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. Using methods of systems biology (including experimentation and modeling), machine learning, and statistics, their long-term goal is to study gene networks and their roles in causing human diseases when disrupted.

One current major project is on feature selection in biological systems. This involves indentifying an optimal subset of features (for examples, genes in microarrays) that represent the critical characteristics of the system. However, large-scale genomic data (including transcriptomics and metabolomics) are high dimensional (>10,000) while containing small number of replicates. This will make analysis difficult and the results can be unpredictable. Conventionally, feature selection in microarrays is usually done by using a filter approach, such as a pre-set threshold of ‘two fold’ or a statistical significance level at 0.05. It is unknown whether these ad hoc methods produce the best results. It is therefore a pressing issue to develop a better solution to this complex question. Dr. Chen and his colleagues and students are utilizing information theory, geometric theory and various computational methods to address this question.

Dr. Chen’s lab is also exploring epigenetics utilizing both experimental and bioinformatic approaches to elucidate epigenetic effects in the genome.

Dr. Chen’s group also has an interest in bioinformatic tool development for genomic analyses, and continues to explore novel methods for effective analysis. They have developed an online computational tool, called LEAP, for detection of copy number variation (accessed through: They are also interested in developing and maintaining biological/medical databases for effective data mining.

Selected publications

  • Sarasua SM, Dwivedi A, Boccuto L, Rollins JD, Chen CF, Rogers RC, Phelan K, DuPont BR, Collins JS. Association between deletion size and important phenotypes expands the genomic region of interest in Phelan-McDermid syndrome (22q13 deletion syndrome). J Med Genet 2011 Nov;48(11):761-6.

  • Kuan CY, Walker TH, Luo PG, Chen CF. Long-Chain Polyunsaturated Fatty Acids Promote Paclitaxel Cytotoxicity via Inhibition of the MDR1 Gene in the Human Colon Cancer Caco-2 Cell Line. J Am Coll Nutr. 2011 Aug;30(4):265-73.

  • Zhou M, Hu Q, Li Z, Li D, Chen CF, Luo H. Expression of a Novel Antimicrobial Peptide Penaeidin4-1 in Creeping Bentgrass (Agrostis stolonifera L.) Enhances Plant Fungal Disease Resistance. PLoS One. 2011;6(9):e24677. Epub 2011 Sep 12.

  • 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): 1-11.
  • 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