Publication List
Scientific Publications
- Leveraging Complementary Computational Models for Prioritizing Chemicals of Developmental and Reproductive Toxicity Concern: An Example of Food Contact Materials, Archives of Toxicology, (), accepted. (2019)
- Transfer Learning for Predicting Human Skin Sensitizers, Archives of Toxicology, 93(4), 931-940. (2019)
- ChemDIS 2: an update of chemical-disease inference system, Database (Oxford), 2018, bay077. (2018)
- ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures, Scientific Reports, 8, 10047. (2018)
- Mechanism-informed Read-across Assessment of Skin Sensitizers Based on SkinSensDB, Regulatory Toxicology and Pharmacology, 94, 276-282. (2018)
- Discovery of Pyrazolo[4,3-c]quinolines Derivatives as Potential Anti-Inflammatory Agents through Inhibiting of NO Production, Molecules, 23(5), 1036. (2018)
- Human immunodeficiency virus Tat-TIP30 interaction promotes metastasis by enhancing the nuclear translocation of Snail in lung cancer cell lines, Cancer Science, 109(10), 3105-3114. (2018)
- An Integrated Web-based System for MEDLINE Analysis: A Case Study of Chronic Kidney Disease, Proceedings of 22nd Pacific Asia Conference on Information Systems (PACIS 2018), 1828-1840. (2018)
- Identification of informative features for predicting proinflammatory potentials of engine exhausts, Biomedical Engineering Online, 16(Suppl 1), 66. (2017)
- Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid, PeerJ, 5, e3175. (2017)
- SkinSensDB: a curated database for skin sensitization assays, Journal of Cheminformatics, 9, 5. (2017)
- Discovery of Indeno[1,2-c]quinoline Derivatives as Potent Dual Antituberculosis and Anti-Inflammatory Agents, Molecules, 22(6), 1001. (2017)
- Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens, Scientific Reports, 7, 41176. (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, 9(6), 888-897. (2017)
- 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) (2016)
- Attenuation of antigen-specific T helper 1 immunity by Neolitsea hiiranensis and its derived terpenoids, PeerJ, 4, e2758. (2016)
- Plasma matrix metalloproteinase 1 improves the detection and survival prediction of esophageal squamous cell carcinoma, Scientific Reports, 6, 30057. (2016)
- Developing a QSAR model for hepatotoxicity screening of the active compounds in traditional Chinese medicines, Food and Chemical Toxicology, 78, 71-77. (2015)
- ChemDIS: a chemical-disease inference system based on chemical-protein interactions, Journal of Cheminformatics, 7, 25. (Highly Accessed) (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. (2015)
- 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. (2014)
- An in silico toxicogenomics approach for inferring potential diseases associated with maleic acid, Chemico-Biological Interactions, 223(5), 38-44. (2014)
- Databases for T-cell epitopes, Methods in Molecular Biology, 1184, 123-134. (2014)
- Public databases of plant natural products for computational drug discovery, Current Computer-Aided Drug Design, 10(3), 191-196. (Editor Choice Article) (2014)
- Interpretable prediction of non-genotoxic hepatocarcinogenic chemicals, Neurocomputing, 145, 68-74. (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) (2014)
- TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants, Database (Oxford), 2014, bau055. (2014)
- Rule-based knowledge acquisition method for promoter prediction in human and drosophila species, The Scientific World Journal, 2014, 327306. (2014)
- Prediction of pupylation sites using the composition of k-spaced amino acid pairs, Journal of Theoretical Biology, 336, 11-17. (2013)
- Identification of biomarkers for esophageal squamous cell carcinoma using feature selection and decision tree methods, The Scientific World Journal, 2013, 782031. (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) (2013)
- TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan, The Scientific World Journal, 2013, 736386. (2013)
- Prediction and analysis of antibody amyloidogenesis from sequences, PLoS One, 8(1), e53235. (2013)
- PupDB: a database of pupylated proteins, BMC Bioinformatics, 13, 40. (Highly Accessed) (2012)
- POPISK: T-cell reactivity prediction using support vector machines and string kernels, BMC Bioinformatics, 12, 446. (Highly Accessed) (2011)
- Prediction of protein subchloroplast locations using Random Forests, Proceeding of World Academy of Science, Engineering and Technology, 41, 903-907. (EI) (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) (2010)
- Human Pol II promoter prediction by using nucleotide property composition features, Proceedings of the International Symposium on Biocomputing, 22. (2010)
- Predicting protein subnuclear localization using GO-amino-acid composition features, Biosystems, 98(2), 73-79. (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) (2009)
- Computational identification of ubiquitylation sites from protein sequences, BMC Bioinformatics, 9, 310. (Highly Accessed) (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. (2008)
- ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization, BMC Bioinformatics, 9, 80. (2008)
- POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties, Bioinformatics, 23(8), 942-949. (2007)
- ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features, Biosystems, 90(2), 573-581. (2007)
- Expression analysis of the ESTs derived from the flower buds of Phalaenopsis equestris, Plant science, Elsevier, 170(3), 426-432. (2006)
Conference Presentations
- Prediction of Skin Sensitizers by Incorporating Mechanism Information, The 1st Winter Camp Congress of The Taiwan Society of Toxicology, Kenting, Taiwan. Jan 26–28 (Oral). (Invited Speaker) (2019)
- A visualization system for navigating neurotoxic effects of chemicals in ChemDIS: Fipronil as a case study, The 12th International Biocuration Conference, Cambridge, UK. Apr 7-10(Poster). (2019)
- Developing a QSAR model for predicting neurotoxic agents, The 15th International Congress of Toxicology (ICTXV), Hawaii, Honolulu. Jul 15–18 (Poster). (2019)
- Computational Screening of Chemicals Toxic to Neuronal Cells, The 1st Winter Camp Congress of The Taiwan Society of Toxicology, Kenting, Taiwan. Jan 26–28 (Poster). (Honorable Mention) (2019)
- Artificial Intelligence as Alternatives to Animal Testing, 15th Annual Meeting of the Chinese-Taipei Society of Laboratory Animal Sciences (CSLAS), Taipei, Taiwan. Nov. 15-16 (Oral). (Invited Speaker) (2018)
- ChemDIS: in silico analysis of chemical-disease association, OpenTox Asia 2018, Tokyo, Japan. May 24-25 (Oral). (Invited Speaker) (2018)
- Leveraging Alternative Assays for Predicting Skin Sensitizers, 2018 International Conference on Computational Chemistry and Toxicology in Environmental Science (2018CCTES), Taichung, Taiwan. May 4-6 (Oral). (Invited Keynote Speaker) (2018)
- An Integrated Web-based System for MEDLINE Analysis: A Case Study of Chronic Kidney Disease, 22nd Pacific Asia Conference on Information Systems (PACIS 2018), Yokohama, Japan. Jun 26-30 (Oral). (2018)
- Knowledge-based Prediction of Chemical-induced Sustained Proliferation, 2017 2nd International Conference on Biomedical Signal and Bioinformatics (ICBSB 2017), Auckland, New Zealand. Nov 27-30 (Oral). (Best Presentation Award) (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). (2017)
- Prediction of non-genotoxic hepatocarcinogens using consensus biomarkers, The 32th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 25-26 (Oral). (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). (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). (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). (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). (2017)
- 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). (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). (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). (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 (Oral). (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). (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). (2016)
- Developing a curated database for skin sensitizers by incorporating adverse outcome pathways, OpenTox Euro 2016, Rheinfelden, Germany. Oct 26-28 (Oral). (2016)
- Attenuation of antigen-specific Th1 immunity by Neolitsea hiiranensis derived sesquiterpenes, EAACI Congress 2016, Vienna, Austria. Jun 11-15 (Poster). (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). (2016)
- 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). (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. Sep. 30 (Oral). (2015)
- Computational Prediction of Skin Permeability of Chemicals, The 30th Joint Annual Conference of Biomedical Science, Taipei, Taiwan. Mar 21-22 (Poster). (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). (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). (2015)
- 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). (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). (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). (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). (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). (2014)
- 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). (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). (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). (2013)
- 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) (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). (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). (2012)
- Prediction of protein subchloroplast locations using Random Forests, International Conference on Computational Biology (ICBB2010), Tokyo, Japan. May 26-28 (Oral). (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). (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). (2010)
- 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). (2009)
- 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). (2008)
- POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties, Academic symposium of biotechnology, National Chiao Tung University, Hsinchu, Taiwan. (Oral). (Invited Speaker) (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). (2007)
- Gene expression during Phalaenopsis embryo development, International Symposium on Agricultural Genomics and Biotechnology. Tainan, Taiwan. Oct 28-30 (Poster). (2004)
Invited Talks
- ChemDIS-Mixture: analyzing potential interaction effects of chemical mixtures, Seminar, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Korea. Oct 10. (2018)
- 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. (2014)