Faculty Profile, National Health Research Institutes, Taiwan

Faculty Profiles

Feng-Chi Chen, Ph.D.

Assistant Investigator
Institute of Population Health Sciences


Ph.D., Department of Life Sciences, National Tsing-Hua University (2001)
B.Sc., Department of Biology, National Taiwan Normal University (1992)


Assistant Investigator, Division of Biostatistics and Bioinformatics, National Health Research Institutes (2006-)
Postdoctoral Research Fellow, Genomics Research Center / Institute of Information Science, Academia Sinica (2003-2006)
Fund Manager, Investment Dept., Sinotek Venture Group (2001-2003)


Dr. Chen's research interests include evolution of hominoids, alternative splicing, and evolution of gene interaction networks. Dr. Chen is currently focusing on unraveling the molecular mechanisms of human-specific diseases using a comparative genomics approach. He compares the genomic sequences between human and other primate species to identify potential key differences underlying the human specificity of disease susceptibility. He aims to incorporate the identified inter-species differences into the context of gene network.


Dr. Chen is the first one to delineate the evolutionary relationships of hominoids using genome-wide sequence sampling. He has estimated the divergence times between human, chimpanzee, gorilla, and orangutan based on the then largest sequence dataset containing the four species. He has also indicated that the common ancestor of human and chimpanzee did not experience severe population bottlenecks. His research article "Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees." has been cited for more than 200 times. Chen has also accurately identified a large number of insertions and deletions between human and chimpanzee, a considerable portion of which are located in coding exons and potentially play important roles in human unique traits. In the field of evolution of alternative splicing, he has discovered that alternatively spliced exons (ASEs) have complex evolutionary features in that different types of ASEs evolve at rates to opposite sides of those of constitutively spliced exons (CSEs). He has also successfully addressed the question whether ASEs evolve faster than CSEs using a large dataset from human-mouse homologous exons. He has found that ASEs are subject to distinct evolutionary pressures at synonymous and nonsynonymous sites, when compared with CSEs.


1. Chen FC, Chen CJ, Li WH, and Chuang TJ. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Research. 17:16-22, 2007.

2. Chen FC and Chuang TJ. The effects of multiple features of alternatively spliced exons on the KA/KS ratio test. BMC Bioinformatics. 7:259, 2006.

3. Chen FC, Chen CJ, Ho JY and Chuang TJ. Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons. BMC Bioinformatics. 7:136, 2006.

4. Chen FC, Wang SS, Chen CJ, Li WH and Chung TJ. Alternatively and constitutively spliced exons are subject to different evolutionary forces. Molecular Biology and Evolution. 23:675-682, 2006.

5. Chen FC and Li WH. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics. 68:444-456, 2001.