Page 69 - 2017 Brochure
P. 69
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
• Visiting Scholar, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan (2011-2012)
• Visiting Scholar, Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA (2010-2011)
• Associate Principle Investigator (Joint appointed), Division of Biostatistics and Bioinformatics, National Health Research Institutes (2010-present)
• Associate Professor (Joint appointed), College of Life Science, National Taiwan University (2014-present)
Research Description (2) Value-added databases/web applications for biomedical research
communities
Our research is motivated by a desire to utilize IT innovations to decipher
the secrets of nature and make life better. All of our published results Recently, our team released new platforms, called “Electronic Laboratory
have been converted into useful web applications or databases for use by Notebook” (ELN, http://eln.iis.sinia.edu.tw) for cloud storage of digitized daily
worldwide research communities since 2003. Over the past five years, we experimental results, and “Multi-Omics online Analysis System” (MOLAS,
have produced 23 SCI papers (22 were in open assess journals, 21 were in http://molas.iis.sinica.edu.tw) for deciphering the regulatory mechanisms
journals ranked in the top quartile, and seven were as first/corresponding hidden within transcriptomic data from next-generation sequencing. Using
author), ten web databases/applications, two standalone software packages, the web platforms/algorithms for omics developed in our laboratory, we
and one technology transfer. In recent years, my research has focused on the have tackled many wide-ranging issues, such as fusion gene discovery in
following areas: clinical biopsy samples (Modern Pathology, 2016), genome assembly and
functional annotation of economically important, non-model organisms
(1) Network analyses in tumorigenesis and infectious disease (two examples include: Giant grouper, http://molas.iis.sinica.edu.tw/
grouper2016, manuscript submitted; and Japanese eel, http://molas.
To explore important nodes/hubs and fragile motifs in a complex biological iis.sinica.edu.tw/jpeel2016, PLoS ONE, 2015), precision phenotyping of
network, we have implemented eleven topological algorithms (http://apps. enterovirus (BMC Genomics, 2015), and identification of mechanisms that
cytoscape.org/apps/cytohubba) as cytohubba. This tool serves as good restrict viral replication for vaccine development (PNAS, 2017). Currently, we
starting point for exploring new therapies and developing novel insights are developing the toolboxes based on Docker platform for high throughput
into basic mechanisms that control normal cellular processes and disease biology with life sciences community in Academia Sinica.
pathologies. Since 2011, the number of downloads is over 9,000 and it has
been cited over 180 times. A new version of cytohubba released in Jan. 2017 and Recombination Detection DineEcenmtebroevr i2ru0s1,”5,BCMoCopGereantoiomnicws,itvholTuemaem1i6n,
was downloaded more than 750 times within the next five months. number Suppl 12, pages S8,
NHRI. *: Corresponding Author. (SCI/4.4, BIOTECHNOLOGY & APPLIED
Publications MICROBIOLOGY/ Q1)
1. Hangfei Qi, Virginia Chu, Nicholas C. Wu, Zugen Chen, Shawna Truong, 7. Hsu HY, Chen SH, Cha YR, Aoyama J, Miller M, Watanabe S, Tsukamoto K,
Gurpreet Brar, Sheng-Yao Su, Yushen Du, Vaithilingaraja Arumugaswami, Lin CY*, Han YS*., “Deciphering the Digestive and Absorptive Capacities
C. Anders Olson, Shu-Hua Chen, Chung-Yen Lin, Ting-Ting Wu, and Ren of Embryo, Pre-leptocephalus, Leptocephalus, and Glass eel stages of the
Sun, “Systematic identification of anti-interferon function on hepatitis C Japanese Eel (Anguilla japonica) Using Next-Generation Sequencing,” PLoS
virus genome reveals p7 as an immune evasion protein,” Proceedings of One, volume 10, number 9, pages e0139105, September 2015, Cooperation
vthoeluNmaeti1o1n4a,lnAucmabdeerm8y, poafgSecsie2n0c1e8s-2o0f2t3h,eJaUnnuiateryd 2S0ta1t7e.s(SoCf IA/m9.e4r)ica (PNAS), with Team in NTU. *:Corresponding author.(SCI/3.73, Journal ranking:
Multidisciplinary Sciences/ Q1: 7/56, 12.5%)
2. Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin
Wang, Pao-Yang Chen, Chung-Yen Lin*, “TEA: The Epigenome platform 8. Jen-Chieh Lee,Yung-Ming Jeng, Sheng-Yao Su, Chen-Tu Wu, Keh-Sung
for Arabidopsis methylome study,” BMC Genomics, volume 17(S13), pages Tsai, Cheng-Han Lee, Chung-Yen Lin, Jodi M. Carter, Jeng-Wen Huang, Shu-
1027, December 2016, Tea website: http://tea.iis.sinica.edu.tw, (SCI/ 4.4, Hwa Chen, Shyang-Rong Shih, Adrián Mariño-Enríquez, Chih-Chih Chen,
BIOTECHNOLOGY & APPLIED MICROBIOLOGY/ Q1) Andrew L. Folpe, Yih-Leong Chang and Cher-Wei Liang, “Identification of
a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic
3. Anderson B. Mayfield, Yu-Bin Wang, Chii-Shiarng Chen, Shu-Hwa Chen, and Mesenchymal MTuamrcohu2r,0”15T,hCe oJlolaubronraaltioofnPwaitthhotleoagmy, volume 235, number 4,
Chung-Yen Lin*, “Dual-compartmental transcriptomic + proteomic analysis pages 539-45, in NTU hospital for rare
of a marine endosymbiosis exposed to environmental change,” Molecular disease (SCI/ 7.33, Journal ranking: Pathology/Q1: 3/76, 3.9%)
Ecology, volume 25, number 23, pages 5944-5958, November 2016, The web
database can be found at http://symbiont.iis.sinica.edu.tw/s_hystrix (SCI/ 5.98) 9. Mayfield, Anderson; Wang, Yu-Bin; Chen, Chii-Shiarng; Lin, Chung-Yen;
Chen, Shu-Hwa, “Compartment-specific transcriptomics in a reef-building
4. Tzu-Po Chuang, Jaw-Yuan Wang, Shu-Wen Jao, Chang-Chieh Wu, Jiann- coral exposed to elevated temperatures,” Molecular Ecology, volume 23,
Hwa Chen, Koung-Hung Hsiao, Chung-Yen Lin, Shu-Hwa Chen, Sheng-Yao number 23, pages 5816-5830, December 2014, Collaboration with Living
Su, Ying-Ju Chen, Yuan-Tsong Chen, Deng-Chyang Wu, Ling-Hui Li, “Over- Oceans Foundation (SCI/ 5.94, Journal ranking: Ecology/Q1: 11/141, 7.8%)
expression of AURKA, SKA3 and DSN1 contributes to colorectal adenoma
to carcinoma progression,” Oncotarget, volume 7, number 29, pages 45803- 10. Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko
45818, June 2016 (SCI/ 6.4 ) *, and Chung-Yen Lin*, “cytoHubba: a Cytoscape Plug-in for Hub Object Analysis
in Network Biology,” BMC Systems Biology, volume 8, number Suppl 4, pages
5. Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, S11, December 2014, Plug-in for cytoscape, accumulated download over 9,000
Chung-Ye n L in a nd Ja n-Ming Ho, “S ubse t se le c tion of high-de pth times (SCI/ 3.65, Journal ranking: MATHEMATICAL & COMPUTATIONAL
next generation sequencing reads for de novo genome assembly using BIOLOGY/Q1: 7/52, 13.5%)
MapReduce framework,” BMC Genomics, volume 16, number Suppl 12,
pages S9, December 2015. (SCI/4.4, BIOTECHNOLOGY & APPLIED
MICROBIOLOGY/ Q1)
6. Lin CH, Chen SH,Wang YB, Hsiung CA, Lin CY*, “Precise Genotyping
67
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
• Visiting Scholar, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan (2011-2012)
• Visiting Scholar, Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA (2010-2011)
• Associate Principle Investigator (Joint appointed), Division of Biostatistics and Bioinformatics, National Health Research Institutes (2010-present)
• Associate Professor (Joint appointed), College of Life Science, National Taiwan University (2014-present)
Research Description (2) Value-added databases/web applications for biomedical research
communities
Our research is motivated by a desire to utilize IT innovations to decipher
the secrets of nature and make life better. All of our published results Recently, our team released new platforms, called “Electronic Laboratory
have been converted into useful web applications or databases for use by Notebook” (ELN, http://eln.iis.sinia.edu.tw) for cloud storage of digitized daily
worldwide research communities since 2003. Over the past five years, we experimental results, and “Multi-Omics online Analysis System” (MOLAS,
have produced 23 SCI papers (22 were in open assess journals, 21 were in http://molas.iis.sinica.edu.tw) for deciphering the regulatory mechanisms
journals ranked in the top quartile, and seven were as first/corresponding hidden within transcriptomic data from next-generation sequencing. Using
author), ten web databases/applications, two standalone software packages, the web platforms/algorithms for omics developed in our laboratory, we
and one technology transfer. In recent years, my research has focused on the have tackled many wide-ranging issues, such as fusion gene discovery in
following areas: clinical biopsy samples (Modern Pathology, 2016), genome assembly and
functional annotation of economically important, non-model organisms
(1) Network analyses in tumorigenesis and infectious disease (two examples include: Giant grouper, http://molas.iis.sinica.edu.tw/
grouper2016, manuscript submitted; and Japanese eel, http://molas.
To explore important nodes/hubs and fragile motifs in a complex biological iis.sinica.edu.tw/jpeel2016, PLoS ONE, 2015), precision phenotyping of
network, we have implemented eleven topological algorithms (http://apps. enterovirus (BMC Genomics, 2015), and identification of mechanisms that
cytoscape.org/apps/cytohubba) as cytohubba. This tool serves as good restrict viral replication for vaccine development (PNAS, 2017). Currently, we
starting point for exploring new therapies and developing novel insights are developing the toolboxes based on Docker platform for high throughput
into basic mechanisms that control normal cellular processes and disease biology with life sciences community in Academia Sinica.
pathologies. Since 2011, the number of downloads is over 9,000 and it has
been cited over 180 times. A new version of cytohubba released in Jan. 2017 and Recombination Detection DineEcenmtebroevr i2ru0s1,”5,BCMoCopGereantoiomnicws,itvholTuemaem1i6n,
was downloaded more than 750 times within the next five months. number Suppl 12, pages S8,
NHRI. *: Corresponding Author. (SCI/4.4, BIOTECHNOLOGY & APPLIED
Publications MICROBIOLOGY/ Q1)
1. Hangfei Qi, Virginia Chu, Nicholas C. Wu, Zugen Chen, Shawna Truong, 7. Hsu HY, Chen SH, Cha YR, Aoyama J, Miller M, Watanabe S, Tsukamoto K,
Gurpreet Brar, Sheng-Yao Su, Yushen Du, Vaithilingaraja Arumugaswami, Lin CY*, Han YS*., “Deciphering the Digestive and Absorptive Capacities
C. Anders Olson, Shu-Hua Chen, Chung-Yen Lin, Ting-Ting Wu, and Ren of Embryo, Pre-leptocephalus, Leptocephalus, and Glass eel stages of the
Sun, “Systematic identification of anti-interferon function on hepatitis C Japanese Eel (Anguilla japonica) Using Next-Generation Sequencing,” PLoS
virus genome reveals p7 as an immune evasion protein,” Proceedings of One, volume 10, number 9, pages e0139105, September 2015, Cooperation
vthoeluNmaeti1o1n4a,lnAucmabdeerm8y, poafgSecsie2n0c1e8s-2o0f2t3h,eJaUnnuiateryd 2S0ta1t7e.s(SoCf IA/m9.e4r)ica (PNAS), with Team in NTU. *:Corresponding author.(SCI/3.73, Journal ranking:
Multidisciplinary Sciences/ Q1: 7/56, 12.5%)
2. Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin
Wang, Pao-Yang Chen, Chung-Yen Lin*, “TEA: The Epigenome platform 8. Jen-Chieh Lee,Yung-Ming Jeng, Sheng-Yao Su, Chen-Tu Wu, Keh-Sung
for Arabidopsis methylome study,” BMC Genomics, volume 17(S13), pages Tsai, Cheng-Han Lee, Chung-Yen Lin, Jodi M. Carter, Jeng-Wen Huang, Shu-
1027, December 2016, Tea website: http://tea.iis.sinica.edu.tw, (SCI/ 4.4, Hwa Chen, Shyang-Rong Shih, Adrián Mariño-Enríquez, Chih-Chih Chen,
BIOTECHNOLOGY & APPLIED MICROBIOLOGY/ Q1) Andrew L. Folpe, Yih-Leong Chang and Cher-Wei Liang, “Identification of
a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic
3. Anderson B. Mayfield, Yu-Bin Wang, Chii-Shiarng Chen, Shu-Hwa Chen, and Mesenchymal MTuamrcohu2r,0”15T,hCe oJlolaubronraaltioofnPwaitthhotleoagmy, volume 235, number 4,
Chung-Yen Lin*, “Dual-compartmental transcriptomic + proteomic analysis pages 539-45, in NTU hospital for rare
of a marine endosymbiosis exposed to environmental change,” Molecular disease (SCI/ 7.33, Journal ranking: Pathology/Q1: 3/76, 3.9%)
Ecology, volume 25, number 23, pages 5944-5958, November 2016, The web
database can be found at http://symbiont.iis.sinica.edu.tw/s_hystrix (SCI/ 5.98) 9. Mayfield, Anderson; Wang, Yu-Bin; Chen, Chii-Shiarng; Lin, Chung-Yen;
Chen, Shu-Hwa, “Compartment-specific transcriptomics in a reef-building
4. Tzu-Po Chuang, Jaw-Yuan Wang, Shu-Wen Jao, Chang-Chieh Wu, Jiann- coral exposed to elevated temperatures,” Molecular Ecology, volume 23,
Hwa Chen, Koung-Hung Hsiao, Chung-Yen Lin, Shu-Hwa Chen, Sheng-Yao number 23, pages 5816-5830, December 2014, Collaboration with Living
Su, Ying-Ju Chen, Yuan-Tsong Chen, Deng-Chyang Wu, Ling-Hui Li, “Over- Oceans Foundation (SCI/ 5.94, Journal ranking: Ecology/Q1: 11/141, 7.8%)
expression of AURKA, SKA3 and DSN1 contributes to colorectal adenoma
to carcinoma progression,” Oncotarget, volume 7, number 29, pages 45803- 10. Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko
45818, June 2016 (SCI/ 6.4 ) *, and Chung-Yen Lin*, “cytoHubba: a Cytoscape Plug-in for Hub Object Analysis
in Network Biology,” BMC Systems Biology, volume 8, number Suppl 4, pages
5. Chih-Hao Fang, Yu-Jung Chang, Wei-Chun Chung, Ping-Heng Hsieh, S11, December 2014, Plug-in for cytoscape, accumulated download over 9,000
Chung-Ye n L in a nd Ja n-Ming Ho, “S ubse t se le c tion of high-de pth times (SCI/ 3.65, Journal ranking: MATHEMATICAL & COMPUTATIONAL
next generation sequencing reads for de novo genome assembly using BIOLOGY/Q1: 7/52, 13.5%)
MapReduce framework,” BMC Genomics, volume 16, number Suppl 12,
pages S9, December 2015. (SCI/4.4, BIOTECHNOLOGY & APPLIED
MICROBIOLOGY/ Q1)
6. Lin CH, Chen SH,Wang YB, Hsiung CA, Lin CY*, “Precise Genotyping
67
