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研究人員 ｜ Research Faculty

● Adjunct Assistant Research Fellow, Division of Biostatistics and Bioin-
林仲彥 Chung-Yen Lin formatics, National Health Research Institutes (2005/10- )
● Adjunct Assistant Professor, Institute of Fishery Science, College of
Life Science, National Taiwan University (2005/08- )
● Assistant Research Fellow, Division of Biostatistics and Bioinformat-
助研究員 Assistant Research Fellow ics, National Health Research Institutes (2004/01- 2005/10)
Ph.D., Zoology, National Taiwan University ● PhD, National Taiwan University (1999)
Tel: +886-2-2788-3799 ext. 1704
Fax: +886-2-2782-4814
Email: cylin@iis.sinica.edu.tw
http://www.iis.sinica.edu.tw/pages/cylin

方式建構複雜的親緣分析關係 (PALM, http://palm.iis.sinica.edu.tw/, PLoS ONE, 2009)。 Recently, we have published our work to select the best model automati- of massive amounts of sequence data, several interesting computational
cally, and help several biomedical research groups to conquer the recon- problems have arisen from WGS sequencing by communities. Issues like
(3) 多源基因體學 (Metagenomics) struction of phylogenetic tree with large dataset (PALM, http://palm.iis. how to compare communities, how to separate sequences from differ-
由於近年來定序技術的大幅進步，以往耗時數月整年的定序工作，可以在數天內完 sinica.edu.tw/, PLoS ONE, 2009). ent organisms in silico, and how to model population structures using
成，這樣的技術，開啟了新一代的研究領域，也就是多源基因體學，又稱環境基 (3) Metagenomics WGS assembly statistics, will present new challenges in the field of bio-
因體學 (Environmental Genomics)，生態基因體學 (Ecogenomics)，群體基因體學 informatics. Our approach involves integrating various databases, gene
(Community Genomics)。這一類的研究，除了快速大規模定序外，就必須依賴生物 Because of the advances in sequencing technology, a large genome, expression analysis, proteomic results and phylogenetic reconstruction
研究簡介 資訊學的協助，來對解析出來的序列進行快速的序列比對、功能註解與建置資料庫 such as the human genome, can be sequenced in a matter of weeks or to achieve a comprehensive view of microbial communities.
平台，進而找出其存在可能的物種與其所具備的功能。為了了解這些微生物間在不 even days, rather than several months or years. Following the generation
目前本研究團隊，現階段主要的研究方向可分為(1)網路生 同棲息環境的消長與互動，本研究團隊將整合與建置自動化分析平台，來剖析巨量
物及系統生物學研究(2)生物資訊加值資料庫與應用系統之 資料中，所代表的複雜的群聚交互作用與預測環境變動後的微生物組成。
建置(3)多源基因體學。
代表著作 Publications
(1)網路生物及系統生物學研究
為了解析人類成癌過程與病原致病機轉之蛋白質交互網路， Research Description 1. Lin, C. Y.*, Chen, S. H, Lo, C.Z., Cho, C.S., Hsiung, C. A., “Primer W. H. Cheng, C. H., Lin, C. Y., Liu, S. M. Chang, C. C. Chaw, S. M.,
我們透過比較蛋白質體學 (Comparative Proteomics) 的方 Design Assistant (PDA): a Web-based Primer Design Tool.,” Nucleic “The Chloroplast Genome of Phalaenopsis aphrodite (Orchidaceae):
法，將現有已知的蛋白質交互作用關係，轉化為序列模組與 In recent years, my research has focused on following important issues: Acids Res., volume 31, pages 3751-3754, July 2003, (SCI/ 7.62) (Ac- Comparative Analysis of Evolutionary Rate with That of Grasses and
模組之間的關係，藉此建立統計模型，來預測可能存在的蛋 cess URL : http://dbb.nhri.org.tw/primer/) Its Phylogenetic Implications.,” Mol. Bio. Evol, volume 23, pages 279
白質交互網路架構，再加上與代謝途徑、基因分類與時空背 (1) Network analysis of human protein interactions for Tumorigenesis and in- 2. Li, L.H., Li, J. C., Lin, Y. F., Lin, C. Y., Chen, C.Y., Tsai, S. F., “Ge- - 291, April 2006, (SCI/ 6.355)
景等相關的註解，便可以協助我們瞭解在不同的發育階段、 fectious diseases in systems biology nomic Shotgun Array: A Procedure Linking Large-Scale DNA Se- 11. Huang, T. W., Lin, C. Y.*, and Kao, C. Y.*, “Reconstruction of human
癌細胞生成轉移及病原感染之際，可能的產生蛋白質網路。 In our current work, we are constructing eukaryotic protein-protein interaction net- quencing with Regional Transcript Mapping.,” Nucleic Acids Res., protein interolog network using evolutionary conserved network,”
另外，與胃部疾病具有高度相關的幽門桿菌 (http://dpi.nhri. works from recently high though-put interactome studies of various species. Mean- volume 32, number 3, pages 27-35, February 2004, (SCI/ 7.62) BMC Bioinformatics, volume 8, number 152, pages 1-14, May 2007,
(SCI/4.96)(*: Corresponding Authors)
org.tw/hp/)，與模式生物果蠅 (http://flydpi.nhri.org.tw)的 while we have also integrated a statistical model into our protein interaction data- 3. Lin, C. Y.*, Lin, F.K., Lin, C.H., Lai, L.W., Hsu, S.J., Chen, S.H., Hsi-
蛋白質交互網路，也於分別於 Bioinformatics (2005) 及BMC base for validation of two-hybrid assays of Helicobacter pylori, and the prediction of ung, C. A., “POWER: PhylOgenetic WEb Repeater - An integrated 12. Chen, S.H., Lo, C.Z., Tsai, M. C., Hsiung C.A., Lin, C.Y.*, “Unique
Bioinformatics (2007) 刊出。目前的研究重點放在不同物種 putative protein interactions not yet discovered experimentally (hp-DPI, http://dpi. and user-optimized framework for bio-molecular phylogenetic analy- Probe Selector (UPS): A Comprehensive Web Service for Probe De-
sign and Oligo Nucleotide Arrays,” BMC Bioinformatics, volume 8,
sis.,” Nucleic Acids Res., volume 33, pages 553-556, July 2005, (SCI/
品系的交互網路與致病性之研究，並試著解析病原與宿主 nhri.org.tw/hp/, Bioinformatics 2005). Using a more sophisticated statistical method 7.62) (Access URL : http://power.nhri.org.tw) number 10, pages S8, January 2008, (URL: http://array.iis.sinica.edu.
間可能產生的交互作用。目前已建置拓樸理論 (Topology)與 with expression profile, we integrated a database called flydpi for the interactome tw/ups)
圖學 (Graph Theory) 等網路生物學 (Network Biology) 的分析 of Drosophila Melanogaster (http://flydpi.nhri.org.tw, BMC Bioinfo, 2006). And we 4. Chen, S. H., Lin, C. Y. and Kuo, C. M., “In silico Analysis of the 13. Lin, C. Y.*, Chin, C. H., Wu, H. H., Chen, S. H., Ho, C. W.,* Ko, M.
Crustacean Hyperglycemic Hormone Family,” Mar. Biotech., volume
平台 (Hubba, http://hub.iis.sinica.edu.tw/, NAR, 2008, HUNTER, also constructed a topological analyzer to extract hubs and motifs from complex 7, number 3, pages 193-206, June 2005, (SCI/ 2.54) T.*, “Hubba: Hub Objects Analyzer : A Framework of Interactome
http://hub.iis.sinica.edu.tw/hunter, BMC Bioinformatics, 2010) network named as Hubba and HUNTER (http://hubba.iis.sinica.edu.tw, NAR, 2008, 5. Lin, C. Y.*, Chen C.L., Cho, C.S., Wang L.M., Chang C. M., Chen P. Hubs Identification for Network Biology,” Nucleic Acids Research,
，預先解析整個蛋白質交互作用網路的整體概況，篩選出關 http://hub.iis.sinica.edu.tw/hunter, BMC Bioinformatics, 2010, respectively). Objec- Y., Lo, C.Z., Hsiung, C. A., “hp-DPI: Helicobacter pylori Database of volume 36, number 2008 Web application Issue, pages W438-W443,
鍵的蛋白質，進而協助新型藥物的開發與治療技術的突破。 tives of our work are to improve understanding of the puzzle during development Protein Interactomes, A Combined Experimental and Inferring Inter- July 2008 (http://hub.iis.sinica.edu.tw) (SCI/6.94)
stage, carcinogenesis and infectious mechanism, and to furthermore introduce a actions,” Bioinformatics, volume 21, pages 1288-1290, April 2005, 14. Chen, S.H., Su,S. Y., Lo, C. Z., Huang, T. J., Kuo, B. H., Lin, C. Y.*,
(2)在生物資訊加值資料庫與應用系統之建置方面： new paradigm for the diagnosis and treatment of human disease to revolutionize (SCI/ 6.701)(http://dpi.nhri.org.tw/hp/) “Phylogenetic reconstruction by Automatic Likelihood Model Selec-
current medical services delivered. tor (PALM) : A Framework for Phylogenetic Analysis with the Best
Primer Design Assistant (PDA) (NAR, 2003, http://dbb.nhri.org. 6. Pan W. H., Lynn K. S., Chen C. H., Wu Y. L., Lin C. Y., Chang H.Y.,
tw/primer/)，大規模 PCR 核酸引子設計線上輔助系統，截自 (2) Developing value-added databases and web applications for biomedical “Using endophenotypes for pathway clusters to map complex disease Substitution Model,” PLoS ONE, volume 4, number 12, pages e8116,
December 2009, http://palm.iis.sinica.edu.tw
2010年三月，共有來自全球各地約十六萬人次上線使用，共 research communities genes.,” Genetic Epidemiology, volume 30, number 2, pages 143-154,
已處理超過八十八萬條序列，除了協助衛生署疾病管制局發 We have developed several web applications and databases related to bioinformat- March 2006, (SCI/ 5.42) 15. Chin, C. H., Chen, S. H., Ho, C. W., Ko, M. T.* Lin, C. Y.*, “A hub-
展快速診斷試劑之外，相關的研究也取得多項專利。結合熱 ics for the biomedical research community. For example, the web application Primer 7. Lin C.Y.* , Chen S. H., Cho C. S., Chen C. L., Lin F. K., Lin C. H., attachment based method to detect functional modules from confi-
dence-scored protein interactions and expression profiles,” BMC Bio-
力學與實驗室經驗，研究團隊也發展出一套可作為基因晶片 Design Assistant (PDA, http://dbb.nhri.org.tw/primer/) can be helpful for large Chen P. Y., Lo C. Z., and Hsiung C.A., “Fly-DPI: Database of Protein informatics, volume 11, number S1, pages S25, January 2010, http://
與雜合探針設計的自動化流程，Unique Probe Selector (UPS, scale PCR in high throughput experiments, such as microarray experiments. From Interactomes for D. melanogaster in the Approach of Systems Biol- hub.iis.sinica.edu.tw/Hunter
http://array.iis.sinica.edu.tw/ups, BMC Bioinformatics, 2008) July 2003 to Oct 2008, the numbers of accumulated website visits and processed ogy.,” BMC Bioinformatics, volume 7, number 5, pages S18, Decem- 16. Shiao, Y.M., Lee, C. C., Hsu, Y. H., Huang, S. F., Lin, C. Y., Li, L. H.,
ber 2006, (SCI/4.96) (URL:http://flydpi.nhri.org.tw)
，經實驗證實可提昇實驗精準度與減低雜訊，提供更穩定 sequences were more than 160,000 and 880,000, respectively. In addition to its use Fann, C. S. J., Tsai, C. Y., Tsai, S. F., Chiu, H. C., “Ectopic and High
可靠的基因表現概況。本研究室亦於2005年七月在 Nucleic by research groups, PDA has been used to develop several diagnostic kits and get 8. Jiang S. S., Chang I. S., Huang L. W., Chen P. C., Wen C. C., Liu S. CXCL13 Chemokine Expression in Myasthenia Gravis with Thymic
C., Chien L. C., Lin C. Y., Hsiung C. A., Juang J. L., “Temporal Tran-
Acid Research，發表一個生物巨分子序列親源關係的分析 patents. For example, in 2004, the Center for Disease Control (CDC), Taiwan used scription Program of Recombinant Autographa californica Multiple Lymphoid Hyperplasia,” Journal of Neuroimmunology, March 2010,
架構自動化平台，POWER: PhylOgenetic WEb Repeater - An PDA to develop a rapid diagnostic kit for SARS. Based on a similar idea, we have Nucleopolyhedrosis Virus.,” Journal of Virology, volume 80, pages Collaborated works with wet lab teams in NHRI and YM University,
integrated and user-optimized framework for bio-molecular developed a platform called “Unique Probe Selector” (UPS) (http://array.iis.sinica. 8989-8999, July 2006, (SCI/ 5.178) Available online 11 March 2010.
phylogenetic analysis (http://power.nhri.org.tw)，獲多個生 edu.tw/ups, BMC Bioinformatics 2008) with various uses in hybridization, such as 9. Wen, C. C., Wu, Y. J., Huang, Y. H., Chen, W. C., Liu, S. C., Jiang, S. 17. Leu, J. H., Chen, S. H., Wang, Y. B., Chen, Y. C., Su, S. Y., Lin, C. Y*.,
物資訊網站推薦使用，如歐洲重要生物資訊網站 Expasy 將 microarrays and blots. Arrays designed by UPS were validated by experiments for S., Juang, J. L., Lin, C. Y., Fang, W. T., Hsiung, C. A., Chang, I. S., “A Ho, J. M*., Lo, C. F*., “A review of the major penaeid shrimp EST
POWER 列入 Life Science Directory 中。目前研究團隊已完成 specificity and sensitivity. Bayes Regression Approach to Array-CGH Data,” Statistical Applica- studies and the construction of a shrimp transcriptome database based
on the ESTs from four penaeid shrimp,” Marine Biotechnology, April
新一代系統的開發，解決親源樹建置過程裡，最佳親緣演化 In 2005, we implemented a phylogenetic platform, called POWER (http://power.nhri. tions in Genetics and Molecular Biology, volume 5, number 1, May 2010, Invited Review, ref website: http://sysbio.iis.sinica.edu.tw/page
統計模型選取的問題，並協助多個國際研究團隊，以簡明的 2006, (http://www.bepress.com/sagmb/vol5/iss1/art3/), (Medline In-
org.tw, Nucleic Acid Research, 2005), for topology construction and visualization. dex)
10. Chang, C. C., Lin, H. C., Lin, I. P., Chang, T. Y., Chen, H. H., Chen,
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