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Research Fellow 林仲彥 研
究
Chung-Yen Lin 人
員
Ph.D., Zoology, National Taiwan University, Taiwan Faculty
T +886-2-2788-3799 ext. 1704 E cylin@iis.sinica.edu.tw
F +886-2-2782-4814 W www.iis.sinica.edu.tw/pages/cylin
・ Research Fellow (2020-present), Associate Research Fellow (2010), Assistant Research
Fellow (2005), Institute of Information Science, Academia Sinica, Taiwan
・ Joint-appointed Associate Principal Investigator(2011-present), Assistant Research
Fellow (2003), Division of Biostatistics and Bioinformatics, Institute of Population Health
Sciences, National Health Research Institutes, Taiwan
・ Joint-appointed Professor (2020-present), Associate Professor (2012), Assistant
Professor (2005), Institute of Fishery Science & Program of Genome and Bioinformatics,
National Taiwan University, Taiwan
・ Awards Winner for Future Tech Breakthrough Award by the Ministry of Science and
Technology, Taiwan (2018) and National Innovation Award by Research Center for
Biotechnology and Medicine Policy, Taipei, Taiwan (2018, 2019)
Research Description
Our research is motivated by a desire to utilize IT innovations to bridge computer science, high-dimensional statistics, and genomics, then
decipher the secrets of nature and make life better. In recent years, our works have focused on the following areas: (1) Network analyses in
tumorigenesis and infectious diseases, (2) Developing value-added databases/web applications for biomedical research communities, (3)
Using Machine learning/AI to decipher the biological problems like smart typing of pathogens, design of new antimicrobial peptides, etc.
All of the published results have been converted into useful web applications/databases/dockers for active use by research communities
worldwide since 2003. Many of our databases/applications are listed on several Bioinformatics portals with accumulated users and processed
sequences around 400,000 and 2,200,000, respectively. Over the past five years, we have published 16 SCI papers (16 on open assess
journals, 15 belonged to Q1, ve as rst/corresponding author) with seven new and over ten previous works as web databases/applications,
several standalone software, and one technology transfer (to Welgene Inc.). One of our e orts, cytohubba (http://apps.cytoscape.org/apps/
cytohubba), which can detect important nodes and subnetworks in a given network by several topological algorithms, has been downloaded
over 20,000 times with near 350 citations since it released in Jan 2017.
Publications
1. Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Gene Profiling Deconvolution Approach to Estimate Immune Brochure 2020
Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin*, Cell Composition from Complex Tissues," BMC Bioinformatics,
"An Intuitive Web-based Framework for Genome-wide DNA volume 19, number (Suppl 4), pages 154, May 2018
Methylation Analysis," to appear in BMC Genomics , Website:
http://symbiosis.iis.sinica.edu.tw/epimolas/molas.html 7. Hsiao-Pei Lu, Po-Yu Liu, Yu-bin Wang, Ji-Fan Hsieh, Han-Chen
Ho, Shiao-Wei Huang, Chung-Yen Lin, Chih-hao Hsieh, Hon-
2. Wen-Chun Huang, Chung-Yen Lin, Masayuki Hashimoto, Jiunn- Tsen Yu, "Functional Characteristics of the Flying Squirrels Cecal
Jong Wu, Ming-Cheng Wang, Wei-Hung Lin, Chang-Shi Chen Microbiota under a Leaf-Based Diet, Based on Multiple Meta-
& Ching-Hao Teng, "The role of the bacterial protease Prc in the Omic Profiling," Frontiers in Microbiology, volume 8, pages
uropathogenesis of extraintestinal pathogenic Escherichia coli," 2622, January 2018.
Journal of Biomedical Science, volume 27, number 14, pages
1-22, January 2020, (IF= 5.2) . 8. Hangfei Qi, Virginia Chu, Nicholas C. Wu, Zugen Chen, Shawna
Truong, Gurpreet Brar, Sheng-Yao Su, Yushen Du, Vaithilingaraja
3. Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Kai-Jiun Arumugaswami, C. Anders Olson, Shu-Hua Chen, Chung-Yen
Lo, Chi-Te Liu, Tzu-Ho Chou, Yang-hsin Shih, "Using high- Lin, Ting-Ting Wu, and Ren Sun, "Systematic identification of
throughput transcriptome sequencing to investigate the anti-interferon function on hepatitis C virus genome reveals p7
biotransformation mechanism of hexabromocyclododecane with as an immune evasion protein," Proceedings of the National
Rhodopseudomonas palustris in water," Science of the Total Academy of Sciences of the United States of America (PNAS),
Environment, volume 692, pages 249-258, November 2019, volume 114, number 8, pages 2018-2023, February 2017,
(IF=5.6) Collaboration with team in UCLA.
4. Li-An Yang, Yu-Jung Chang, Shu-Hwa Chen, Chung-Yen Lin 9. Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang,
and Jan-Ming Ho, "SQUAT: A Sequencing Quality Assessment Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin*, "TEA: The
Tool for Data Quality Assessments before and after Genome Epigenome platform for Arabidopsis methylome study," BMC
Assemblies," BMC Genomics, volume 19, number Suppl 9, pages Genomics , volume 17(S13), pages 1027, December 2016, Tea
238, April 2019, Open Access website: http://tea.iis.sinica.edu.tw icon
5. Tsung-Chieh Yao, Ren-Hua Chung, Chung-Yen Lin, et al., 10. Anderson B. Mayfield, Yu-Bin Wang, Chii-Shiarng Chen,
"Genetic Loci Determining Total Immunoglobulin E from Birth Shu-Hwa Chen, and Chung-Yen Lin*, "Dual-compartmental
through Adulthood Identified from Genome-wide Association transcriptomic + proteomic analysis of a marine endosymbiosis
Study of Asians," Allergy , volume 1, number 4, pages 1-4, exposed to environmental change," Molecular Ecology, volume
November 2018, (IF:6.08) 25, number 23, pages 5944-5958, November 2016, the web
database can be found at http://symbiont.iis.sinica.edu.tw/s_
6. Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, hystrix (IF: 5.98)
Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin*, "A
161
究
Chung-Yen Lin 人
員
Ph.D., Zoology, National Taiwan University, Taiwan Faculty
T +886-2-2788-3799 ext. 1704 E cylin@iis.sinica.edu.tw
F +886-2-2782-4814 W www.iis.sinica.edu.tw/pages/cylin
・ Research Fellow (2020-present), Associate Research Fellow (2010), Assistant Research
Fellow (2005), Institute of Information Science, Academia Sinica, Taiwan
・ Joint-appointed Associate Principal Investigator(2011-present), Assistant Research
Fellow (2003), Division of Biostatistics and Bioinformatics, Institute of Population Health
Sciences, National Health Research Institutes, Taiwan
・ Joint-appointed Professor (2020-present), Associate Professor (2012), Assistant
Professor (2005), Institute of Fishery Science & Program of Genome and Bioinformatics,
National Taiwan University, Taiwan
・ Awards Winner for Future Tech Breakthrough Award by the Ministry of Science and
Technology, Taiwan (2018) and National Innovation Award by Research Center for
Biotechnology and Medicine Policy, Taipei, Taiwan (2018, 2019)
Research Description
Our research is motivated by a desire to utilize IT innovations to bridge computer science, high-dimensional statistics, and genomics, then
decipher the secrets of nature and make life better. In recent years, our works have focused on the following areas: (1) Network analyses in
tumorigenesis and infectious diseases, (2) Developing value-added databases/web applications for biomedical research communities, (3)
Using Machine learning/AI to decipher the biological problems like smart typing of pathogens, design of new antimicrobial peptides, etc.
All of the published results have been converted into useful web applications/databases/dockers for active use by research communities
worldwide since 2003. Many of our databases/applications are listed on several Bioinformatics portals with accumulated users and processed
sequences around 400,000 and 2,200,000, respectively. Over the past five years, we have published 16 SCI papers (16 on open assess
journals, 15 belonged to Q1, ve as rst/corresponding author) with seven new and over ten previous works as web databases/applications,
several standalone software, and one technology transfer (to Welgene Inc.). One of our e orts, cytohubba (http://apps.cytoscape.org/apps/
cytohubba), which can detect important nodes and subnetworks in a given network by several topological algorithms, has been downloaded
over 20,000 times with near 350 citations since it released in Jan 2017.
Publications
1. Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Gene Profiling Deconvolution Approach to Estimate Immune Brochure 2020
Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin*, Cell Composition from Complex Tissues," BMC Bioinformatics,
"An Intuitive Web-based Framework for Genome-wide DNA volume 19, number (Suppl 4), pages 154, May 2018
Methylation Analysis," to appear in BMC Genomics , Website:
http://symbiosis.iis.sinica.edu.tw/epimolas/molas.html 7. Hsiao-Pei Lu, Po-Yu Liu, Yu-bin Wang, Ji-Fan Hsieh, Han-Chen
Ho, Shiao-Wei Huang, Chung-Yen Lin, Chih-hao Hsieh, Hon-
2. Wen-Chun Huang, Chung-Yen Lin, Masayuki Hashimoto, Jiunn- Tsen Yu, "Functional Characteristics of the Flying Squirrels Cecal
Jong Wu, Ming-Cheng Wang, Wei-Hung Lin, Chang-Shi Chen Microbiota under a Leaf-Based Diet, Based on Multiple Meta-
& Ching-Hao Teng, "The role of the bacterial protease Prc in the Omic Profiling," Frontiers in Microbiology, volume 8, pages
uropathogenesis of extraintestinal pathogenic Escherichia coli," 2622, January 2018.
Journal of Biomedical Science, volume 27, number 14, pages
1-22, January 2020, (IF= 5.2) . 8. Hangfei Qi, Virginia Chu, Nicholas C. Wu, Zugen Chen, Shawna
Truong, Gurpreet Brar, Sheng-Yao Su, Yushen Du, Vaithilingaraja
3. Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Kai-Jiun Arumugaswami, C. Anders Olson, Shu-Hua Chen, Chung-Yen
Lo, Chi-Te Liu, Tzu-Ho Chou, Yang-hsin Shih, "Using high- Lin, Ting-Ting Wu, and Ren Sun, "Systematic identification of
throughput transcriptome sequencing to investigate the anti-interferon function on hepatitis C virus genome reveals p7
biotransformation mechanism of hexabromocyclododecane with as an immune evasion protein," Proceedings of the National
Rhodopseudomonas palustris in water," Science of the Total Academy of Sciences of the United States of America (PNAS),
Environment, volume 692, pages 249-258, November 2019, volume 114, number 8, pages 2018-2023, February 2017,
(IF=5.6) Collaboration with team in UCLA.
4. Li-An Yang, Yu-Jung Chang, Shu-Hwa Chen, Chung-Yen Lin 9. Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang,
and Jan-Ming Ho, "SQUAT: A Sequencing Quality Assessment Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin*, "TEA: The
Tool for Data Quality Assessments before and after Genome Epigenome platform for Arabidopsis methylome study," BMC
Assemblies," BMC Genomics, volume 19, number Suppl 9, pages Genomics , volume 17(S13), pages 1027, December 2016, Tea
238, April 2019, Open Access website: http://tea.iis.sinica.edu.tw icon
5. Tsung-Chieh Yao, Ren-Hua Chung, Chung-Yen Lin, et al., 10. Anderson B. Mayfield, Yu-Bin Wang, Chii-Shiarng Chen,
"Genetic Loci Determining Total Immunoglobulin E from Birth Shu-Hwa Chen, and Chung-Yen Lin*, "Dual-compartmental
through Adulthood Identified from Genome-wide Association transcriptomic + proteomic analysis of a marine endosymbiosis
Study of Asians," Allergy , volume 1, number 4, pages 1-4, exposed to environmental change," Molecular Ecology, volume
November 2018, (IF:6.08) 25, number 23, pages 5944-5958, November 2016, the web
database can be found at http://symbiont.iis.sinica.edu.tw/s_
6. Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, hystrix (IF: 5.98)
Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin*, "A
161
