Chin-Fu Chen, PhD

Assistant Research Scientist

Dr. Chen joined the GGC's Center for Bioinformatic and Epidemiological Studies in 2010. His lab's research interests and expertise are primarily in bioinformatic data analysis and functional genomics. Dr. Chen's lab combines statistical and computational methods with experimental approaches to study human genetic diseases.

I. Current bioinformatic projects

1.  Using feature selection and machine learning approaches for analysis of metabolic and genomic data produced by the autism studies at the Greenwood Genetic Center.

2. Analysis of microRNA network in the autism spectrum disorders and other human genetic diseases.

3. Continuing improvement of an on-line metal-tool, MICO, for integration of the predictions on the functional consequences of human non-synonymous variants. MICO is accessible via: Dr. Chen's group is also developing novel computational methods for effective analysis human mutations.

II. Experimental approach
Dr. Chen's lab is focusing on understanding roles of circadian rhythms and microRNAs play in pathogenesis of autism spectrum disorders and other human genetic diseases.


Selected publications


  • Alexander M, Steck SE, Burch JB, Chen C-F, Hurley TG, Cavicchia P, Ray M,Nitin Shivappa N, Guess J, Zhang H, Youngstedt SD, Creek KE, Lloyd SC, Yang X, Hebert JR. 2014. Case-Control Study of the PERIOD3 Clock Gene Length Polymorphism and Colorectal Adenoma Formation. Oncol Rep (In press).
  • Tabung FK, Steck SE, Burch JB, Chen C-F, Zhang H, Hurley TG, Cavicchia P, Alexander M, Nitin Shivappa N, Creek KE, Lloyd SC, Hebert JR. 2014. A Healthy Lifestyle Index is associated with reduced risk of colorectal adenomatous polyps among non-users of non-steroidal anti-inflammatory drugs. J Prim Prev (In press).
  • Lee, G, Chen, C-F. 2014. MICO: A meta-tool for prediction of the effects of non-synonymous mutations. Bioinformation 10 (7): 469-471.
  • Zhou P, Zhang G, Chen S, Jiang Z, Tang Y, Henrissat B, Yan Q, Yang S, Chen C-F, Zhang B, Du Z. 2014. Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei. BMC Genomics 15:294.
  • Sarasua SM, Boccuto L, Sharp JL, Chen C-F, Dwivedi A, Rollins JD, Collins JS, Rogers RC, Phelan K, Dupont BR. 2014. Original Investigation Clinical and genomic evaluation of 201 patients with Phelan– McDermid syndrome. Hum Genet 133(7):847-59.
  • Sarasua SM, Dwivedi A, Boccuto L, Chen C-F, Sharp JL, Rollins JD, Collins JS, Rogers RC, Phelan K, Dupont BR. 2013. 22q13.2q13.32 genomic regions associated with severity of speech delay, developmental delay, and physical features in Phelan-McDermid syndrome. Genet Med 16(4):318-28.
  • Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C.-J.,• Brown N, Carlson JE, Tien M, Liang H. 2013. Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide. Plant Cell Rep 32:1827-41.
  • Schwartz CE, Chen C-F. 2013. Progress in Detecting Genetic Alterations and Their Association with Human Disease. J Mol Biol 425: 3914–3918.
  • Boccuto L, Chen C-F, Pittman AR, Skinner CD,McCartney HJ, Kelly Jones K, Bochner BR, Stevenson RE, Schwartz CE. 2013. Decreased tryptophan metabolism in patients with autism spectrum disorders. Molecular Autism 4:16
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Chen, C-F. 2008. Robustness in Systems Biology: A Brief Review. J Biomechatron Engineer 1(2): 1-12.
  • 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.
  • 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.
  • 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.
  • Luo F, Yang, Y, Chen C-F, Chang R, Zhou J, Scheuermann RH. 2007. Modular organization of protein interaction networks. Bioinformatics 23: 207–214.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Thomas MA, Chen C-F, Jensen-Seaman MI, Tonellato PJ, Twigger SN. 2003. Phylogenetics of rat inbred strains. Mammalian Genomics 14: 61-64.
  • 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.
  • Chen C–F, Katz ER. 2000. The mediation of cell-substratum adhesion by RasG in Dictyostelium J Cell Biochem 79:139-149.
  • 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.
  • Chen C-F, Katz ER. 1998. Expression vector containing an N-terminal epitope tag for Dictyostelium discoideum. BioTechniques 25: 22-24.

Contact Information

Office (864) 388-1723
Fax (864) 388-1706


  • B.S. National Taiwan University
  • M.S. National Taiwan University
  • M.S. SUNY at Stony Brook
  • Ph.D. SUNY at Stony Brook (Genetics)
  • Postdoctoral Fellow, University of Pennsylvania School of Medicine (Hematology & Oncology)

Areas of Expertise