Location: 4.100 - CCC


Epidemiology and Biostatistics

Chen, Yidong, Ph.D.


Personal Statement:

Currently, Dr. Chen is the director of the computational biology and bioinformatics program at Greehey Children’s Cancer Research Institute (GCCRI), and Professor in the Department of Epidemiology and Biostatistics (DEB, School of Medicine) at the UTHSCSA. Prior to joining the DEB, Dr. Chen was a staff scientist at the National Cancer Institute/NIH specializing in Bioinformatics, and Associate Investigator at National Human Genome Research Institute/NIH leading the bioinformatics efforts for microarray technology. He currently leads the bioinformatics effort in hepatoblastoma (HB) research (funded by Cancer Prevention and Research Institute of Texas (CPRIT).


Ph.D., Rochester Institute of Technology, Rochester, New York


Dr. Chen’s research focuses on bioinformatics, computational modeling, and biostatistics for the application of gene expression, miRNA, DNA copy number, SNP and other genome-wide profiling for cancer research, especially for pediatric cancer studies. In addition, his lab is continuing efforts on developing new data analysis methods for next-generation sequencing. microarray, and other high-throughput technologies, and is providing statistical analysis tools for research results of integrative data analysis, utilizing NCBI GEO data or TCGA data for comparative studies.


  • Co-director, Next-generation sequencing shared resources, Cancer Therapy and Research Center, San Antonio, TX
  • Faculty Advisor, Genome Sequencing Facility, UTHSCSA, San Antonio, TX
  • Professor, Dept. of Epidemiology and Biostatistics, UTHSCSA, San Antonio, TX


Complete List of Publications

  • Hsu YC, Chiu YC, Chen Y, Hsiao TH, Chuang EY. 2016. A simple gene set-based method accurately predicts the synergy of drug pairs. BMC systems biology. 10 Suppl 3:66. PMCID: PMC5009556
  • Chen HI, Jin Y, Huang Y, Chen Y. 2016. Detection of high variability in gene expression from single-cell RNA-seq profiling. BMC genomics. 17 Suppl 7:508. PMCID: PMC5001205
  • Cui X, Meng J, Zhang S, Rao MK, Chen Y, Huang Y. 2016. A hierarchical model for clustering m(6)A methylation peaks in MeRIP-seq data. BMC genomics. 17 Suppl 7:520. PMCID: PMC5001242
  • Ma C, Sastry KS, Flore M, Gehani S, Al-Bozom I, Feng Y, Serpedin E, Chouchane L, Chen Y, Huang Y. 2016. CrossLink: a novel method for cross-condition classification of cancer subtypes.
    BMC genomics. 17 Suppl 7:549. PMCID: PMC5001207
  • Wu HL, Hsiao TH, Chen PJ, Wong SH, Kao JH, Chen DS, Lu JY, Lu TP, Chen Y, Chuang EY, Tu HC, Liu CJ. 2016. Liver Gene Expression Profiles Correlate with Virus Infection and Response to Interferon Therapy in Chronic Hepatitis B Patients. Scientific reports. 6:31349. PMCID: PMC4992874
  • Liu Y, Wilson D, Leach RJ, Chen Y. 2016. MBDDiff: an R package designed specifically for processing MBDcap-seq datasets. BMC genomics. 17 Suppl 4:432. PMCID: PMC5001203
  • Rajamanickam S, Panneerdoss S, Gorthi A, Timilsina S, Onyeagucha B, Kovalskyy D, Ivanov D, Hanes MA, Vadlamudi RK, Chen Y, Bishop AJ, Arbiser JL, Rao MK. 2016. Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis. Clinical cancer research : an official journal of the American Association for Cancer Research. 22(14):3524-36. PMCID: PMC4947433
  • Cui X, Meng J, Zhang S, Chen Y, Huang Y. 2016. A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data. Bioinformatics (Oxford, England). 32(12):i378-i385. PMCID: PMC4908365
  • Toledo RA, Qin Y, Cheng ZM, Gao Q, Iwata S, Silva GM, Prasad ML, Ocal IT, Rao S, Aronin N, Barontini M, Bruder J, Reddick RL, Chen Y, Aguiar RC, Dahia PL. 2016. Recurrent Mutations of Chromatin-Remodeling Genes and Kinase Receptors in Pheochromocytomas and Paragangliomas. Clinical cancer research : an official journal of the American Association for Cancer Research. 22(9):2301-10. PMCID: PMC4854762
  • Hsiao TH, Chiu YC, Hsu PY, Lu TP, Lai LC, Tsai MH, Huang TH, Chuang EY, Chen Y. 2016. Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. Scientific reports. 2016; 6:23035. PMCID: PMC478978