Research Fellow/Professor  |  Lin, Chung-Yen  
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Chung-Yen Lin received B.S., M.S. and Ph.D. in zoology, fishery science and zoology from National Taiwan University (NTU) in 1991, 1993 and 1999, respectively. In 1995, he and his colleague published the first book to introduce internet in Chinese. And he also joined the team in NTU to edit and publish the textbook for Bioinformatics in 1999. After 4 years postdoc training in Division of Biostatistics and Bioinformatics, National Health Research Institutes (NHRI), he became an assistant researcher in the same departments in the end of 2004. During 2002- 2004, he contributed to his knowledge on IT and life science to help Center of Disease Control (CDC, Taiwan) for constructing pathogens surveillance framework (for Enterovirus and SARS) and developing rapid detective kits for SARS and other pathogens in his own developing algorithm (PDA,, NAR, 2003). In Oct 2005, he joined the institute as an assistant research fellow. And he became an associate research fellow in 2011. Meanwhile, two of his research projects (Electronic Lab notebook and Genome ‐ wide DNA methylation on Cloud) are awarded by Microsoft Inc. for cloud applications from 2011 to 2013. Recently he puts  focus on implemention of online analysis platform for genome/ transcriptome research (human and non-model organisms) and development of new pipeline for gene fusion event detection in clinical biopsy specimens.  In 2014, the platform named as MOLAS (Multi-Omics onLine Analysis System, for deciphering gene expression profiling online was licensed to a biotech company which provides services on next generation sequencing for biomedical community in Taiwan. Since 2009, he has published 23 SCI papers (23 on open access journals, 20 belonged to Q1 journals) and implemented more than 10 web databases/ 10 applications open for research community worldwide. One of his works released in 2009 named as cytohubba (, web version, hubba,, NAR, 2008), as a Java plugin of cytoscape, which was integrated 3 self-developed algorithms and 8 common used approaches with intuitive inferface to identify important nodes/hubs identification and sub-network, has been downloaded near 8,500 times according to the download statistics of cytoscape. Recently, he puts his focus on the implementation of platforms for Omics studies and develops new approaches to speed up the analyses on biological big data. With his expertise on aquatic physiology and biology, he and his colleagues are deciphering the genome and transcriptome of economic important aquatic animals and fungus. By integration of IT and biological thinking, a platform for Omics studies named as MOLAS ( is implemented. Based on this framework, his team has published several publications for cancer researches, non-model organisms and symbiosis, and  provided online database/ web application (please see the publication list).  

In summary, the objective of his researches is to using IT innovations to make the life better. His interests include interactome of host-pathogens, Systems Biology, Network Biology, precision medicine, and metagenomics.