Our mission
Using IT innovations to increase the quality of life (QoL)
Introduction on what we have done and what we want to do
At recent years, we put focuses on following important issues:
(1) Network analysis of human protein interactions for Tumorigenesis and infectious diseases in the approach of systems biology
We have implemented a statistical model into our protein interaction database for validation of two-hybrid assays of Helicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally. By this approach, we can compare the interacting network of various strains with different virulence to decipher the secret between hosts and pathogens (http://dpi.nhri.org.tw/hp/, Bioinformatics 2005). Using the more sophisticated statistical method with expression profile, we integrated a database named as flydpi for the interactome of Drosophila Melanogaster (http://flydpi.nhri.org.tw, BMC Bioinfo, 2006). And we also constructed a topological analyzer for complex network named as Hubba (NAR, 2008, http://hubba.iis.sinica.edu.tw). Objectives of our work are to improve our understanding of the puzzle during development stage, carcinogenesis and infectious mechanism, and to furthermore introduce a new paradigm for the diagnosis and treatment of human disease to revolutionize current medical services delivered.
(2) Developing value-added databases and web applications for biomedical research communities
We have published several web applications and databases related with bioinformatics for biomedical research community. For example, the web application, Primer Design Assistant (PDA) (NAR, 2003, , http://dbb.nhri.org.tw/primer/), can be helpful to large scale PCR for high throughput experiments like microarray experiments. From July 2003 to Mar 2008, the accumulated visits and processed sequences go beyond 100,000 and 620,000, respectively. PDA is not only served for research groups, but also was used to develop the rapid diagnostic kit for SARS for Central of Disease Control (CDC), Taiwan in 2004. Until now, there are several diagnostic kits developed by PDA. Based on similar idea, we have implemented a platform for unique probe design for various uses in hybridization, like microarray and blots named as "Unique Probe Selector, UPS" ( http://array.iis.sinica.edu.tw/ups , BMC Bioinfo 2008).
In 2005, we have implemented a phylogenetic platform for topology construction and visualization named as POWER (http://power.nhri.org.tw, NAR, 2005). We are working on the best model selection in automatic way and try to integrate two systems for biomedical research groups.
(3) Metagenomics
According to the advance in sequencing technology, time for sequencing large genome like human genome would not take several months/years but weeks/days. Several shotgun sequencing projects of various communities have been completed and started. Following the flood of massive sequence data, there are several interesting computational problems that arise from WGS sequencing of communities. Those issues related with how to compare communities, how to separate sequence from different organisms in silico, and how to model population structures using WGS assembly statistics, will be new challenges in the field of bioinformatics. Our approach here is to integrate various databases, gene expression analysis, proteomic results and phylogenetic reconstruction to achieve a comprehensive view of microbial communities.
List of Publications
1. 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., volume 31, pages 3751-3754, July 2003, (SCI/ 7.62) (Access URL : http://dbb.nhri.org.tw/primer/)
2. Chen, S. H., Lin, C. Y., Huang, F. L. and Kuo, C. M., "Cloning of Two Crustacean Hyperglycemic Hormone Isoforms from the Freshwater Giant Prawn, Macrobrachium rosenbergii: Evidence of Alternative Splicing," Mar. Biotech., volume 6, number 1, pages 83-94, October 2004, (SCI/ 1.4)
3. 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., volume 32, number 3, pages 27-35, February 2004, (SCI/ 7.62)
4. 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., volume 33, pages 553-556, July 2005, (SCI/ 7.62) (Access URL : http://power.nhri.org.tw)
5. Chen, S. H., Lin, C. Y. and Kuo, C. M., "In silico Analysis of the Crustacean Hyperglycemic Hormone Family," Mar. Biotech., volume 7, number 3, pages 193-206, June 2005, (SCI/ 1.4)
6. 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, volume 21, pages 1288-1290, April 2005, (SCI/ 6.701)(http://dpi.nhri.org.tw/hp/)
7. Lin C.Y. , Chen S. H., Cho C. S., Chen C. L., Lin F. K., Lin C. H., Chen P. Y., Lo C. Z., and Hsiung C.A., "Fly-DPI: Database of Protein Interactomes for D. melanogaster in the Approach of Systems Biology.," BMC Bioinformatics, volume 7, number 5, pages S18, December 2006, (SCI/4.96) (URL:http://flydpi.nhri.org.tw)
8. Jiang S. S., Chang I. S., Huang L. W., Chen P. C., Wen C. C., Liu S. C., Chien L. C., Lin C. Y., Hsiung C. A., Juang J. L., "Temporal Transcription Program of Recombinant Autographa californica Multiple Nucleopolyhedrosis Virus.," Journal of Virology, volume 80, pages 8989-8999, July 2006, (SCI/ 5.178)
9. Wen, C. C., Wu, Y. J., Huang, Y. H., Chen, W. C., Liu, S. C., Jiang, S. S., Juang, J. L., Lin, C. Y., Fang, W. T., Hsiung, C. A., Chang, I. S., "A Bayes Regression Approach to Array-CGH Data," Statistical Applications in Genetics and Molecular Biology, volume 5, number 1, May 2006, (http://www.bepress.com/sagmb/vol5/iss1/art3/), (Medline Index)
10. 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, volume 23, pages 279 - 291, April 2006, (SCI/ 6.355)
11. Tao-Wei Huang, Chung-Yen Lin* and Cheng-Yan Kao*, "Reconstruction of human protein interolog network using evolutionary conserved network," BMC Bioinformatics, volume 8, number 152, pages 1-14, May 2007, (SCI/4.96)(*: Corresponding Authors)
12. Chen, S.H., Lo, C.Z., Tsai, M. C., Hsiung C.A., Lin, C.Y., "Unique Probe Selector (UPS): A Comprehensive Web Service for Probe Design and Oligo Nucleotide Arrays," BMC Bioinformatics, volume 8, number 10, pages S8, January 2008, (URL: http://array.iis.sinica.edu.tw/ups)
13. Lin, C. Y.*, Chin, C. H., Wu, H. H., Chen, S. H., Ho, C. W.,* Ko, M. T.*, "Hubba: Hub Objects Analyzer : A Framework of Interactome Hubs Identification for Network Biology," Nucleic Acids Research, volume 36, number 2008 Web application Issue, pages W438-W443, July 2008, Nucleic Acids Research Advance Access published online on May 24, 2008 (http://hub.iis.sinica.edu.tw) (SCI/6.94)
14. Chen, S.H., Su,S. Y., Lo, C. Z., Huang, T. J., Kuo, B. H., Lin, C. Y.*, "Phylogenetic reconstruction by Automatic Likelihood Model Selector (PALM) : A Framework for Phylogenetic Analysis with the Best Substitution Model," PLoS ONE, volume 4, number 12, pages e8116, December 2009, http://palm.iis.sinica.edu.tw
15. Chin, C. H., Chen, S. H., Ho, C. W., Ko, M. T.* Lin, C. Y.*, "A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles," BMC Bioinformatics, volume 11, number S1, pages S25, January 2010, http://hub.iis.sinica.edu.tw/Hunter
16. Shiao, Y.M., Lee, C. C., Hsu, Y. H., Huang, S. F., Lin, C. Y., Li, L. H., Fann, C. S. J., Tsai, C. Y., Tsai, S. F., Chiu, H. C., "Ectopic and High CXCL13 Chemokine Expression in Myasthenia Gravis with Thymic Lymphoid Hyperplasia," Journal of Neuroimmunology, March 2010, Collaborated works with wet lab teams in NHRI and YM University, Available online 11 March 2010
17. Leu, J. H*., Chen, S. H*., Wang, Y. B., Chen, Y. C., Su, S. Y., Lin, C. Y., Ho, J. M., Lo, C. F., "A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp," Marine Biotechnology, April 2010, Invited Review, ref website: http://sysbio.iis.sinica.edu.tw/page
Contact person: Chung-Yen Lin Ph.D