Chin-Fu Chen

Assistant Research Professor

Contact Information

113 Gregor Mendel Circle
Office of Bioinformatics and Epidemiology
Center for Molecular Studies
Greenwood Genetics Center

Phone: 864-388-1723
Fax: 864-388-1707



  • Post-doctoral Fellow, University of Pennsylvania School of Medicine
  • Ph.D. in Genetics, SUNY at Stony Brook
  • M.A. in Ecology and Evolution, SUNY at Stony Brook
  • M.S. in Forest Ecology, National Taiwan University
  • B.S. in Forestry, National Taiwan University

Research Interests

My laboratory utilizes Systems Biology approaches to study human genetic diseases with a focus on autism and intellectual disability. We are particularly interested in the following two major areas:

  1. Bioinformatic, statistical, and computational analyses on the gene expression, protein-protein interaction network, DNA methylation , single nucleotide polymorphism data that are generated via the high throughput technologies such as microarrays and next generation sequencing. We are in developing methods and algorithms for linking the disease phenotype (clinical presentations) with the genotype (mutations) in autism and intellectual disability.
  2. Functional (experimental) analyses of important cellular pathways such as tryptophan metabolism, circadian rhythm, and vitamin D that might be causing the pathogenesis of autism and intellectual disability. We also maintain a general interest in multiple aspects of bioinformatics and other human diseases. Current collaborative projects currently include semantic analysis of Gene Ontology and development of DNA methylation markers for colon cancer.

Selected Publications

  1. Sarasua SM, Dwivedi A, Boccuto L, Rollins JD, Chen C-F, Rogers C, Phelan K, DuPont B, Collins JS. 2011. Association between deletion size and important phenotypes expands the genomic region of interest in PhelaneMcDermid syndrome (22q13 deletion syndrome). J Med Genet. 48:761-766.
  2. Kuan C-Y, Walker TH, Luo P, Chen C-F. 2011. Long-chain polyunsaturated fatty acids promote paclitaxel cytotoxicity via inhibition of the MDR1 gene in the human colon cancer Caco-2 cell line. J Amer College Nutri 30:265-273.
  3. Zhou M, Hu Q, Li Z, Li D, Chen C-F, Luo H. 2011. Expression of a novel antimicrobial peptide Penaeidin4-1 in creeping bentgrass (Agrostis stolonifera L.) enhances plant fungal disease resistance. PLoS ONE6(9): e24677. doi:10.1371/journal.pone.0024677.
  4. Cheng C-H, Leung AY, Chen C-F. 2010. The effects of two different Ganoderma species (lingzhi) on gene expression in human monocytic THP-1 cells. Nutrition& Cancer 62(5): 648-658.
  5. Du Z, Li L, Chen C-F, Yu PS, Wang JZ. 2009. G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res 37:W345-9.
  6. Pawlowski P, Heringer-Walther S, Cheng C-H. , Archie J, Chen C-F, Walther T, Srivastava A. 2009. Microarray Expression Profiling Identifies Differential Expression of Genes in the Developing Brain of Agtr2-/y Mice. Genomics 94:188-195.
  7. Chen C-F, Cheng C-H. 2009. Regulation of cellular metabolism and cytokines by the medicinal herb feverfew in the human monocytic THP-1 Cells. Evidence-based Complementary and Alternative Medicine (eCAM) 61: 91-98.
  8. Chen, C-F. 2008. Robustness in Systems Biology: A Brief Review. J Biomechatron Engineer 1(2): 1-12.
  9. Weston Glenn JL, Chen C-F, Lewandowski A, Cheng C-H, Ramsdell CM, Bullard-Dillard R, Chen J, Dewey MJ, Glenn TC. 2008. Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping. BMC Genomics 9: 300; doi:10.1186/1471-2164-9-300.
  10. Chen C-F, Leung AY. 2007. Gene response of human monocytic cells for the detection of the anti-migraine activity of feverfew extracts. Can J Physiol Pharmacol 85: 1108-1115.
  11. Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F. 2007. A new method to measure the semantic similarity of GO Terms. Bioinformatics 23: 1274–1281.
  12. Luo F, Yang, Y, Chen C-F, Chang R, Zhou J, Scheuermann RH. 2007. Modular organization of protein interaction networks. Bioinformatics 23: 207–214.
  13. Chen C-F, Xin F, Szeto J. 2006. Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach. Comput Biol Chem. 30: 372-381.
  14. de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen C-F, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H. 2005. The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 33: D485-91.
  15. Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen C-F, Thomas MA, Haussler D, Jacob HJ. 2004. Comparative recombination rates in the rat, mouse, and human Genomes. Genome Res. 14: 528–538.
  16. Chen C-F, Feng X. 2003. A New Hybrid Self-Organizing Map and Fuzzy Logic Data Mining Approach for Understanding Macrophage Signaling Pathways through DNA Microarray Data. Proceedings of the 7th World Multiconference on Systematics, Cybernetics and Informatics, July 27-30, Orlando, Florida, USA. Vol. VIII 324-329.
  17. Li P, Struble CA, Chen C-F. 2003. Identifying Biological Processes in Microarray Data Using Singular Value Decomposition and the Gene Ontology Database. Proceedings of the 7th World Multiconference on Systematics, Cybernetics and Informatics, July 27-30, Orlando, Florida, USA. Vol. VIII 339-344.
  18. Jacob WT, Feng X, Sobczak N, Jiang H, Chen C-F, Kirova R, Struble C, Jiang N, Wang X, Tonellato P J. 2003. Multiple Approaches to Data-mining of Proteomic Data based on Statistical and Pattern Classification Methods. Proteomics 3(9): 1704-1709.
  19. Thomas MA, Chen C-F, Jensen-Seaman MI, Tonellato PJ, Twigger SN. 2003. Phylogenetics of rat inbred strains. Mammalian Genomics 14: 61-64.
  20. Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen C-F, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. 2002 Rat Genome Database (RGD): mapping disease onto the genome. Nucleic. Acids Res. 30: 125-128.
  21. Chen C–F, Katz ER. 2000. The mediation of cell-substratum adhesion by RasG in Dictyostelium J Cell Biochem 79:139-149.
  22. Stenton G R., Kim MK, Nohara O, Chen C-F, Hirji N, Wills FL, Gilchrist M, Hwang P-H, Park J-G, Finlay W, Jones RL, Befus AD, Schreiber AD. 2000. Aerosolized Syk antisense suppresses Syk expression, mediator release from macrophages and pulmonary inflammation J Immunology 164: 3790-3797.
  23. Chen C-F, Katz ER. 1998. Expression vector containing an N-terminal epitope tag for Dictyostelium discoideum. BioTechniques 25: 22-24.

Professional Affiliations

  • International Society for Computational Biology (ISCB), 2003- present
  • The New York Academy of Science, 2010-present
  • American Society of Hematology (ASH), 2004- present
  • Society for Leukocyte Biology (SLB), 2004- present