Faculty Profile, National Health Research Institutes, Taiwan

Faculty Profiles


Chung-Yen Lin, Ph.D.

Joint-appointed Assistant Investigator
Institute of Population Health Sciences
cylin@nhri.org.tw

EDUCATION

Ph.D., Institute of Zoology, National Taiwan University, Taiwan, 1999
M.S., Institute of Fishery Science, National Taiwan University, Taiwan, 1993
B.S., Department of Zoology, National Taiwan University, 1991

PROFESSIONAL EXPERIENCES

- Assistant research fellow, Institute of Information Science, Academia Sinica, Taiwan (2005-present)
- Joint-appointed Assistant Investigator, Division of Biostatistics and Bioinformatics, National Health Research Institutes, Taiwan (2005-present)
- Joint-appointed Assistant Professor, College of Life Science, National Taiwan University, Taiwan (2005-present)
- Assistant Investigator, Division of Biostatistics and Bioinformatics, National Health Research Institutes, Taiwan (2004-2005)
- Postdoctoral Fellow, Division of Biostatistics and Bioinformatics, National Health Research Institutes, Taiwan (1999-2003)

RESEARCH INTERESTS

At recent years, Dr. Lin puts his focuses on the following important issues:
1. Deciphering the protein network of tumorigenesis and stem cells differentiation in the approach in Network biology and Systems Biology.
2. Developing value-added databases and web applications for biomedical research communities.
3. Developing Electronic Laboratory Notebook (ELN) in OpenSource for post-genomics and large scale experiments.
4. Metagenomics on extreme biology.

RESEARCH ACTIVITIES & ACCOMPLISHMENTS

Dr. Lin focuses on the following researches and has achieved significant results:
1. Network analysis of human protein interactions for tumorigenesis and infectious diseases in the approach of systems biology
2. Developing value-added databases and web applications for biomedical research communities including
2.1 Genomic researches, design PCR primer and probe for hybridization:
a. Primer Design Assistant (PDA) (NAR, 2003, http://dbb.nhri.org.tw/primer/)
b. Unique Probe Selector (UPS) (BMC Bioinformatics, 2008, http://array.iis.sinica.edu.tw/ups)

2.2 Protein interactome network,
a. Interactome of Helicobacter pylori (hp-DPI), (Bioinformatics 2005, http://dpi.nhri.org.tw/hp/)
b. Interactome of Drosophila melanogaster (flyDPI),(BMC Bioinformatics, 2006, http://flydpi.nhri.org.tw)

2.3 Phylogenetic platform for topology construction and visualization, Phylogenetic Web Repeater (POWER), (NAR 2005, http://power.nhri.org.tw)

SELECTED PUBLICATIONS

1. Chen, S.H., Tsai, M.K., Lo, C.Z., Hsiung, C. A., Lin, C. Y*. Unique Probe Selector (UPS): A Comprehensive Web Service for Probe Design and Oligo Nucleotide Arrays. BMC Bioinformatics, 9 (Suppl 1):S8, 2008. (ref site: http://array.iis.sinica.edu.tw/ups) (*=Corresponding Author)

2. Huang, T. W., Lin, C.Y. *, and Kao, C.Y.*. Reconstruction of human protein interolog network using evolutionary conserved network, BMC Bioinformatics, 8 (152): 1-14, 2007. (*=Corresponding Author)

3. Lin, C. Y., Chen, S.H., Chen C.L., Cho, C.S., Lin, F.K., Lin, C.H., Chen P. Y., Lo, C.Z., Hsiung, C. A. Fly-DPI: Database of Protein Interactomes for D. melanogaster in the Approach of Systems Biology. BMC Bioinformatics. 7(S5):S18, 2006. (ref site: http://flydpi.nhri.org.tw)

4. Chang, C. C., Lin, H. C., Lin, I. P., Chang, T. Y., Chen, H. H., Chen, W. H. Cheng, C. H., Lin, C. Y., Liu, S. M. Chang, C. C. Chaw, S. M. The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae): Comparative Analysis of Evolutionary Rate with That of Grasses and Its Phylogenetic Implications. Mol. Bio. Evol. 23:279-291, 2006.

5. Pan W. H., Lynn K. S., Chen C. H., Wu Y. L., Lin C. Y., Chang H.Y. Using endophenotypes for pathway clusters to map complex disease genes. Gen. Epi. 30(2):143-154, 2006.

6. Lin, C. Y., Lin, F.K., Lin, C.H., Lai, L.W., Hsu, S.J., Chen, S.H., Hsiung, C. A. POWER: PhylOgenetic WEb Repeater-An integrated and user-optimized framework for bio-molecular phylogenetic analysis. Nucleic Acids Res. 33:553-556, 2005. (ref site: http://power.nhri.org.tw)

7. Lin, C. Y., Chen C.L., Cho, C.S., Wang L.M., Chang C. M., Chen P. Y., Lo, C.Z., Hsiung, C. A. hp-DPI: Helicobacter pylori Database of Protein Interactomes, A Combined Experimental and Inferring Interactions. Bioinformatics. 21:1288-1290, 2005. (ref site: http://dpi.nhri.org.tw/hp/)

8. Li, L.H., Li, J. C., Lin, Y. F., Lin, C. Y., Chen, C.Y., Tsai, S. F. Genomic Shotgun Array: A Procedure Linking Large-Scale DNA Sequencing with Regional Transcript Mapping. Nucleic Acids Res. 32(3):e27, 2004.

9. Lin, C. Y., Chen, S. H, Lo, C.Z., Cho, C.S., Hsiung, C. A. Primer Design Assistant (PDA): a Web-based Primer Design Tool. Nucleic Acids Res. 31:3751-3754, 2003.(ref site: http://dbb.nhri.org.tw)

PATENT

l. Juang, J.L., Hsiung ,C.A., Lin, C.Y. “Cross-species nucleic acid probes” 2007. Taiwan Serial No. 92103058.