BioCompLab

Publication List

Scientific Publications


  1. C.C. Wang, Y.C. Lin, Y.H. Cheng and C.W. Tung* (2017) Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid, PeerJ, 5, e3175.
  2. C.C. Wang, Y.C. Lin, S.S. Wang, C. Shih, Y.H. Lin and C.W. Tung* (2017) SkinSensDB: a curated database for skin sensitization assays, Journal of Cheminformatics, 9, 5.
  3. S.H. Huang and C.W. Tung* (2017) Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens, Scientific Reports, 7, 41176.
  4. C.W. Chang, C.W. Tung, C.C. Tsai, Y.T. Wu* and M.C. Hsu* (2017) Determination of cannabinoids in hemp nuts products in Taiwan by HPLC-MS/MS coupled with chemometric analysis: Quality evaluation and a pilot human study, Drug Testing and Analysis, in press.
  5. C.C. Wang, Y.C. Lin, Y.C. Lin, S.R. Jhang and C.W. Tung* (2016) Prediction of Proinflammatory Potentials of Engine Exhausts by Integrating Chemical and Biological Features, Chapter in Bioinformatics and Biomedical Engineering. Lecture Notes in Computer Science, Springer, 9656, 293-303. (EI)
  6. Y.H. Cheng, I.S. Chen, Y.C. Lin, C.W. Tung, H.S. Chang and C.C. Wang* (2016) Attenuation of antigen-specific T helper 1 immunity by Neolitsea hiiranensis and its derived terpenoids, PeerJ, 4, e2758.
  7. Y.K. Chen, C.W. Tung, J.Y. Lee, Y.C. Hung, C.H. Lee, S.H. Chou, H.S. Lin, M.T. Wu and I.C. Wu* (2016) Plasma matrix metalloproteinase 1 improves the detection and survival prediction of esophageal squamous cell carcinoma, Scientific Reports, 6, 30057.
  8. S.H. Huang, C.W. Tung, F. Fülöp and J.H. Li* (2015) Developing a QSAR model for hepatotoxicity screening of the active compounds in traditional Chinese medicines, Food and Chemical Toxicology, 78, 71-77.
  9. C.W. Tung* (2015) ChemDIS: a chemical-disease inference system based on chemical-protein interactions, Journal of Cheminformatics, 7, 25. (Highly Accessed)
  10. C.W. Tung*, P. Lin and C.C. Wang (2015) Toxicoinformatics Tools for Studying Endocrine Disruption Effects of Pesticides, Chapter in 104年農藥內分泌干擾作用專題研討會論文集 (蔡韙任 林嬪嬪 費雯綺 李悅怡, ed.), 行政院農業委員會農業藥物毒物試驗所, 67-77.
  11. M. Chen, C.W. Tung, Q. Shi, L. Guo, L. Shi, H. Fang, J. Borlak and W. Tong* (2014) A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model, Archives of Toxicology, 88(7), 1439-1449.
  12. Y.C. Lin, C.C. Wang and C.W. Tung* (2014) An in silico toxicogenomics approach for inferring potential diseases associated with maleic acid, Chemico-Biological Interactions, 223(5), 38-44.
  13. C.W. Tung* (2014) Databases for T-cell epitopes, Methods in Molecular Biology, 1184, 123-134.
  14. C.W. Tung* (2014) Public databases of plant natural products for computational drug discovery, Current Computer-Aided Drug Design, 10(3), 191-196.
  15. C.W. Tung* and J.L. Jheng (2014) Interpretable prediction of non-genotoxic hepatocarcinogenic chemicals, Neurocomputing, 145, 68-74.
  16. C.W. Tung* (2014) Acquiring decision rules for predicting Ames-negative hepatocarcinogens using chemical-chemical interactions, Chapter in Pattern Recognition in Bioinformatics, Lecture Notes in Computer Science, Springer, 8626, 1-9. (EI)
  17. C.W. Tung*, Y.C. Lin, H.S. Chang, C.C. Wang, I.S. Chen, J.L. Jheng and J.H. Li (2014) TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants, Database (Oxford), 2014, bau055.
  18. W.L. Huang, C.W. Tung, C. Liaw, H.L. Huang and S.Y. Ho* (2014) Rule-based knowledge acquisition method for promoter prediction in human and drosophila species, The Scientific World Journal, 2014, 327306.
  19. C.W. Tung* (2013) Prediction of pupylation sites using the composition of k-spaced amino acid pairs, Journal of Theoretical Biology, 336, 11-17.
  20. C.W. Tung, M.T. Wu, Y.K. Chen, C.C. Wu, W.C. Chen, H.P. Li, S.H. Chou, D.C. Wu and I.C. Wu* (2013) Identification of biomarkers for esophageal squamous cell carcinoma using feature selection and decision tree methods, The Scientific World Journal, 2013, 782031.
  21. C.W. Tung* (2013) Prediction of non-genotoxic hepatocarcinogenicity using chemical-protein interactions, Chapter in Pattern Recognition in Bioinformatics, Lecture Notes in Computer Science, Springer, 7986, 231-241. (EI)
  22. Y.C. Lin, C.C. Wang, I.S. Chen, J.L. Jheng, J.H. Li and C.W. Tung* (2013) TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan, The Scientific World Journal, 2013, 736386.
  23. C. Liaw, C.W. Tung and S.Y. Ho* (2013) Prediction and analysis of antibody amyloidogenesis from sequences, PLoS One, 8(1), e53235.
  24. C.W. Tung* (2012) PupDB: a database of pupylated proteins, BMC Bioinformatics, 13, 40. (Highly Accessed)
  25. C.W. Tung, M. Ziehm, A. Kämper, O. Kohlbacher* and S.Y. Ho* (2011) POPISK: T-cell reactivity prediction using support vector machines and string kernels, BMC Bioinformatics, 12, 446. (Highly Accessed)
  26. C.W. Tung, C. Liaw, S.J. Ho and S.Y. Ho* (2010) Prediction of protein subchloroplast locations using Random Forests, Proceeding of World Academy of Science, Engineering and Technology, 41, 903-907. (EI)
  27. C. Liaw, C.W. Tung, S.J. Ho and S.Y. Ho* (2010) Sequence-based prediction of gamma-turn types using a physicochemical property-based decision tree method, Proceeding of World Academy of Science, Engineering and Technology, 41, 898-902. (EI)
  28. W.L. Huang, C.W. Tung and S.Y. Ho* (2010) Human Pol II promoter prediction by using nucleotide property composition features, Proceedings of the International Symposium on Biocomputing, 22.
  29. W.L. Huang, C.W. Tung, H.L. Huang and S.Y. Ho* (2009) Predicting protein subnuclear localization using GO-amino-acid composition features, Biosystems, 98(2), 73-79.
  30. K.T. Hsu, H.L.. Huang, C.W. Tung, Y.h. Chen and S.Y. Ho* (2009) Analysis of physicochemical properties on prediction of R5, X4 and R5X4 HIV-1 coreceptor usage, Proceeding of World Academy of Science, Engineering and Technology, 53, 1120-1127. (EI)
  31. C.W. Tung and S.Y. Ho* (2008) Computational identification of ubiquitylation sites from protein sequences, BMC Bioinformatics, 9, 310. (Highly Accessed)
  32. W.L. Huang, C.W. Tung, S.W. Ho and S.Y. Ho* (2008) ProLoc-rGO: Using rule-based knowledge with Gene Ontology terms for prediction of protein subnuclear localization, Computational Intelligence in Bioinformatics and Computational Biology, 2008. CIBCB'08. IEEE Symposium on, 201-206.
  33. W.L. Huang, C.W. Tung, S.W. Ho, S.F. Hwang and S.Y. Ho* (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization, BMC Bioinformatics, 9, 80.
  34. C.W. Tung and S.Y. Ho* (2007) POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties, Bioinformatics, 23(8), 942-949.
  35. W.L. Huang, C.W. Tung, H.L. Huang, S.F. Hwang and S.Y. Ho* (2007) ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features, Biosystems, 90(2), 573-581.
  36. W.C. Tsai, Y.Y. Hsiao, S.H. Lee, C.W. Tung, D.P. Wang, H.C. Wang, W.H. Chen and H.H. Chen* (2006) Expression analysis of the ESTs derived from the flower buds of Phalaenopsis equestris, Plant science, Elsevier, 170(3), 426-432.

Conference Presentations


  1. C.W. Tung* (2017) Effect of maleic acid on microrna expression in human neuroblastoma cells, 12th International Neuroscience and Biological Psychiatry Regional ISBS Conference, Yokohama, Japan. Jul 24-25 (Oral).
  2. S.H. Huang and C.W. Tung* (2017) Prediction of non-genotoxic hepatocarcinogens using consensus biomarkers, The 32th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 25-26 (Oral).
  3. S.H. Hsu, C.W. Tung* and O.Y. Fu (2017) The effects of antiresorptive agents on the survival of patients with breast cancer and bone metastasis– a single medical center experience, The 22nd Taiwan Joint Cancer Conference, Taipei, Taiwan. May 6-7 (Poster).
  4. W.L. Hsu and C.W. Tung* (2017) Predicting the risk for drug-induced G6PD-deficiency related hemolysis, The 32th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 25-26 (Poster).
  5. R.C. Hsiao, C.W. Tung, K.P. Hsieh and C.C. Wang* (2017) The inferred off-target effects of anti-osteoporosis drugs by ChemDIS and CTD, The 32th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 25-26 (Poster).
  6. Y.H. Cheng, Y.C. Lin, C.W. Tung and C.C. Wang* (2017) Caryophyllene oxide attenuates local and systemic T cell-mediated immune responses in ovalbumin-sensitized BALB/c mouse models, The 32th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 25-26 (Poster).
  7. H.F. Wu, Y.C. Chang and C.W. Tung* (2016) Mining structural and physicochemical features for drug-induced glucose-6-phosphate dehydrogenase deficiency-related hemolysis, The 31th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 26-27 (Oral).
  8. C.C. Wang, Y.C. Lin, Y.C. Lin, S.R. Jhang and C.W. Tung* (2016) Prediction of proinflammatory potentials of engine exhausts by integrating chemical and biological features, 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), Granada, Spain. Apr 20-22 (Oral).
  9. C.W. Tung*, M.J. Tsai, W.N. Chen and Y.H. Lin (2016) Developing an Integrative Pharmacogenomics Analysis Framework for Personalized Medicine, Fifteenth Annual Bio-IT World Conference & Expo (Bio-IT 2016), Boston, USA. Apr 5-7 (Poster).
  10. M.J. Tsai*, C.W. Tung, W.N. Chen and Y.H. Lin (2016) An Integrative Approach for Identifying Cancer-Specific Immunogenic Epitopes, Fifteenth Annual Bio-IT World Conference & Expo (Bio-IT 2016), Boston, USA. Apr 5-7 (Poster).
  11. W.L. Hsu and C.W. Tung* (2016) Investigating interaction networks for drug-induced G6PD-deficiency related hemolysis, The 31th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 26-27 (Poster).
  12. C.W. Tung*, C.C. Wang, Y.C. Lin and S.S. Wang (2016) Developing a curated database for skin sensitizers by incorporating adverse outcome pathways, OpenTox Euro 2016, Rheinfelden, Germany. Oct 26-28 (Oral).
  13. Y.H. Cheng, C.C. Wang*, I.S. Chen, Y.C. Lin and C.W. Tung (2016) Attenuation of antigen-specific Th1 immunity by Neolitsea hiiranensis derived sesquiterpenes, EAACI Congress 2016, Vienna, Austria. Jun 11-15 (Poster).
  14. C.R. Chen and C.W. Tung* (2016) 開發用於分析 Aminoglycoside 藥物血中濃度監測量表, 2016 Cross-Strait Predictive Toxicology Conference: Environment, Food and Health, National Chung Hsing University, Taichung, Taiwan. May 5-7 (Poster).
  15. C.W. Tung*, Y.C. Wang and C.C. Wang (2015) 以計算方法預測化合物穿皮能力, 8th Cross-Strait Toxicology Conference, Wuhan, China. Oct 25-28 (Poster).
  16. C.W. Tung*, Y.C. Wang and C.C. Wang (2015) Computational Prediction of Skin Permeability of Chemicals, The 30th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 21-22 (Poster).
  17. Y.H. Kuo and C.W. Tung* (2015) 藉由蛋白質交互作用研究抗發炎藥物可能的脫靶效應, Annual Meeting of the Pharmaceutical Society of Taiwan, Tainan, Taiwan. Nov 14 (Poster).
  18. S.H. Huang and C.W. Tung* (2015) Identification of consensus biomarkers for non-genotoxic hepatocarcinogens, 7th Asian Association of Schools of Pharmacy (AASP) Conference, Taipei City, Taiwan. Oct 30-Nov 2 (Poster).
  19. H.F. Wu, 楊璦瑜, Y.C. Chang, 黃學楊 and C.W. Tung* (2014) 導致G6PD缺乏症溶血性貧血藥物類別分析, Annual Meeting of the Pharmaceutical Society of Taiwan, Kaohsiung, Taiwan. Dec 13 (Poster).
  20. Y.C. Wang and C.W. Tung* (2014) Computational Prediction of Skin Permeability Coefficient of Chemicals and Evaluation of Important Structure Descriptors, Annual Meeting of the Pharmaceutical Society of Taiwan, Kaohsiung, Taiwan. Dec 13 (Poster).
  21. C.W. Tung* (2014) Acquiring decision rules for predicting Ames-negative hepatocarcinogens using chemical-chemical interactions, Eighth IAPR International Conference on Pattern Recognition in Bioinformatics, Stockholm, Sweden. Aug 21-23 (Oral).
  22. C.W. Tung*, Y.C. Lin, I.S. Chen, C.C. Wang, J.L. Jheng and J.H. Li (2014) Three-dimensional structure database of phytochemicals from Taiwan indigenous plants, The 29th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 15-16 (Poster).
  23. Y.C. Lin*, C.Y. Lu and C.W. Tung (2014) Proteomic analyses of Staphylococcus aureus biofilm from a porcine mucosal infection model, Gordon Research Conferences on New Antibacterial Discovery & Development, Ventura, CA, USA. Mar 16-21 (Poster).
  24. C.W. Tung* (2013) Comparative analysis of prediction models for non-genotoxic hepatocarcinogenicity using chemical-protein interactions and toxicogenomics, 7th Cross-Strait Toxicology Conference, Taipei, Taiwan. Sep 13-14 (Poster).
  25. C.W. Tung* (2013) Prediction of non-genotoxic hepatocarcinogenicity using chemical-protein interactions, Eighth IAPR International Conference on Pattern Recognition in Bioinformatics, Valrose Castle, Nice, France. Jun 17-20 (Oral).
  26. Y.C. Lin, C.C. Wang, I.S. Chen, J.H. Li, J.L. Jheng and C.W. Tung* (2013) The database of anti-cancer, anti-platelet, and anti-tuberculosis phytochemicals from indigenous plants in Taiwan, The 28th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 23-24 (Poster).
  27. C.W. Tung* (2012) Computational identification and analysis of pupylation sites, International Conference on Bioinformatics and Computational Biology (BIOCOMP BG 2012), Varna, Bulgaria. Sep 20-21 (Poster). (Poster award: 3rd place)
  28. C. Liaw, C.W. Tung and S.Y. Ho* (2012) Computational identification of important features for predicting antibody amyloidogenesis, The 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB2012), Shenzhen, China. Dec 20-21 (Poster).
  29. S.H. Huang, C.W. Tung and J.H. Li* (2012) In silico screening the hepatotoxic potential of the active compounds of traditional Chinese medicines, Annual Meeting of the Pharmaceutical Society of Taiwan, Taichung, Taiwan. Nov 25 (Poster).
  30. C.W. Tung, C. Liaw, S.J. Ho and S.Y. Ho* (2010) Prediction of protein subchloroplast locations using Random Forests, International Conference on Computational Biology (ICBB2010), Tokyo, Japan. May 26-28 (Oral).
  31. C. Liaw, C.W. Tung, S.J. Ho and S.Y. Ho* (2010) Sequence-based prediction of gamma-turn types using a physicochemical property-based decision tree method, International Conference on Computational Biology (ICBB2010), Tokyo, Japan. May 26-28 (Oral).
  32. W.L. Huang, C.W. Tung and S.Y. Ho* (2010) Human Pol II promoter prediction by using nucleotide property composition features, International Symposium on Biocomputing (ISB '10), Calicut, Kerala, India. Feb 15-17 (Oral).
  33. K.T. Hsu, H.L.. Huang, C.W. Tung, Y.h. Chen and S.Y. Ho* (2009) Analysis of physicochemical properties on prediction of R5, X4 and R5X4 HIV-1 coreceptor usage, International Conference on Bioinformatics and Bioengineering (ICBB), Tokyo, Japan. May 27-29 (Oral).
  34. W.L. Huang, C.W. Tung, S.W. Ho and S.Y. Ho* (2008) ProLoc-rGO: Using rule-based knowledge with Gene Ontology terms for prediction of protein subnuclear localization, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'08), Sun Valley Idaho, USA, Sep 15-17 (Oral).
  35. C.W. Tung and S.Y. Ho* (2007) Mining physicochemical properties for predicting immunogenicity of MHC class II binding peptides, 18th International Conference on Genome Informatics (GIW2007), Biopolis, Singapore. Dec 3-5 (Poster).
  36. Y.Y. Hsiao, W.C. Tsai, C.W. Tung, Y.F. Chiu, Z.J.. Pan, W.H. Chen and H.H. Chen* (2004) Gene expression during Phalaenopsis embryo development, International Symposium on Agricultural Genomics and Biotechnology. Tainan, Taiwan. Oct 28-30 (Poster).

Invited Talks


  1. C.W. Tung (2016) ChemDIS:化合物相關疾病分析系統, 2016 Cross-Strait Predictive Toxicology Conference: Environment, Food and Health, National Chung Hsing University, Taichung, Taiwan. May 5-7.
  2. C.W. Tung (2015) Toxicoinformatics Tools for Studying Endocrine Disruption Effects of Pesticides, 104年農藥內分泌干擾作用專題研討會, 行政院農業委員會農業藥物毒物試驗所, Taichung, Taiwan. September 30.
  3. C.W. Tung (2014) Chemical-disease inference using Comparative Toxicogenomics Database, 毒理學家研習課程 Regulatory Toxicology and Toxinformatics, National Taiwan University, Taipei, Taiwan. September 4.
  4. C.W. Tung (2007) POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties, Academic symposium of biotechnology, National Chiao Tung University, Hsinchu, Taiwan.