Journal papers

1. Chen, H. H., Hsueh, C. W., Lee, C. H., Hao, T. Y., Tu, T. Y., Chang, L. Y., Lee, J. C., Lin, C. Y.* (2023) SWEET: a single-sample network inference method for deciphering individual features in disease. Briefings in Bioinformatics, bbad032 [LINK]

2. Lin, C. Y., Chen, Y. J., Hsu, C. H., Lin, Y. H., Chen, P. T., Kuo, T. H., Ho, C. T., Chen, H. H., Huang, S. J., Chiu, H. C., Chen, C. C., Hwang, E.* (2022) Erinacine S from Hericium erinaceus Mycelium Promotes Neuronal Regeneration by Inducing Neurosteroids Accumulation.  Journal of Food and Drug Analysis, in press.

3. Tsai, M. L.,  Lee, C. H.,  Huang, L. C., Chen, Y. H., Liu, W. N., Lin, C. Y., Hsu, K. W., Lee, A. W., and Lin, C. L.,*  (2022) CRISPR-mediated knockout of VEGFR2/KDR inhibits cell growth in a squamous thyroid cancer cell line. FEBS Open Bio, 12(5):993-1005.

4.  Lin, C. L., Tsai, M. L., Chen, Y. H., Liu, W. N., Lin, C. Y., Hsu, K. W., Hung, C. Y., Chang, Y. J., Wei, P. L., Chen, S. H., Huang, L. C.,* and  Lee, C. H.* (2021) Platelet-Derived Growth Factor Receptor-α Subunit Targeting Suppresses Metastasis in Advanced Thyroid Cancer In Vitro and In Vivo. Biomolecules & Therapeutics, 1;29(5):551-561.

5.  Li, R., Lin, C. Y., Guo, W.-F., Akutsu, T.* (2021) Weighted Minimum Feedback Vertex Sets and Implementation in Human Cancer Genes Detection. BMC Bioinformatics, 22:143.

6. Liu, P., Song, J., Lin, C. Y., and Akutsu, T.* (2021) ReCGBM: a gradient boosting-based method for predicting human Dicer cleavage sites. BMC Bioinformatics, 22:63. 

7.  Chen, S. H., Hsieh, Y.-Y., Tzeng, H. E., Lin, C. Y., Hsu, K. W., Chiang, Y. S., Lin, S. M., Su, M. J., Hsieh, W. S., Lee, C. H.* (2020) ABL Genomic Editing Sufficiently Abolishes Oncogenesis of Human Chronic Myeloid Leukemia Cells In Vitro and In Vivo. Cancers , 12, 1399. 

8.  Chuang, Y. H.#, Lee, C. H.#, Lin, C. Y.#, Liu, C. L., Huang, S. H., Lee, J. Y., Chiu, Y. Y., Lee, J. C.*, and Yang, J. M.* (2020) An integrated genomic strategy to identify CHRNB4 as a diagnostic/prognostic biomarker for targeted therapy in head and neck cancer, Cancers, 12, 1324 #These authors contributed equally

9.  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.*, and Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers, Nature Communications, 10:3131  [LINK] [PDF]

10.  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 , 17(3) , 1940005 *These authors jointly directed this work

11.  Lee, J. Y., Lin, S. Y., Lin, C. Y., Chuang, Y. H., Huang, S. H., Tseng, Y. Y., Wang, H. J. and Yang, J. M. (2019) Identification of the PCA29 gene signature as a predictor in prostate cancer, Journal of Bioinformatics and Computational Biology, 17(3) , 1940006

12.  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.

13.  Lin, C. L., Tsai, M. L., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., Huang, L. C., and Lee, C. H.* (2019) HDAC1 and HDAC2 Double Knockout Triggers Cell Apoptosis in Advanced Thyroid Cancer, International Journal of Molecular Sciences, 20(2), 454. 

14.  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., and 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. 

15.  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., and Lee, C. H.* (2018) CRISPR/Cas9 genome editing of Epidermal Growth Factor Receptor sufficiently abolished oncogenicity in Anaplastic Thyroid cancer, Disease Markers, 3835783.

16.  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.

17.  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.

18.  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.

19.  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.

20.  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.

21.  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.

22.  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.

23.  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.

24.  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

1.  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

2.  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

3.  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

4.  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

5.  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

Patents 

1.  Yang, J. M., Lin, C. Y., Chiu, Y. Y., Lee, J. Y., Ho, Y. S., and Lee, C. H., Uses of bupropion and pharmaceutical composition for manufacture of medicament for treatment of cancer and method for inhibiting migration of tumor cells (安非他酮和醫藥組合物在製備治療癌症之藥物的用途及抑制腫瘤細胞遷移的方法), 中華民國專利, 107127866, 2020/12/21

Posters 

2.  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)

3.  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. (The best poster award)

4.  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 Conference, Taiwan, May, 2012. (The best poster award)

5.  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. (The best poster award)