowledge representation, literature mining
Qi Miao
Ph.D. student, UT School of Public Health
Research interests: Single-cell CyTOF data analysis
Yuanxin Wang
Ph.D. student, MD Anderson UTHealth Graduate School
Research interests: cellular transitions, cell expression/communication
Shengbin Ye
Ph.D. student from Rice Statistics, joint with Prof. Meng Li
Research interests: Modeling complex relationship
Kun Hee Kim
Ph.D. student, MD Anderson UTHealth Graduate School
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
Shan (Chloe) He
Ph.D. student, MD Anderson UTHealth Graduate School, Biostat track
Research interest: Data-driven immunological state characterization
Yujia Wang
Ph.D. student, MD Anderson UTHealth Graduate School, Biostat track
Research interest: Tumor ecosystem modeling
Margaret He
King Foundation High School Summer Program, rising freshman at Rice University
Research interests: Structural flexibility and cross-reactivity of TCR
Satvik Elayavalli
CPRIT CURE/UPWARDS summer intern from Emory University, Georgia
Research interest: Statistical methods for differential expressed gene test and cellular plasticity characterization
Postdoctoral and graduate research assistant positions are often available
We always welcome inquiry from trainees interested in our research and collaboration.
Former Members
Yuefan Huang, Ph.D. obtained in May 2023 from Biostats at UT School of Public Health, single-cell metabolism, cancer genomics, immunotherapy, now at GRAIL
Holly Hill, Ph.D. obtained May 2023 from Epidemiology at UT School of Public Health, cancer genomics, personalized medicine, now postdoc at Rice University
Yang Zhang, BCM Ph.D. student, 3rd rotation, 2023 Spring, cancer clonal-spatial evolution
Samhita Vinay, Undergraduate student from CS at Rice University, cancer/clinical cenomics, supervised by Holly
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 postdoc at CMU.
Haonan Feng, Rotation Ph.D. student, MD Anderson UTHealth Graduate School, 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 MDA 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, MD Anderson UTHealth Graduate School), Bioinformatics
Haodong Xu (postdoc, proteomics/machine-learning), now assistant professor at UTHealth
Chenjie Lyu (MS student from MD Anderson UTHealth Graduate School, 2019-2021), machine learning
Junke Wang (2021 Spring rotation Ph.D. student, MD Anderson UTHealth Graduate School), 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
Jincheng Han (2019 spring rotation Ph.D. student, MD Anderson UTHealth Graduate School), 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
Nam Sy Vo (Postdoctoral fellow), immunoinformatics; now Director, Center for Biomedical Informatics, VinBigdataAffiliate Faculty, College of Engineering and Computer Science, VinUniversity, 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 tenure-track assistant professor at U. Alabama Birmingham in March 2017.
Mike Spurgat (summer intern from Univ. of Houston), 2016, now Ph.D. student at UT Medical Branch at Galveston (UTMB)
Jack Leighton (rotation Ph.D. student, MD Anderson UTHealth Graduate School), neoantigen prediction
Tenghui Chen (Ph.D. 5/2016 from MD Anderson UTHealth Graduate School), recipients of the MD Anderson UTHealth 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, MD Anderson UTHealth Graduate School)
Naveen Ramesh (rotation Ph.D. student, MD Anderson UTHealth Graduate School), double-hit mutations
Smruthy Sivakumar (rotation Ph.D. student, MD Anderson UTHealth Graduate School), 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, MD Anderson UTHealth Graduate School), quantification of experimental assays
Han Chen (MS student from MD Anderson UTHealth Graduate School), cancer pathway/module identification
Rajendra Bahadur Shahi (visiting graduate student from Vrije University Brussel), genomics of non-small cell lung cancer