Biostatistics and Bioinformatics Shared Resource

Jeff W. Chou, Ph.D.

Bioinformatician IV
Department of Biostatistical Sciences 
Cancer Genomics Core and Biostatistics Core
Comprehensive Cancer Center
Center for Public Health Genomics
Wake Forest University School of Medicine
Medical Center Blvd.
Winston-Salem, NC 27157
Tel: (336) 713-1156
Email: jchou@wakehealth.edu

Education

North Carolina State University – PhD, Physics
North Carolina State University – MS, Computer Science
Shanghai Jiao Tong University - BA, Physics
Postdoctoral Fellowship, Brookhaven National Lab

Research Topics

  • Analysis of RNA/DNA-seq genomic and microarray gene expression dat
  • High dimensional statistical analysis; Data mining; Machine learning
    • Classification and prediction

Current Research

Dr. Chou is a bioinformatician with expertise in genomic data analysis and High dimensional statistical analysis. He has developed methods for unsupervised pattern extraction and bi-clustering with applications to microarray gene expression data.  He helps in developing RNA/DNA-seq analysis pipeline for Cancer Genomics Core and Center for Public Health Genomics. He provides analytic support for researchers both at Comprehensive Cancer Center and Wake Forest University School of Medicine. 

Selected Publications

  1. Chou JW, Paules RS, Bushel PR. Systematic Variation Normalization in microarray data to get gene expression comparison unbiased. J Bioinform Comput Biol, 2005 Apr;3(2):225-41.  PMID: 15852502.
  2. Zhou T, Chou JW, Simpson DA, Zhou Y, Mullen TE, Medeiros M, Bushel PR, Paules RS, Yang X, Hurban P, Lobenhofer EK, Kaufmann WK. Profiles of global gene expression in Ionizing-radiation-damaged human diploid fibroblasts reveal synchronization behind the G1 checkpoint in a G0-like state of quiescence. Environ Health Perspect, 2006 Apr;114(4):553-9.  PMCID:  PMC1440780.
  3. Zhou T, Chou JW, Mullen TE, Elkon RE, Zhou Y, Simpson DA, Bushel PR, Paules RS, Lobenhofer EK, Hurban P, Kaufmann WK. Identification of primary transcriptional regulation of cell-cycle-regulated genes upon DNA damage. Cell Cycle 2007, Apr 15;6(8):972-81.  PMCID: PMC2117899.
  4. Auman JT, Chou JW, Gerrish K, Huang Q, Jayadev S, Blanchard K, Paules RS. Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue. Environ Health Perspect. 2007 Apr; 115(4):572-8.  PMCID:  PMC18522695.
  5. Zhou T, Chou JW, Zhou Y, Simpson DA, Cao F, Bushel PR, Paules RS, Kaufmann WK. ATM-dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts. Molecular Cancer Research 2007, 5:813-822.
  6. Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. BMC Bioinformatics 2007, Nov 2;8:427.  PMCID:  PMC2194742.
  7. Zhou T, Chou JW, Watkins PB, Kaufmann WK. Toxicogenomics: transcription profiling for toxicology assessment. EXS. 2009; 99:325-66. DOI: 10.1007/978-3-7643-8336-7_12.  
  8. Chou JW, Bushel PR. Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes. BMC Genomics 2009 Jun 18;10:272.  PMCID:  PMC2706894.
  9. Bostrom MA, Lu L, Chou J, Hicks PJ, Xu J, Langefeld CD, Bowden DW, Freedman BI. Candidate genes for non-diabetic ESRD in African Americans: a genome-wide association study using pooled DNA. Hum Genet. 2010 Aug;128(2):195-204. PMCID: PMC3144421
  10. Miller LD, Coffman LG, Chou JW, Black MA, Bergh J, D'Agostino R Jr, Torti SV, Torti FM. An Iron Regulatory Gene Signature Predicts Outcome in Breast Cancer. Cancer Res. 2011 Nov 1;71(21):6728-37. PMCID: PMC3206152
  11. Loeser RF, Olex A, McNulty MA, Carlson CS, Callahan M, Ferguson C, Chou J, Leng X, Fetrow JS. Microarray analysis reveals age-related differences in gene expression during the development of osteoarthritis in mice. Arthritis Rheum. 2012 Mar;64(3):705-17. PMCID: PMC3269534
  12. Rajani KR, Pettit Kneller EL, McKenzie MO, Horita DA, Chou JW, Lyles DS. Complexes of vesicular stomatitis virus matrix protein with host rae1 and nup98 involved in inhibition of host transcription. PLoS Pathog. 2012 Sep;8(9):e1002929. PMCID: PMC3460625
  13. Turner CP, Gutierrez S, Liu C, Miller L, Chou J, Finucane B, Carnes A, Kim J, Shing E, Haddad T, Phillips A. Strategies to defeat ketamine-induced neonatal brain injury. Neuroscience. 2012 May 17;210:384-92. PMCID: PMC3358446
  14. Bailey JN, Lu L, Chou JW, Xu J, McWilliams DR, Howard TD, Freedman BI, Bowden DW, Langefeld CD, Palmer ND. The Role of Copy Number Variation in African Americans with Type 2 Diabetes-Associated End Stage Renal Disease. J Mol Genet Med. 2013 Jul 31;7:61. PMCID: PMC3973178.
  15. Alistar A, Chou JW, Nagalla S, Black MA, D'Agostino R Jr, Miller LD.  Dual roles for immune metagenes in breast cancer prognosis and therapy prediction. Genome Med. 2014 Oct 28;6(10):80. doi: 10.1186/s13073-014-0080-8. eCollection 2014. PMID: 25419236

Quick Reference

Biostatistics and Bioinformatics Shared Resource
Executive Director
Ralph D'Agostino Jr., PhD

336-716-9410
336-716-9011

rdagosti@wakehealth.edu

Co-Director
Xiaobo Zhou, PhD

xizhou@wakehealth.edu

Senior Biostatisticians
Janet Tooze, PhD

jtooze@wakehealth.edu

Doug Case, PhD

dcase@wakehealth.edu

Fang-Chi Hsu, PhD

fhsu@wakehealth.edu

Senior Bioinformaticians
Carl Langefeld, PhD

clangefe@wakehealth.edu

Guangxu Jin, PhD

gjin@wakehealth.edu

Jing Su, PhD

jsu@wakehealth.edu

Biostatisticians
Scott Isom, MS

sisom@wakehealth.edu

Greg Russell, MS

grussell@wakehealth.edu

Beverly Levine, PhD

blevine@wakehealth.edu

Bioinformaticians
Jeff Chou, PhD

jchou@wakehealth.edu

Liang Lui, PhD

lliu@wakehealth.edu

Dave McWilliams, PhD

dmcwilli@wakehealth.edu

Jian Zhang, PhD

jizhang@wakehealth.edu

Administrator
Tina Martin, BSBA

timartin@wakehealth.edu

 

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