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Chun-Yu Lin, Ph.D. (林峻宇, リンシュンウ)

My major research interests are bioinformatics and systems biology for molecular interaction networks with the aim to explore cell behaviors and disease mechanisms. Recently, my research focused on translational medicine for unmet clinical needs by integrating computational, biological and clinical research, including protein-protein interaction, module, and network analysis and clinical systems biology for translational cancer research.

Lab in NCTU

JSPS Post-Doctoral Research Fellow/Guest Research Associate (JSPS外国人特別研究員 )

Bioinformatics Center (Akutsu Laboratory)

Institute for Chemical Research, Kyoto University, Japan

Office: 京都大学宇治キャンパス内総合研究実験棟ＩＣＢ３２０号室

Room CB320, Bioinformatics Center, Institute for Chemical Research, Kyoto University. Uji, Kyoto 611-0011, Japan.

Tel: +81-774-38-3017

E-mail: chunyu AT kuicr.kyoto-u.ac.jp

Positions

2017.10 –

JSPS Post-Doctoral Research Fellow/Guest Research Associate (JSPS外国人特別研究員)

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan

(Prof. Akutsu's Laboratory)

2016.2 –2017.9

Assistant Research Fellow (助研究員)

Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, Taiwan

2014.9 –2016.1

Post-Doctoral Research Fellow (博士後研究員)

Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsinchu, Taiwan

(Prof. Jinn-Moon Yang's Laboratory)

Education

2010 – 2014

Ph.D.,

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan (Supervisor: Prof. Jinn-Moon Yang)

2008 – 2010

M.Sc.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan (Supervisor: Prof. Jinn-Moon Yang)

2004 – 2008

B.Sc.,

Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan

(Supervisor: Prof. Hui Liang Wang (Senior Vice President) )

Publications

Journal papers

Lin, C. Y.^#, Lee, C. H.^#, Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee Wu, Y. H., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S.*, Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers, Nature Communications, (Accepted) ^#These authors contributed equally
Lin, C. Y.#,*, Ruan, P. Y.#, Li, R. M., Yang, J. M., See, S., Song, J. N., and Akutsu, T.* (2019) Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes, Journal of Bioinformatics and Computational Biology (Accepted) *These authors jointly directed this work
Chen, S. H., Chow, J. M., Hsieh, Y. Y., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., Shabangu, B. M., and Lee, C. H.* (2019) HDAC1,2 Knock-Out and HDACi Induced Cell Apoptosis in Imatinib-Resistant K562 Cells, International Journal of Molecular Sciences, 20(9), 2271.
Lin, C. L., Tsai, M. L., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., Huang, L. C., Lee, C. H.* (2019) HDAC1 and HDAC2 Double Knockout Triggers Cell Apoptosis in Advanced Thyroid Cancer, International Journal of Molecular Sciences, 20(2), 454 .
Hsu, K. W., Huang, C. Y., Tam, K. W., Lin, C. Y., Huang, L. C., Lin, C. L., Hsieh, W. S., Chi, W. M., Chang, Y. J., Wei, P. L., Lee, C. H.* (2018) The application of Non-Invasive Apoptosis Detection Sensor (IADS) on Histone Deacetylation Inhibitors (HDACi) Induced Breast Cancer Cell Death, International Journal of Molecular Sciences, 19(2), 452 .
Lin, C. L., Huang, L. C., Liu, W. N., Lin, C. Y., Hsu, K. W., Tam, K. W., Hsieh, W. S., Chi, W. M., Lee, A. W., Yang, J. M., Lee, C. H.* (2018) CRISPR/Cas9 genome editing of Epidermal Growth Factor Receptor sufficiently abolished oncogenicity in Anaplastic Thyroid cancer, Disease Markers, 3835783
Huang, L. C., Lin, C. L., Qiu, J. Z., Lin, C. Y., Hsu, K. W., Tam, K. W., Lee, J. Y., Yang, J. M., and Lee, C. H.* (2017) Nicotinic Acetylcholine Receptor Subtype Alpha-9 Mediates Triple-Negative Breast Cancers Based on a Spontaneous Pulmonary Metastasis Mouse Model, Frontiers in Cellular Neuroscience, 11:336.
Tu, S. H., Hsieh, Y. C., Huang, L. C., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., and Lee, C. H.* (2017) A rapid and quantitative method to detect human circulating tumor cells in a preclinical animal model, BMC Cancer, 17:440.
Lin, C. Y., Lee, T. L., Chiu, Y. Y., Lin, Y. W., Lo, Y. S., Lin, C. T., and Yang J. M.* (2015) Module organization and variance in protein-protein interaction networks, Scientific Reports 5, 9386.
Lo, Y. S., Huang, S. H., Luo, Y. C., Lin, C. Y., and Yang, J. M.* (2015) Reconstructing Genome-Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping, PLOS ONE 10(1), e0116347.
Lin, C. Y., Chen, Y. C., Lo, Y. S., and Yang, J. M.* (2013) Inferring homologous protein-protein interactions through pair position specific scoring matrix, BMC Bioinformatics 14, Suppl 2:S11.
Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M.* (2012) MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates, Nucleic Acids Research 40, W263-W270.
Chiu, Y. Y., Lin, C. Y., Lin, C. T., Hsu, K. C., Chang, L. Z., and Yang, J. M.* (2012) Space-related pharma-motifs for fast search protein binding motifs and polypharmacological targets, BMC Genomics 13, Suppl 7:S21.
Lo, Y. S., Lin, C. Y., and Yang, J. M.* (2010) PCFamily: a web server for searching homologous protein complexes, Nucleic Acids Research 38, W516-W522.
Chen, C. C., Lin, C. Y., Lo, Y. S., and Yang, J. M.* (2009) PPISearch: a web server for searching homologous protein-protein interactions across multiple species, Nucleic Acids Research 37, W369-W375.

Conference papers

Lin, C. Y.^#, Ruan, P. Y.^#, Li, R. M., Yang, J. M., See S., and Akutsu, T (2018) Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes, IEEE 18th International Conference on BioInformatics and BioEngineering (BIBE), 147-150 , October ^#These authors contributed equally
Lee, J. Y., Lin, S. Y., Chuang, Y. H., Huang, S. H., Tseng, Y. Y., Lin, C. Y., Wang, H. J. and Yang, J. M. (2018) Identification of the PCa28 Gene Signature as a Predictor in Prostate Cancer, IEEE 18th International Conference on BioInformatics and BioEngineering (BIBE), 155-158, October
Tamura, T., Lin, C. Y., Yang, J. M., and Akutsu, T. (2016) Finding influential genes using gene expression data and Boolean models of metabolic networks, IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE), 57-63, October
Lin, C. Y., Chen, Y. C., Lo, Y. S., and Yang, J. M.* (2013) Inferring homologous protein-protein interactions through pair position specific scoring matrix, The Eleventh Asia Pacific Bioinformatics Conference (APBC), January
Chiu, Y. Y., Lin, C. Y., Lin, C. T., Hsu, K. C., Chang, L. Z., and Yang, J. M.* (2012) Space-related pharma-motifs for fast search protein binding motifs and polypharmacological targets, Asia Pacific Bioinformatics Network (APBioNet) Eleventh International Conference on Bioinformatics (InCoB), October

Posters

Lin, C. Y., Yang, J. M., and Akutsu, T. Pan-cancer module network analysis for identifying dominating networks across human cancers, The 7th joint Conference on Informatics In Biology, Medicine and Pharmacology (IIBMP 2018), Japan, Sep, 2018. (The best poster award)
Lin, C. Y., Chen, Y. C., Lo, Y. S., Lee, T. L., and Yang, J. M., Inferring homologous protein-protein interactions through pair position specific scoring matrix, The 2013 poster contest of the college of biological and technology, NCTU, May, 2013.
Lo, Y. S., Lin, C. Y., Huang, S. H., and Yang, J. M., Structural interactomes of multiple genomes reveal drug-gene-pathway-disease relationships, The 2013 poster contest of the college of biological and technology, NCTU, May, 2013.
Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M., Evolutionary module-module interaction networks reveal cell behaviors, The 17th Biophysics Conferenc, Taiwan, May, 2012.
Lin, C. Y., Chen, C. C., Lo, Y. S., and Yang, J. M., Template-driven approaches for protein-protein interaction families, The 2010 poster contest of the college of biological and technology, NCTU, May, 2010.

Awards

MOST Grant for the Einstein Program, Taiwan
BioICT Junior Chair Professor, National Chiao Tung University (Taiwan), 2018
The best poster award, The 7th joint Conference on Informatics In Biology, Medicine and Pharmacology (IIBMP 2018), Japan, 2018
JSPS Postdoctoral Fellowship for Research in Japan, 2017 (Selection Ratio = 125/1252 = 10%)
Outstanding performance of minor alliance between academia and industry, Ministry of Science and Technology (Taiwan), 2015 (The top 6 of 106 alliances)
The third place of poster competition, The 17th Biophysics Conference, 2012
Outstanding performances in the poster contest of the college of biological and technology, National Chiao Tung University (Taiwan), 2010 and 2013
The 1st place in my graduating class of the Institute of Bioinformatics and Systems Biology, National Chiao Tung University (Taiwan), 2010
Academic achievement award in the Institute of Bioinformatics and Systems Biology, National Chiao Tung University (Taiwan), 2009

Web service release

MoNetFamily

A web server to infer homologous modules and module-module interaction networks in vertebrates

http://monetfamily.life.nctu.edu.tw/

Reference: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W263-70.

PCFamily

A web server for searching homologous protein complexes

http://pcfamily.life.nctu.edu.tw/

Reference: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W516-22.

PPISearch

A web server for searching homologous protein-protein interactions across multiple species

http://gemdock.life.nctu.edu.tw/PPISearch/

Reference: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W369-75

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Chun-Yu Lin, Ph.D. (林峻宇, リン シュン ウ)