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副研究員
林仲彥 Chung-Yen Lin
Associate Research Fellow
Ph.D., Zoology, National Taiwan University
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
Research Description ● Visiting Scholar, Computational
Biology Research Center, The
Our research is motivated by a desire to utilize IT innovations to decipher the secrets of life. At the same National Institute of Advanced In-
time, all of our published results have been converted into useful web applications/databases for active dustrial Science and Technology
(AIST), Japan (2011/8–2012/7)
use by research communities worldwide. Over the past ve years, we have published 15 SCI papers (7,
rst/corresponding author) with 4 web databases, 4 web applications, 2 standalone software, and 2 ● Visiting Scholar, Molecular &
patents. In recent years, my research has focused on the following areas: Medical Phamacology , David
Geffen School of Medicine at
(1) Network analysis of protein interactions involved in tumorigenesis and infectious diseases (systems UCLA, United States (2010/8–
biology): 2011/1)
In our current work, we are constructing a new statistical model based on domain- domain interactions ● Joint-appointed Associate Princi-
to reconstruct protein-protein interaction networks for any given organism, using data from recent ple Investigator, National Health
high through-put interactome studies. To decipher complex networks, our team has also developed Research Institutes, Division of
several algorithms which can successfully identify hubs/sub-networks with various topological fea- Biostatistics and Bioinformatics,
tures (please see the publication list for details). Taiwan (2005/11–present)
(2) Developing value-added databases and web applications for biomedical research communities: ● Joint-appointed Associate Profes-
sor , National Taiwan University,
We have developed several web applications and databases related to bioinformatics for the biomedi- College of Life Science, Taiwan
cal research community since 2003. For example, the web application Primer Design Assistant (PDA, (2005/2–present)
http://dbb.nhri.org.tw/primer/) can be helpful for large-scale PCR in high throughput experiments,
such as microarray experiments. From July 2003 to May 2014, the numbers of accumulated website vis-
its and processed sequences were over 205,000 and 1,250,000, respectively. Recently, our team also re-
leased new platforms called “Electronic Laboratory Notebook” (ELN, http://eln.iis.sinia.edu.tw) and “Multi-Omics online Analysis System” (MOLAS, http://
molas.iis.sinica.edu.tw) for digitizing daily experimental results and deciphering the regulatory mechanisms hidden within complex transcriptomic data
generated through next-generation sequencing, respectively.
Publications
1. Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, number 10, pages 2788–2799, October 2012, Article first published
Wen-Lian Hsu, Yu-Chun Wang, Der-Tsai Lee, Feipei Lai, Chih-Wei online: 29 MAY 2012 (SCI/ 5.84)
Huang and Yu-Jung Chang, “CloudDOE: A Quick and Easy Tool for
Setting up Hadoop on Private/Public Clouds and Analyzing High- 6. Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Mar-
Throughput Sequencing Data via MapReduce,” to appear in PLoS tin Wu, Chih-hao Hsieh and Hon-Tsen Yu, “Metagenomic analysis re-
One, http://clouddoe.iis.sinica.edu.tw/ veals a functional signature for biomass degradation by cecal microbi-
ota in the leaf-eating flying squirrel (Petaurista alborufus lena),”BMC
2. Shu-Hwa Chen, Kun-Lin Li, I-Hsuan Lu, Yu-Bin Wang,Che-Huang Genomics, volume 13, pages 466, September 2012.
Tung, Hsiu-Chi Ting, Ching-Yi Lin, Chung-Yen Lin*, Yi-Hsien Su*,
Jr-Kai Sky Yu, “Sequencing and analysis of the transcriptome of the 7. Yu-Bin Wang, Shu-Hwa Chen, Chung-Yen Lin and Jr-Kai Yu, “EST
acorn worm Ptychodera flava, an indirect developing hemichordate,” and transcriptome analysis of cephalochordate amphioxus - past, pre-
to appear in Marine Genomics, Web database: http://molas.iis.sinica. sent, and future,” Brief in Functional Genomics, volume 11, number
edu.tw/hemichordate 2, pages 96-106, March 2012, (SCI/ 4.126)
3. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Reme- 8. Chin-I Chang, Pei-Hsin Hung, Chia-Che Wu, Ta Chih Cheng, Jyh-
nyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin Ming Tsai, King-Jung Lin and Chung-Yen Lin, “Simultaneous Detec-
CY, Zhong W, Lloyd-Smith JO, Sun R., “A quantitative high-resolu- tion of Multiple Fish Pathogens Using a Naked-Eye Readable DNA
tion genetic profile rapidly identifies sequence determinants of viral Microarray,” Sensors, volume 12, number 3, pages 2710-2728, Febru-
fitness and drug sensitivity,” PLoS Pathogens, volume 10, number 4, ary 2012.
pages e1004064, April 2014, Collaboration with Team in UCLA 9. Jiann-Horng Leu, Shu-Hwa Chen, Yu-Bin Wang, Yen-Chen Chen,
Sheng-Yao Su, Chung-Yen Lin*, Jan-Ming Ho, Chu-Fang Lo*, “A
4. Chia-Hao Chin, Shu-Hwa Chen, Chun-Yu Chen, Chao. A Hsiung,
Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin, “Spotlight: Assem- Review of the Major Penaeid Shrimp EST Studies and the Construc-
bly of Protein Complexes by Integrating Graph Clustering Methods,” tion of a Shrimp Transcriptome Database Based on the ESTs from
Gene, volume 518, number 1, pages 42-51, April 2013, Collabora- Four Penaeid Shrimp,” Marine Biotechnology, volume 13, number 4,
tion with scientists in NHRI and NCU, http://hub.iis.sinica.edu.tw/ pages 608-21, August 2011. http://sysbio.iis.sinica.edu.tw/page
spotlight 10. Chen, S. H., Lo, C. Z., Su, S. Y., Kuo, B. H., Hsiung, A. C., Lin, C.
5. Lei-Chin Chen, Jung-Chi Chen, Jwu-Ching Shu, Chien-Yen Chen, Y.*, “UPS 2.0: Unique Probe Selector for Probe Design and Oligonu-
Ssu-Ching Chen, Shu-Hwa Chen, Chung-Yen Lin, Chi-Yu Lu, and cleotide Microarrays in Pangenomic/ Genomic Level,” BMC Genom-
Chien-Cheng Chen, “Interplay of RsbM and RsbK controls the theta B ics, volume 11, number 8, pages S6, December 2010, http://array.iis.
activity of Bacillus cereus,” Environmental Microbiology, volume 14, sinica.edu.tw/ups
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