We are a computational biology group in the Department of Bioinformatics and Computational Biology at UT MD Anderson Cancer Center in Houston, Texas.
We are interested in developing computational methods to systematically and accurately characterize the genomics and the transcriptomics of human cell populations using high throughput sequencing technology. For example, we have developed approaches that successfully discovered and reconstructed structural variation in a variety of cancer genomes. We are also interested in developing integrative approaches that help understand the etiology of cancer.  We are actively involved in several large-scale genomics projects such as the Cancer Genome Atlas (TCGA) and the 1000 Genomes projects.  Since 2012, we have worked with the Khalifa Institute of Personalized Cancer Therapy to establish routine genome sequencing at MD Anderson cancer center.

Achievements

  • Ramiz (Ph.D. student) awarded an NLM fellowship to perform knowledge modeling/acquisition from electronic medical record EMR data, 2019
  • Ken Chen (PI) received an award from CPRIT to investigate cancer genome instability and related therapeutics, 2018
  • Ken Chen (PI) received an award from Chan-Zuckerberg Initiative for developing novel single-cell data analysis methods, 2018
  • A nice story about how our tool novoBreak is optimized in the cancer genome cloud.
  • Zechen started as a tenure-track assistant professor at University of Alabama, Birmingham, March 2017 
  • Zechen (postdoc)'s first author paper (novoBreak) published in Nature Methods, 2016
  • Hamim (student)'s first author paper (Monovar) published in Nature Methods, 2016
  • Ken Chen (PI) awarded Andrew Sabin Family Fellow, 2016-2017
  • Our systematic study of 1,000 cancer patients identified pathogenic germline variants missed by standard testing, Meric et al., 2015
  • Zechen Chong (postdoc) awarded Keck fellow, 2015
  • We obtained R01 supplement award to test NCI Cloud Pilot Centers
  • The T200 (MD Anderson Institute of Personalized Cancer Therapy) platform paper led by our group published in Chen et al., Clinical Chemistry, 2015.  So far, this platform has been applied to study over 10,000 MD Anderson tumor samples, 2015.
  • Tenghui Chen (student) received GSBS President's research scholarship award, 2015
  • Tenghui Chen (student) received GSBS Deans Gee Family Legacy award, 2015
  • Wanding Zhou (postdoc) and Tenghui Chen (student) published co-first author paper (TransVar) in Nature Methods, 2015
  • SV tools developed by this group identified a driver gene fusion in sporadic Medullary Thyroid Carcinoma, Grubbs et al., 2014.
  • Zechen Chong (postdoc) ranked No. 1 in ICGC-TCGA DREAM 8.5 somatic mutation calling structural variation sub-challenge, 2014
  • Xian Fan (student) published 2 first author paper, 2014
  • Wanding Zhou (postdoc) awarded MD Anderson Odyssey Fellow
  • Ken Chen (PI) awarded a U01 sub-award to establish informatics for routine patient genomic profiling
  • Ken Chen (PI) awarded a U41 sub-award with the Human Genome Structural Variation Consortium (formerly, 1000 Genomes SV group) from NHGRI to study structural variation in human population using the 2nd and 3rd generation sequencing
  • Ken Chen (PI) award a NCI R01 grant to delineate structural heterogeneity in cancer genomes, 2012