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 in department of Bioinformatics and Computational Biology at MD Anderson Cancer Center in Houston, TX. 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 cell populations with a focus on structural variants, towards understanding the heterogeneity and the evolution of cancer as a consequence of the genetics and the environment. 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: integrated omics, cancer target discovery in the context of targeted/immunotherapy
Jinzhuang Dou
Associate Computational Scientist, Applied Math/Bioinformatics
Research interests: single-cell multiomics, immunotherapy
Xianli Jiang
Postdoc, biology/bioinformatics
Research interests: protein-protein-interaction, AI, single-cell analysis
Merve Dede
Postdoc, bioinformatics,
MD
Research interests: systems biology, functional genomics
Yukun Tan
Postdoc, electrical
engineering
Research interests: single-cell, dynamic systems
Haijing Jin
CPRIT TRIUMPH postdoc fellow
Research interests: Genome
clonal evolution in cancer and associated translational impact
Qingnan Liang
Postdoc, Human genetics
Research interest: computational single cell genetics/regulation
Nejla Ozirmak Lermi
Associate Comp. Scientist
Liason of TMP-IL
Ramiz Iqbal
Bioinformatics Ph.D. student in UT GSBS
Research interests: cancer knowledge representation, literature mining
Qi Miao
Ph.D. student from UT School of Public Health
Research interests: single-cell CyTOF data analysis
Yuefan Huang
Ph.D. student from UT SPH
Research interests: single-cell, metabolism
Yuanxin Wang
Ph.D. student from GSBS
Research interests: single-cell, cell expression/communication
Holly Hill
Ph.D. student from UTSPH
Research interests: bioinformatics, epidemiology, lymphoma
Shengbin Ye
Ph.D. student from Rice Statistics, joint with Prof. Meng Li
Research interests: modeling complex relationship
Kun Hee Kim
Ph.D. student from GSBS
Research interests: math/statistical genomics, single-cell immunology
Yuchen Pan
Ph.D. student from UTSPH
Research interests: single-cell immunology
Shan (Chloe) He
Ph.D. student, UT GSBS, Biostat track
Research interest: geneset-phenotype association, biofunctional-statistics
Yujia Wang, UT GSBS Ph.D. student, 2nd rotation
Yang Zhang, BCM Ph.D. student, 3rd rotation
Samhita Vinay, Undergraduate student from CS at Rice University, TX
Alice Feng, Remote Intern from Harvard University, MA
Sahil Chowdhury, Remote Intern from Junior high, Dulles High school, Sugar Land, TX
Former Members
Shaoheng Liang, Ph.D. obtained 2022/12 in Rice CS, Research interests: single-cell statistics/machine-learning
Haonan Feng, Rotation Ph.D. student, UT GSBS, 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.
Sahil Chowdhury, 2022 Summer Intern, Junior high, Dulles High school, Sugar Land, TX
Siqi Lai (2021 Fall rotation Ph.D. student, UT GSBS), Bioinformatics
Haodong Xu (postdoc, proteomics/machine-learning), now assistant professor at UTHealth
Chenjie Lyu (MS student from GSBS, 2019-2021), machine learning
Junke Wang (2021 Spring rotation Ph.D. student, UT GSBS), 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, UT GSBS), 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 PhD student @UT Medical Branch at Galveston (UTMB)
Jack Leighton (rotation Ph.D. student, UT GSBS), neoantigen prediction
Tenghui Chen (Ph.D. 5/2016 from UT GSBS program), recipients of the GSBS 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 GSBS)
Naveen Ramesh (rotation Ph.D. student, UT GSBS), double-hit mutations
Smruthy Sivakumar (rotation Ph.D. student, UT GSBS), 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 BAML (Bank of America, Merrill Lynch).
Kevin Zhu (rotation Ph.D. student, UT GSBS), quantification of experimental assays
Han Chen (MS student from UT GSBS), cancer pathway/module identification
Rajendra Bahadur Shahi (visiting graduate student from Vrije University Brussel), genomics of non-small cell lung cancer