Skip to main content
Publications

Publications

Journal articles · Conference papers · Patents · Books

Journal articles are synchronised weekly from ORCID and Crossref. Conference papers, patents and books are maintained by hand, because no registry carries them. This is the complete record.

Journal Articles

117 of 117 entries

YearTitleVenueAuthors
2026 Movement Anywhere: An Open-Source Distributed 2D Video-Based Movement Analysis Platform Empowered by Active Learning IEEE Journal of Biomedical and Health Informatics, 1-14 Ho, M. Y.; Tseng, Y. J.
2025 A robust and interpretable graph neural network-based protocol for predicting p-glycoprotein substrates Briefings in Bioinformatics, 26(4) Hsu, K. C.; Wang, P. H.; Su, B. H.; Tseng, Y. J.
2025 Advantages of two quantum programming platforms in quantum computing and quantum chemistry Journal of Cheminformatics, 17(1) Wang, P. H.; Wu, W. Y.; Lee, C. Y.; Hong, J. C.; et al.
2025 Altered gut microbial networks and metabolic pathways in multiple system atrophy: a comparative 16S rRNA study Frontiers in Neuroscience, 19 Liu, P. C.; Cheng, S. Y.; Li, C. C.; Wang, Y. K.; et al.
2025 Analyzing Generative AI and Machine Learning in Auto-Assessing Schizophrenia’s Negative Symptoms Schizophrenia Bulletin, 52(4) Liu, C. M.; Chan, Y. H.; Ho, M. Y.; Liu, C. C.; et al.
2025 Curated CYP450 Interaction Dataset: Covering the Majority of Phase I Drug Metabolism Scientific Data, 12(1) Ni, Y. H.; Su, Y. W.; Yang, S. C.; Hong, J. C.; et al.
2025 DeePFAS: Deep-Learning-Enabled Rapid Annotation of PFAS: Enhancing Nontargeted Screening through Spectral Encoding and Latent Space Analysis Environmental Science & Technology, 59(46), 24841-24852 Wang, H.; Kuo, T. C.; Tseng, Y. J.
2025 Identifying novel metabolites in children with attention-deficit hyperactivity disorder through metabolome profiling Translational Psychiatry, 15(1) Hung, Y. A.; Kuo, T. C.; Tseng, Y. J.; Shang, C. Y.; et al.
2025 SPARK Taiwan: a decade of insights in adapting US translational medicine and commercialization methods Nature Biotechnology, 43(4), 647-650 Lo, T. F.; Huang, Y. C.; Cho, N. Y.; Tseng, Y. J.
2024 A Clinical Breathomics Dataset Scientific Data, 11(1) Kuo, P. H.; Jhong, Y. C.; Kuo, T. C.; Hsu, Y. T.; et al.
2024 Digital annealing optimization for natural product structure elucidation Briefings in Bioinformatics, 25(6) Lee, C.; Wang, P. H.; Tseng, Y. J.
2024 Every Pixel Has Its Moments: Ultra-High-Resolution Unpaired Image-to-Image Translation via Dense Normalization Lecture Notes in Computer Science, 312-328 Ho, M. Y.; Wu, C. M.; Wu, M. S.; Tseng, Y. J.
2024 FastEval Parkinsonism: an instant deep learning–assisted video-based online system for Parkinsonian motor symptom evaluation npj Digital Medicine, 7(1) Yang, Y. Y.; Ho, M. Y.; Tai, C. H.; Wu, R. M.; et al.
2024 Mapping new psychoactive substances: Leveraging GIS technology for advanced global surveillance and policy support Regulatory Toxicology and Pharmacology, 153, 105713 Ku, T. J.; Kuo, T. C.; Lin, O. A.; Tseng, Y. J.
2024 Pathological Gait Analysis With an Open-Source Cloud-Enabled Platform Empowered by Semi-Supervised Learning-PathoOpenGait IEEE Journal of Biomedical and Health Informatics, 28(2), 1066-1077 Ho, M. Y.; Kuo, M. C.; Chen, C. S.; Wu, R. M.; et al.
2023 Biopharma innovation trends during COVID-19 and beyond: an evidence from global partnerships and fundraising activities, 2011-2022 Globalization and Health, 19(1) Yu, T. H.; Mei, Y. Y.; Tseng, Y. J.
2023 Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles Gut Microbes, 15(2) Li, C. C.; Hsu, W. F.; Chiang, P. C.; Kuo, M. C.; et al.
2023 Comparison of controlled drugs and new psychoactive substances (NPS) regulations in East and Southeast Asia Regulatory Toxicology and Pharmacology, 138, 105338 Lin, O. A.; Chuang, P. J.; Tseng, Y. J.
2023 MetaMOPE: a web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics Bioinformatics Advances, 3(1) Tsai, D. M.; Chang, C. Y.; Lin, S. M.; Kuo, T. C.; et al.
2023 MSIr: Automatic Registration Service for Mass Spectrometry Imaging and Histology Analytical Chemistry, 95(6), 3317-3324 Lin, B. J.; Kuo, T. C.; Chung, H. H.; Huang, Y. C.; et al.
2023 Recent Advances in Quantum Computing for Drug Discovery and Development IEEE Nanotechnology Magazine, 17(2), 26-30 Wang, P. H.; Chen, J. H.; Yang, Y. Y.; Lee, C.; et al.
2023 The evolution of the spike protein and hACE2 interface of SARS-CoV-2 omicron variants determined by hydrogen bond formation Briefings in Functional Genomics, 22(3), 291-301 Yang, Y. Y.; Tseng, Y. J.
2023 When Machine Learning and Deep Learning Come to the Big Data in Food Chemistry ACS Omega, 8(18), 15854-15864 Tseng, Y. J.; Chuang, P. J.; Appell, M.
2022 A pilot study of metabolomic pathways associated with fatigue in patients with colorectal cancer receiving chemotherapy European Journal of Oncology Nursing, 56, 102096 Chou, Y. J.; Kober, K. M.; Yeh, K. H.; Cooper, B. A.; et al.
2022 Author Correction: Intelligent pharmaceutical patent search on a near-term gate-based quantum computer Scientific Reports, 12(1) Wang, P.; Chen, J.; Tseng, Y. J.
2022 Coexisting gastrointestinal and hepatobiliary tract anomalies in omphalocele and gastroschisis: A twenty-year experience in a single tertiary medical center Pediatrics & Neonatology, 63(5), 468-473 Wen, C. C.; Kuo, T. C.; Lee, H. C.; Yeung, C. Y.; et al.
2022 Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors Briefings in Bioinformatics, 23(5) Lee, C.; Su, B. H.; Tseng, Y. J.
2022 Development of antiviral carbon quantum dots that target the Japanese encephalitis virus envelope protein Journal of Biological Chemistry, 298(6), 101957 Chen, H. H.; Lin, C. J.; Anand, A.; Lin, H. J.; et al.
2022 Exosomal Proteins and Lipids as Potential Biomarkers for Lung Cancer Diagnosis, Prognosis, and Treatment Cancers, 14(3), 732 Hsu, M. T.; Wang, Y. K.; Tseng, Y. J.
2022 Exploring molecular moieties on carbonized polymer dots from flavonoid glycosides with activity against enterovirus A71 Carbon, 192, 285-294 Lin, C. J.; Unnikrishnan, B.; Lehman, C. W.; Wang, P. H.; et al.
2022 Intelligent pharmaceutical patent search on a near-term gate-based quantum computer Scientific Reports, 12(1) Wang, P. H.; Chen, J. H.; Tseng, Y. J.
2022 RSDB: A rare skin disease database to link drugs with potential drug targets for rare skin diseases Scientific Data, 9(1) Kuo, T. C.; Wang, P. H.; Wang, Y. K.; Chang, C. I.; et al.
2022 Taiwan Controlled Substances Database Journal of the Formosan Medical Association, 121(12), 2649-2652 Huang, Y. W.; Lin, O. A.; Su, B. H.; Hsieh, P. H.; et al.
2021 A general optimization protocol for molecular property prediction using a deep learning network Briefings in Bioinformatics, 23(1) Chen, J. H.; Tseng, Y. J.
2021 Ensemble modeling with machine learning and deep learning to provide interpretable generalized rules for classifying CNS drugs with high prediction power Briefings in Bioinformatics, 23(1) Yu, T. H.; Su, B. H.; Battalora, L. C.; Liu, S.; et al.
2021 Identification of traumatic acid as a potential plasma biomarker for sarcopenia using a metabolomics‐based approach Journal of Cachexia, Sarcopenia and Muscle, 13(1), 276-286 Tsai, J.; Wang, S.; Chang, C.; Chen, C.; et al.
2021 Lipidomics of children and adolescents exposed to multiple industrial pollutants Environmental Research, 201, 111448 Chen, C. H. S.; Kuo, T. C.; Kuo, H. C.; Tseng, Y. J.; et al.
2020 A Pilot Study of Metabolomic Pathways Associated With Fatigue in Survivors of Colorectal Cancer Biological Research For Nursing, 23(1), 42-49 Chou, Y. J.; Kober, K. M.; Kuo, C. H.; Yeh, K. H.; et al.
2020 Advances in the prediction of mouse liver microsomal studies: From machine learning to deep learning WIREs Computational Molecular Science, 11(1) Renn, A.; Su, B.; Liu, H.; Sun, J.; et al.
2020 Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development Briefings in Bioinformatics, 22(3) Hsiao, Y.; Su, B. H.; Tseng, Y. J.
2020 Different molecular enumeration influences in deep learning: an example using aqueous solubility Briefings in Bioinformatics, 22(3) Chen, J. H.; Tseng, Y. J.
2020 Essential Step Toward Mining Big Polymer Data: PolyName2Structure, Mapping Polymer Names to Structures ACS Applied Polymer Materials, 2(8), 3107-3113 Lin, C.; Wang, P. H.; Hsiao, Y.; Chan, Y. T.; et al.
2020 Human Breathomics Database Database, 2020 Kuo, T. C.; Tan, C. E.; Wang, S. Y.; Lin, O. A.; et al.
2020 PanGPCR: predictions for multiple targets, repurposing and side effects Bioinformatics, 37(8), 1184-1186 Liu, L. C.; Ho, M. Y.; Su, B. H.; Wang, S. Y.; et al.
2019 IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting Journal of Cheminformatics, 11(1) Wang, P. H.; Tseng, Y. J.
2019 Metabolomics of Children and Adolescents Exposed to Industrial Carcinogenic Pollutants Environmental Science & Technology, 53(9), 5454-5465 Chen, C. H. S.; Kuo, T. C.; Kuo, H. C.; Tseng, Y. J.; et al.
2019 PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors Bioinformatics, 35(20), 4193-4195 Wang, P. H.; Tu, Y. S.; Tseng, Y. J.
2019 Quantum chemical investigation of the detection properties of alternariol and alternariol monomethyl ether Structural Chemistry, 30(5), 1749-1759 Tu, Y. S.; Tseng, Y. J.; Appell, M.
2018 LeadOp+R: Structure-Based Lead Optimization With Synthetic Accessibility Frontiers in Pharmacology, 9 Lin, F. Y.; Esposito, E. X.; Tseng, Y. J.
2018 LipidPedia: a comprehensive lipid knowledgebase Bioinformatics, 34(17), 2982-2987 Kuo, T. C.; Tseng, Y. J.
2018 Resistance Training Improves Muscle Function and Cardiometabolic Risks But Not Quality of Life in Older People With Type 2 Diabetes Mellitus: A Randomized Controlled Trial Journal of Geriatric Physical Therapy, 41(2), 65-76 Hsieh, P. L.; Tseng, C. H.; Tseng, Y. J.; Yang, W. S.
2018 Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods Molecular Simulation, 44(16), 1344-1352 Tu, Y. S.; Tseng, Y. J.; Appell, M.
2017 An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm Journal of Cheminformatics, 9(1) Su, B. H.; Shen, M. Y.; Harn, Y. C.; Wang, S. Y.; et al.
2017 Directly monitor protein rearrangement on a nanosecond-to-millisecond time-scale Scientific Reports, 7(1) Chen, E. H. L.; Lu, T. T. Y.; Hsu, J. C. C.; Tseng, Y. J.; et al.
2017 Effects of sarcosine and N, N-dimethylglycine on NMDA receptor-mediated excitatory field potentials Journal of Biomedical Science, 24(1) Lee, M. Y.; Lin, Y. R.; Tu, Y. S.; Tseng, Y. J.; et al.
2017 G.A.M.E.: GPU-accelerated mixture elucidator Journal of Cheminformatics, 9(1) Schurz, A.; Su, B. H.; Tu, Y. S.; Lu, T. T. Y.; et al.
2017 NP-StructurePredictor: Prediction of Unknown Natural Products in Plant Mixtures Journal of Chemical Information and Modeling, 57(12), 3138-3148 Harn, Y. C.; Su, B. H.; Ku, Y. L.; Lin, O. A.; et al.
2017 Trowaglerix Venom Polypeptides As a Novel Antithrombotic Agent by Targeting Immunoglobulin-Like Domains of Glycoprotein VI in Platelet Arteriosclerosis, Thrombosis, and Vascular Biology, 37(7), 1307-1314 Chang, C. H.; Chung, C. H.; Tu, Y. S.; Tsai, C. C.; et al.
2017 Using precursor ion scan of 184 with liquid chromatography-electrospray ionization-tandem mass spectrometry for concentration normalization in cellular lipidomic studies Analytica Chimica Acta, 971, 68-77 Chao, H. C.; Chen, G. Y.; Hsu, L. C.; Liao, H. W.; et al.
2016 A novel thromboxane receptor antagonist, nstpbp5185, inhibits platelet aggregation and thrombus formation in animal models Thrombosis and Haemostasis, 116(08), 285-299 Huang, S. W.; Kuo, H. L.; Hsu, M. T.; Tseng, Y. J.; et al.
2016 A Portable Micro Gas Chromatography System for Lung Cancer Associated Volatile Organic Compound Detection IEEE Journal of Solid-State Circuits, 51(1), 259-272 Tzeng, T. H.; Kuo, C. Y.; Wang, S. Y.; Huang, P. K.; et al.
2016 Distinct metabolic changes in human lung cancer cells with differential radiation sensitivities Translational Cancer Research, 5(6), 738-747 Shen, C. Y.; Kuo, C. H.; Wang, S. Y.; Yang, W. Q.; et al.
2016 Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis PLOS ONE, 11(2), e0148900 Hsu, K. H.; Su, B. H.; Tu, Y. S.; Lin, O. A.; et al.
2016 Steps toward a virtual rat: Predictive absorption, distribution, metabolism, and toxicity models ACS Symposium Series
2016 Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data Analytical Chemistry, 88(21), 10395-10403 Tian, T. F.; Wang, S. Y.; Kuo, T. C.; Tan, C. E.; et al.
2015 21.5 A portable micro gas chromatography system for volatile compounds detection with 15ppb of sensitivity 2015 IEEE International Solid-State Circuits Conference - (ISSCC) Digest of Technical Papers, 1-3 Tzeng, T. H.; Kuo, C. Y.; Wang, S. Y.; Huang, P. K.; et al.
2015 A matrix-induced ion suppression method to normalize concentration in urinary metabolomics studies using flow injection analysis electrospray ionization mass spectrometry Analytica Chimica Acta, 864, 21-29 Chen, G. y.; Liao, H. w.; Tseng, Y. J.; Tsai, I. l.; et al.
2015 An efficient and robust fatty acid profiling method for plasma metabolomic studies by gas chromatography–mass spectrometry Clinica Chimica Acta, 451, 183-190 Chiu, H. H.; Tsai, S. J.; Tseng, Y. J.; Wu, M. S.; et al.
2015 CypRules: a rule-based P450 inhibition prediction server Bioinformatics, 31(11), 1869-1871 Shao, C. Y.; Su, B. H.; Tu, Y. S.; Lin, C.; et al.
2015 Development and application of a comparative fatty acid analysis method to investigate voriconazole-induced hepatotoxicity Clinica Chimica Acta, 438, 126-134 Chen, G. y.; Chiu, H. h.; Lin, S. w.; Tseng, Y. J.; et al.
2015 Exploring possible mechanisms of action for the nanotoxicity and protein binding of decorated nanotubes: interpretation of physicochemical properties from optimal QSAR models Toxicology and Applied Pharmacology, 288(1), 52-62 Esposito, E. X.; Hopfinger, A. J.; Shao, C. Y.; Su, B. H.; et al.
2015 Fasting but not changes of plasma metabolome during oral glucose tolerance tests improves the diagnosis of severe coronary arterial stenosis Clinical Endocrinology, 83(4), 483-489 Hung, C.; Li, H.; Kuo, C.; Lin, M.; et al.
2015 Ion Trace Detection Algorithm to Extract Pure Ion Chromatograms to Improve Untargeted Peak Detection Quality for Liquid Chromatography/Time-of-Flight Mass Spectrometry-Based Metabolomics Data Analytical Chemistry, 87(5), 3048-3055 Wang, S. Y.; Kuo, C. H.; Tseng, Y. J.
2015 Mass-Spectrometry-Based Serum Metabolomics of a C57BL/6J Mouse Model of High-Fat-Diet-Induced Non-alcoholic Fatty Liver Disease Development Journal of Agricultural and Food Chemistry, 63(35), 7873-7884 Lai, Y. S.; Chen, W. C.; Kuo, T. C.; Ho, C. T.; et al.
2015 Rule-Based Classification Models of Molecular Autofluorescence Journal of Chemical Information and Modeling, 55(2), 434-445 Su, B. H.; Tu, Y. S.; Lin, O. A.; Harn, Y. C.; et al.
2015 Rule-Based Prediction Models of Cytochrome P450 Inhibition Journal of Chemical Information and Modeling, 55(7), 1426-1434 Su, B. H.; Tu, Y. s.; Lin, C.; Shao, C. Y.; et al.
2015 Synthesis and inhibitory effects of novel pyrimido-pyrrolo-quinoxalinedione analogues targeting nucleoproteins of influenza A virus H1N1 European Journal of Medicinal Chemistry, 102, 477-486 Lin, M. I.; Su, B. H.; Lee, C. H.; Wang, S. T.; et al.
2015 The metabolome profiling and pathway analysis in metabolic healthy and abnormal obesity International Journal of Obesity, 39(8), 1241-1248 Chen, H. H.; Tseng, Y. J.; Wang, S. Y.; Tsai, Y. S.; et al.
2015 Tu1474 Reduced 2-Hydroxybutyric Acid and Increased Malic Acid Correlate With Diabetes Remission After Roux-en-Y Gastric Bypass Gastroenterology, 148(4), S-901-S-902 Liao, W. C.; Kuo, C. H.; Wang, S. Y.; Tai, C. M.; et al.
2015 Using the Matrix-Induced Ion Suppression Method for Concentration Normalization in Cellular Metabolomics Studies Analytical Chemistry, 87(19), 9731-9739 Chen, G. Y.; Liao, H. W.; Tsai, I. L.; Tseng, Y. J.; et al.
2014 Comparison of warfarin therapy clinical outcomes following implementation of an automated mobile phone-based critical laboratory value text alert system BMC Medical Genomics, 7(S1) Lin, S. W.; Kang, W. Y.; Lin, D. T.; Lee, J. C. S.; et al.
2013 3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data BMC Systems Biology, 7(1) Kuo, T. C.; Tian, T. F.; Tseng, Y. J.
2013 Cheminformatics aspects of high throughput screening: from robots to models: symposium summary Journal of Computer-Aided Molecular Design, 27(5), 443-453 Jane Tseng, Y.; Martin, E.; G. Bologa, C.; Shelat, A. A.
2013 Correction to Metabolomic Characterization of Laborers Exposed to Welding Fumes Chemical Research in Toxicology, 26(2), 301-301 Wang, K. C.; Kuo, C. H.; Tian, T. F.; Tsai, M. H.; et al.
2013 Dependence of QSAR Models on the Selection of Trial Descriptor Sets: A Demonstration Using Nanotoxicity Endpoints of Decorated Nanotubes Journal of Chemical Information and Modeling, 53(1), 142-158 Shao, C. Y.; Chen, S. Z.; Su, B. H.; Tseng, Y. J.; et al.
2013 Metabolomic Analysis of Complex Chinese Remedies: Examples of Induced Nephrotoxicity in the Mouse from a Series of Remedies Containing Aristolochic Acid Evidence-Based Complementary and Alternative Medicine, 2013, 1-10 Tsai, D. M.; Kang, J. J.; Lee, S. S.; Wang, S. Y.; et al.
2013 Metabolomic characterization of rhubarb species by capillary electrophoresis and ultra‐high‐pressure liquid chromatography ELECTROPHORESIS, 34(19), 2918-2927 Tseng, Y. J.; Kuo, C.; Wang, S.; Liao, H.; et al.
2013 Metabolomic Dynamic Analysis of Hypoxia in MDA-MB-231 and the Comparison with Inferred Metabolites from Transcriptomics Data Cancers, 5(2), 491-510 Tsai, I. L.; Kuo, T. C.; Ho, T. J.; Harn, Y. C.; et al.
2013 Metabolomics of Ginger Essential Oil against Alcoholic Fatty Liver in Mice Journal of Agricultural and Food Chemistry, 61(46), 11231-11240 Liu, C. T.; Raghu, R.; Lin, S. H.; Wang, S. Y.; et al.
2013 Oversampling to Overcome Overfitting: Exploring the Relationship between Data Set Composition, Molecular Descriptors, and Predictive Modeling Methods Journal of Chemical Information and Modeling, 53(4), 958-971 Chang, C. Y.; Hsu, M. T.; Esposito, E. X.; Tseng, Y. J.
2013 Plasma metabolomic profiles predict near-term death among individuals with lower extremity peripheral arterial disease Journal of Vascular Surgery, 58(4), 989-996.e1 Huang, C. C.; McDermott, M. M.; Liu, K.; Kuo, C. H.; et al.
2013 Screening and Confirmation of 62 Drugs of Abuse and Metabolites in Urine by Ultra-High-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry Journal of Analytical Toxicology, 37(9), 642-651 Tsai, I. L.; Weng, T. I.; Tseng, Y. J.; Tan, H. K. L.; et al.
2013 Template-Based de Novo Design for Type II Kinase Inhibitors and Its Extended Application to Acetylcholinesterase Inhibitors Molecules, 18(11), 13487-13509 Su, B. H.; Huang, Y. S.; Chang, C. Y.; Tu, Y. S.; et al.
2013 True ion pick (TIPick): a denoising and peak picking algorithm to extract ion signals from liquid chromatography/mass spectrometry data Journal of Mass Spectrometry, 48(2), 234-242 Ho, T.; Kuo, C.; Wang, S.; Chen, G.; et al.
2012 Batch Normalizer: A Fast Total Abundance Regression Calibration Method to Simultaneously Adjust Batch and Injection Order Effects in Liquid Chromatography/Time-of-Flight Mass Spectrometry-Based Metabolomics Data and Comparison with Current Calibration Methods Analytical Chemistry, 85(2), 1037-1046 Wang, S. Y.; Kuo, C. H.; Tseng, Y. J.
2012 Computational Chemistry And Drug Discovery: A Call To Action Future Medicinal Chemistry, 4(15), 1893-1896 Jansen, J. M.; Amaro, R. E.; Cornell, W.; Tseng, Y. J.; et al.
2012 Distribution-Based Classification Method for Baseline Correction of Metabolomic 1D Proton Nuclear Magnetic Resonance Spectra Analytical Chemistry, 85(2), 1231-1239 Wang, K. C.; Wang, S. Y.; Kuo, C. h.; Tseng, Y. J.
2012 Metabolomic Characterization of Laborers Exposed to Welding Fumes Chemical Research in Toxicology, 25(3), 676-686 Kuo, C. H.; Wang, K. C.; Tian, T. F.; Tsai, M. H.; et al.
2012 Predictive Toxicology Modeling: Protocols for Exploring hERG Classification and Tetrahymena pyriformis End Point Predictions Journal of Chemical Information and Modeling, 52(6), 1660-1673 Su, B. H.; Tu, Y. s.; Esposito, E. X.; Tseng, Y. J.
2012 Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases Journal of Molecular Graphics and Modelling, 38, 360-362 Jansen, J. M.; Cornell, W.; Tseng, Y. J.; Amaro, R. E.
2011 A Comprehensive Support Vector Machine Binary hERG Classification Model Based on Extensive but Biased End Point hERG Data Sets Chemical Research in Toxicology, 24(6), 934-949 Shen, M. y.; Su, B. H.; Esposito, E. X.; Hopfinger, A. J.; et al.
2011 Structure-Based Fragment Hopping for Lead Optimization Using Predocked Fragment Database Journal of Chemical Information and Modeling, 51(7), 1703-1715 Lin, F. Y.; Tseng, Y. J.
2011 The great descriptor melting pot: mixing descriptors for the common good of QSAR models Journal of Computer-Aided Molecular Design, 26(1), 39-43 Tseng, Y. J.; Hopfinger, A. J.; Esposito, E. X.
2010 Chromaligner: a web server for chromatogram alignment Bioinformatics, 26(18), 2338-2339 Wang, S. Y.; Ho, T. J.; Kuo, C. H.; Tseng, Y. J.
2010 In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage Journal of Chemical Information and Modeling, 50(7), 1304-1318 Su, B. H.; Shen, M. y.; Esposito, E. X.; Hopfinger, A. J.; et al.
2010 Rapid determination of aristolochic acids I and II in herbal products and biological samples by ultra-high-pressure liquid chromatography–tandem mass spectrometry Talanta, 80(5), 1672-1680 Kuo, C. H.; Lee, C. W.; Lin, S. C.; Tsai, I. L.; et al.
2008 Categorical QSAR models for skin sensitization based on local lymph node assay measures and both ground and excited state 4D-fingerprint descriptors Journal of Computer-Aided Molecular Design, 22(6-7), 345-366 Liu, J.; Kern, P. S.; Gerberick, G. F.; Santos-Filho, O. A.; et al.
2008 ChemInform Abstract: Membrane‐Interaction Quantitative Structure—Activity Relationship (MI‐QSAR) Analyses of Skin Penetration Enhancers. ChemInform, 39(35) Zheng, T.; Hopfinger, A. J.; Esposito, E. X.; Liu, J.; et al.
2008 Membrane-Interaction Quantitative Structure−Activity Relationship (MI-QSAR) Analyses of Skin Penetration Enhancers Journal of Chemical Information and Modeling, 48(6), 1238-1256 Zheng, T.; Hopfinger, A. J.; Esposito, E. X.; Liu, J.; et al.
2007 Categorical QSAR Models for Skin Sensitization based upon Local Lymph Node Assay Classification Measures Part 2: 4D-Fingerprint Three-State and Two-2-State Logistic Regression Models Toxicological Sciences, 99(2), 532-544 Li, Y.; Pan, D.; Liu, J.; Kern, P. S.; et al.
2007 QSAR Analyses of Skin Penetration Enhancers. ChemInform, 38(34) Iyer, M.; Zheng, T.; Hopfinger, A. J.; Tseng, Y. J.
2006 4D-Fingerprint Categorical QSAR Models for Skin Sensitization Based on the Classification of Local Lymph Node Assay Measures Chemical Research in Toxicology, 20(1), 114-128 Li, Y.; Tseng, Y. J.; Pan, D.; Liu, J.; et al.
2006 Prediction and Mechanistic Interpretation of Human Oral Drug Absorption Using MI-QSAR Analysis Molecular Pharmaceutics, 4(2), 218-231 Iyer, M.; Tseng, Y. J.; Senese, C. L.; Liu, J.; et al.
2004 4D-Fingerprints, Universal QSAR and QSPR Descriptors Journal of Chemical Information and Computer Sciences, 44(5), 1526-1539 Senese, C. L.; Duca, J.; Pan, D.; Hopfinger, A. J.; et al.
2004 4D‐QSAR Analysis of a Series of Antifungal P450 Inhibitors and 3D‐Pharmacophore Comparisons as a Function of Alignment. ChemInform, 35(6) Liu, J.; Pan, D.; Tseng, Y.; Hopfinger, A. J.
2004 Characterization of a Ligand−Receptor Binding Event Using Receptor-Dependent Four-Dimensional Quantitative Structure−Activity Relationship Analysis Journal of Medicinal Chemistry, 47(12), 3075-3088 Pan, D.; Liu, J.; Senese, C.; Hopfinger, A. J.; et al.
2003 Quantitative Structure‐Based Design: Formalism and Application of Receptor‐Dependent RD‐4D‐QSAR Analysis to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase. ChemInform, 34(51) Pan, D.; Tseng, Y.; Hopfinger, A. J.

Conference Papers

  1. YT Hsu, PW Du, JC Hong, CW Tsai, TC Kuo, PK Hsiao, HP Kao, SC Lin, YJ Tseng* (2026, Aug). Development of the Guided Risk Evaluation and Environmental Navigation (GreenN) System: A Computational Approach for Greener Chemical Evaluation and Visualization. ACS Fall 2026 National Meeting & Exposition, Chicago, IL. August 23-27, 2026.
  2. YC Chen, YJ Tseng* (2024, Nov). Predicting Microsatellite Instability from Histology Images with Dilated Neighborhood Attention Transformer in Colorectal Cancer, The IEEE International Conference on Bioinformatics & Bioengineering (BIBE2024), Kragujevac, Serbia. Nov 27-29, 2024.
  3. YJ Tseng* (2024, Aug). Quantum Computing for Natural Product Structure Elucidation. ACS Fall 2024 National Meeting & Exposition, Denver, CO. August 18-22, 2024.
  4. PY Yao, TC Kuo, YK Wang, HH Chung, YH Chen, CH Chen, DZ Luo, CC Hsu, WS Lai, YJ Tseng* (2024, Jun). AI-enhanced Spatial Metabolomics Utilizing Mass Spectrometry Imaging in Schizophrenic Mouse Brain. Metabolomics 2024, Osaka, Japan. June 16-20, 2024.
  5. CY Chang, MC Kuo, YJ Tseng* (2024, Apr). Exploring Lipid Disturbances and its Spatial Association with a-Synuclein Aggregation in MSA Patient Brain Regions via Desorption Electrospray Ionization Mass Spectrometry Imaging. 2024 AAN Annual Meeting, Denver, CO. April 13-18, 2024.
  6. MY Ho, MC Kuo, CS Chen, RM Wu, CC Chuang, CS Shih, YJ Tseng* (2024, Apr). Pathological Gait Analysis with an Open-source Cloud-enabled Platform Empowered by Semi-supervised Learning—PathoOpenGait. 2024 AAN Annual Meeting, Denver, CO. April 13-18, 2024.
  7. C Lee, PH Wang, YJ Tseng* (2023, Aug). Exploration of Quantum-Inspired Computing for Natural Product Structure Elucidation. ACS Fall 2023 National Meeting & Exposition, San Francisco, CA.
  8. PH Kuo, YC Jhong, TC Kuo, CH Kuo, YJ Tseng* (2023, Jun). CBDB: A clinical breathomics database. Metabolomics 2023, Niagara Falls, Canada.
  9. CY Chang, MC Kuo, YK Wang, HH Chun, YS Chen, ZX Chen, CC Hsu, YJ Tseng* (2023, Jun). Metabolomic Alterations in Different Brain Regions of Multiple System Atrophy using DESI-MSI. Metabolomics 2023, Niagara Falls, Canada.
  10. CY Chang, YJ Tseng* (2023, Jun). Correlating α-Synuclein Accumulation with Metabolomic Alterations in Different Brain Regions of Multiple System Atrophy using DESI-MSI. Metabolomics 2023, Niagara Falls, Canada.
  11. CC Li*, YJ Tseng, AM Wo (2023, May). Association of bacterial extracellular vesicles in human stool, plasma and gut microbiota using a composite purification method. ISEV2023 Annual Meeting, Seattle, WA.
  12. PH Wang, YY Yang, YJ Tseng* (2022, Aug). QSAR model of carcinogenicity based on data from GreenScreen Hazard Assessment. ACS Fall 2022 National Meeting & Exposition, Chicago, IL.
  13. TC Kuo, PH Wang, YK Wang, YY Yang, CY Chang, PY Yao, YC Jhong, CY Lee, YJ Tseng* (2022, Aug). Benchmark Dataset for Hazardous Substances for Safer Alternative Chemicals. ACS Fall 2022 National Meeting & Exposition, Chicago, IL.
  14. YK Wang, CY Chang, YY Yang, YJ Tseng* (2022, Aug). Current Trends in Safer Alternatives and Risk Assessment. ACS Fall 2022 National Meeting & Exposition, Chicago, IL.
  15. YJ Tseng* (2022, Aug). Sustainability and green technology – in silico databases, and tools. ACS Fall 2022 National Meeting & Exposition, Chicago, IL.
  16. YJ Tseng* (2022, Mar). Big data and deep learning in agriculture and food chemistry - considerations and practice. ACS Spring 2022 National Meeting & Exposition, San Diego, CA.
  17. C Lee, YJ Tseng* (2022, Mar). Competitive analysis of trending deep-learning-based protein modelling methods on G-protein coupling receptors. ACS Spring 2022 National Meeting & Exposition, San Diego, CA.
  18. YY Yang, YJ Tseng* (2022, Mar). Competitive analysis of different SARS-CoV-2 variants in United Kingdom, Israel, South Africa, Brazil and Peru. ACS Spring 2022 National Meeting & Exposition, San Diego, CA.
  19. H Liu, CW Lee, YJ Tseng* (2021, Aug). Optimizing all properties – A novel multi-objective ADMET modeling for structure optimization using reinforcement graph constitutional neural networks. ACS Fall 2021 National Meeting & Exposition, Atlanta, GA.
  20. YJ Tseng* (2021, Mar). Sustainability: Advances and Applications of Chemicals Prediction Tools in Food Safety and Security. ACS Spring 2021 National Meeting & Exposition, San Antonio, TX.
  21. H Liu, CW Lee, BH Su, YJ Tseng* (2020, Aug). Training strategy for unbalanced small datasets in deep learning. ACS Fall 2020 National Meeting & Exposition, San Francisco, CA.
  22. H Liu, YC Tien, TS Cho, BH Su, YJ Tseng* (2020, Aug). Graph Convolution Neural Network in Environmental Carcinogenicity Prediction. ACS Fall 2020 National Meeting & Exposition, San Francisco, CA.
  23. H Liu, CW Lee, BH Su, YJ Tseng* (2020, Aug). A New explainable graph convolution network based on discrete method: using water solubility as an example. ACS Fall 2020 National Meeting & Exposition, San Francisco, CA.
  24. H Liu, CW Lee, BH Su, YJ Tseng* (2020, Aug). Explainable AI in toxicity prediction. ACS Fall 2020 National Meeting & Exposition, San Francisco, CA.
  25. YJ Tseng* (2020, Aug). Graph convolution neural network in environmental carcinogenicity prediction. ACS Fall 2020 National Meeting & Exposition, San Francisco, CA, August 17-20, 2020.
  26. A Renn, BH Su, H Liu, YJ Tseng* (2019, Apr). Mouse-Liver Microsomal Stability Prediction using Graph Convolutional Neural Networks. Spring 2019 ACS National Meeting, Orlando, FL.
  27. H Liu, BH Su, TS Cho, YC Tien, YJ Tseng* (2019, Apr). Graph based neural network model for predicting aqueous solubility. Spring 2019 ACS National Meeting, Orlando, FL.
  28. PH Wang, YS Tu, YJ Tseng* (2019, Apr). PgpRules: a Decision Tree Based Prediction Server for P-glycoprotein Substrates and Inhibitors. Spring 2019 ACS National Meeting, Orlando, FL.
  29. TW Shieh, BH Su, YJ Tseng* (2019, Apr). Predicting human liver microsomal stability. Spring 2019 ACS National Meeting, Orlando, FL.
  30. YS Tu, YJ Tseng, M Appell (2018, Aug). Quantum molecular dynamics and cheminformatics study of mycotoxin toxicity and detection to improve food safety. 256th American Chemical Society National Meeting and Exposition, Boston, Massachusetts.
  31. YS Tu, YJ Tseng, M Appell (2018, Mar). Density functional theory and ab initio investigation of the detection properties of cyromazine. 255th American Chemical Society National Meeting and Exposition, New Orleans, Louisiana.
  32. MT Hsu, LP Chow, TY Ling, HW Chen, CH Kuo, YJ Tseng* (2017, Jun). Molecular Landscape of Lung Cancer Stem Cell-Derived Exosomes. 2017 Exosomes and Liquid Biopsies Asia, Taoyuan, Taiwan.
  33. PH Wang, YJ Tseng* (2017, Apr). Auto Generation of Markush Structure for Maximizing Composition Patent Claim. 253rd American Chemical Society National Meeting & Expo, San Francisco, California.
  34. BH Su, D Huang, OA Lin, YJ Tseng* (2017, Apr). Computationally Predicted Signatures of EGFR Exon 20 Insertions In Non-Small Cell Lung Cancer and Its Response to Irreversible Inhibitors. 253rd American Chemical Society National Meeting & Expo, San Francisco, California.
  35. Wang, S. Y., Tseng, Y. J.*, Tseng, T. H., Kuo, C. Y., Huang, P. K., Huang, Y. M., Hsieh, W. C., Huang, Y. J., Kuo, P. H., Yu, S. A., Tian, W. C., Lee, S. C., and Lu, S.-S., “Lung Cancer Associated Volatile Organic Compounds Detection Using a Novel Portable Gas Chromatographic Device Integrated MEMS and CMOS Technology,” 12th International Conference of the Metabolomics Society, Dublin, Ireland, June 27-30. 2016.
  36. Tseng, Y. J. , Scaffold analysis of Ames mutagenicity, 251th ACS National Meeting & Exposition, San Francisco, San Diego, March. 13-17. 2016.
  37. Su, B. H.; Tu, Y. S.; Lin, O. A.; Harn, Y. C.; Shen, M. Y.; Tseng, Y. J.* , In-silico Rule-based Models for Design of Fluorophores Area, Pacifichem, December 15-20, 2015.
  38. Tzeng, T. H., Kuo, C. Y., Wang, S. Y., Huang, P. K., Kuo, P. H., Huang, Y. M., Tseng, Y. J.* , Tian, W. C., Lee, S. C., & Lu, S. S.. 21.5 A portable micro gas chromatography system for volatile compounds detection with 15ppb of sensitivity, IEEE International Solid-State Circuits Conference, San Francisco, California, Feb. 22-26. 2015.
  39. Shao, C. Y., Su, B. H., Tu, Y.S., Lin, C., Lin, O. A., Tseng, Y. J.* , CypRules: A rule-based P450 inhibition prediction server, 248th ACS National Meeting & Exposition, San Francisco, California, Aug. 10-14. 2014.
  40. Wang, S. Y., Kuo, C. H., Tseng, Y. J.* , An ion trace detection algorithm to extract pure ion chromatogram to improve untargeted peak detection quality for LC/TOF-MS-based metabolomics data, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014.
  41. Tsai, D. M., Kuo, C. H., Tseng, Y. J.* , Strategy of UPLC/MS-based Targeted Metabolomics, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014.
  42. Tan, C. E., Chung, Y. Y., Tseng, Y. J.* , IDMass: GC/MS Data Management and Analyzes Software for Metabolomics Studies, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014.
  43. Lin, S. W., Kang, W. Y., Lin, D. T., Lee, J., Wu, F. L., Chen, C. L. Tseng, Y. J.* , Comparison of warfarin therapy clinical outcomes following implementation of an automated mobile phone-based critical laboratory value text alert system, Translational Bioinformatics Conference, Seoul, Korea, October 2-4, 2013.
  44. Tseng, Y. J.* , BaselineCorrector: A distribution-based classification method for baseline correction of metabolomic 1D proton nuclear magnetic resonance spectra, 246th ACS National Meeting & Exposition, Indianapolis, Indiana, September 8-12, 2013.
  45. Tseng, Y. J.* , GAME: Gpu accelerated mixture elucidator 246th ACS National Meeting & Exposition, Indianapolis, Indiana, September 8-12, 2013.
  46. Tseng, Y. J.* , “Drug discovery through Teach-Discover-Treat initiative, 246th ACS National Meeting & Exposition, Indianapolis, Indiana, September 8-12, 2013.
  47. Wang, S. Y., Wu, M. S., Kuo, C. H., Liao, W. C., Tseng, Y. J.* , Metabolomics study of metabolite changes in the serum of morbidly obese patients after the gastric bypass surgery, 4th AOMSC & 10th TSMS Annual Conference, TICC, Taipei, Taiwan, July 10-12, 2013.
  48. Tsai, D. M., Chen, G. Y., Kuo, C. H., Tseng, Y. J.* , Development of a hydrophilic interaction chromatography coupled with mass spectrometry method for metabolomic analysis, 4th AOMSC & 10th TSMS Annual Conference, TICC, Taipei, Taiwan, July 10-12, 2013.
  49. Kuo, P. H., Chang, N. W., Kuo, C. H., Tseng, Y. J.* , Metabolomic analysis of exhaled breath condensates (EBC) in healthy volunteers and patients with chronic obstructive pulmonary disease (COPD) and bronchiectasis, 4th AOMSC & 10th TSMS Annual Conference, TICC, Taipei, Taiwan, July 10-12, 2013.
  50. Wang, S. Y., Tseng, Y. J.* , BN server: a web-based service for LC/TOFMS-based metabolomics data normalization and statistical analysis, 9th International conference of the Metabolomics Society, Glasgow, SECC, Glasgow, Scotland, July 1-4, 2013.
  51. Chung, Y. Y, Kuo, C. H., Tseng, Y. J.* , Noise reduction of GC/TOF-MS using spectrum domain baseline removal and chromatogram segment filtering, 9th Annual Conference of the Metabolomics Society, SECC, Glasgow, Scotland, July 1- 4, 2013.
  52. Kuo, T. C., Tsai, D. M., Kuo, H. C., Kuo, C. H., Tseng, Y. J. , Establish Targeted Lipidomics Workflow Using TIPick, 9th International Conference of the Metabolomics Society, SECC, Glasgow, Scotland, July 1-4, 2013.
  53. Chang, N. W., Kuo, C. H., Tseng, Y. J. , Metabolomics characterisation of Angelica species by comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GCxGC-TOFMS), 9th International conference of the Metabolomics Society, SECC, Glasgow, Scotland, July 1-4, 2013.
  54. Liu, J. W., Kuo, C. H., Tseng, Y. J.* , The Retention Time Alignment for non-targeted LC/MS analysis Using Kernel Density Estimation with a Novel Bandwidth Estimator, 9th International conference of the Metabolomics Society, SECC, Glasgow, Scotland, July 1-4, 2013.
  55. Hsu, K. H., Tseng, Y. J.* , A new approach of traditional Chinese medicine taxonomy: using marker ingredients as bases, 245th ACS National Meeting & Exposition, New Orleans, Louisiana, April 7-11, 2013.
  56. Shao, C. Y., Tseng, Y. J.* , Exploration of mechanism between nanotoxicity and protein targets: QSAR models using nanotoxicity endpoints of decorated nanotubes, 245th ACS National Meeting & Exposition, New Orleans, Louisiana, April 7-11, 2013.
  57. Tu, Y. S., Harn, Y. C., Shen, M. Y., Tseng, Y. J.* , Classification tree and random forest based prediction models on molecular autofluorescence, 245th ACS National Meeting & Exposition, New Orleans, Louisiana, April 7-11, 2013.
  58. Tseng, Y. J.* , LeadOp: Structure-based fragment hopping for lead optimization using pre-docked fragment database, 244th ACS National Meeting & Exposition, Philadelphia, Pennsylvania, August 19-23, 2012. (Invited talk, Drug Discovery Symposium).
  59. Chen, S. Z., Tseng, Y. J.* , Predictive toxicity protocol for cell-viability high throughput data, 244th ACS National Meeting & Exposition, Philadelphia, Pennsylvania, August 19-23, 2012.
  60. Tseng, Y. J.* , Kuo, C. H., Yang, W. Q., Wang, S. Y., Metabolic Signatures Associated with the Progression of Breast Cancer by Ultra High Pressure Liquid Chromatography Time-of-Flight Mass Spectrometry, 8th International conference of the Metabolomics Society, Washington D.C., June 25-28, 2012.
  61. Yang, W. Q., Ho, C. C., Tseng, Y. J. , Kuo, C. H., Development of a Solid-Phase Microextraction Gas Chromatography Time-of-Flight Mass Spectrometry Method for Profiling Volatile Metabolic Patterns of Exhaled Breath Condensate, the 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20–24, 2012.
  62. Tseng, Y. J.* , Kuo, C. H., Tian, T. F., An Alignment Algorithm for Comprehensive Two-dimensional Gas Chromatography-Mass Spectrometry, 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20–24, 2012.
  63. Chang, C. Y., Tseng, Y. J.* , Virtual screening the natural products for FKBP12 inhibition, 243rd ACS National Meeting & Exposition, San Diego, California, March 25 - 29, 2012.
  64. Tu, Y. S., Esposito, E. X., Tseng, Y. J.* , Predictive Toxicology Modeling: Protocols for Exploring Tetrahymena Pyriformis Endpoint Predictions, 243rd ACS National Meeting & Exposition, San Diego, California, March 25 - 29, 2012.
  65. Su, B. H., Harn, Y. C., Tseng, Y. J.* , An efficient dynamic programming algorithm to predict natural product structures, 243rd ACS National Meeting & Exposition, San Diego, California, March 25 - 29, 2012.
  66. Jansen, J. M., Tseng, Y. J.* , Rommie E Amaro, Teach - Discover - Treat: A COMP initiative to provide high quality computational chemistry tutorials that impact education and drug discovery for neglected diseases, 242nd ACS National Meeting & Exposition, Denver, USA, August 28 - Sept. 1, 2011. (invited talk, Collaborative Drug Discovery for Neglected Diseases session in COMP).
  67. Su, B. H., Chen, S. Z., Tu, Y. S., Tseng, Y. J.* , Natural products screening for alpha-glucosidase inhibitors, 242nd ACS National Meeting & Exposition, Denver, USA, August 28 - Sept. 1, 2011.
  68. Tseng, Y. J.* , The symposium of "Cheminformatics aspects of high throughput screening: from robots to models”, 242nd ACS National Meeting & Exposition, Denver, USA, August 28 - Sept. 1, 2011. (Invited Talk for special symposium).
  69. Wang SY, Kuo CH, and Tseng YJ*, An ion trace detection algorithm to extract pure ion chromatogram to improve untargeted peak detection quality for LC/TOF-MS-based metabolomics data, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014
  70. Tsai DM, Kuo CH, and Tseng YJ*, Strategy of UPLC/MS-based Targeted Metabolomics, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014
  71. Tan CE, Chung YY, and Tseng YJ*, IDMass: GC/MS Data Management and Analyzes Software for Metabolomics Studies, 10th International conference of the Metabolomics Society, Tsuruoka, Japan, June 26-29, 2014
  72. Lin SW, Kang WY, Lin DT, Lee J, Wu FL, Chen CL and Tseng YJ*, Comparison of warfarin therapy clinical outcomes following implementation of an automated mobile phone-based critical laboratory value text alert system, Translational Bioinformatics Conference, Seoul, Korea, October 2-4, 2013
  73. Tseng YJ*, GAME: Gpu accelerated mixture elucidator 246th ACS National Meeting, Indianapolis, Indiana, September 8-12, 2013
  74. Tseng YJ*, “Drug discovery through Teach-Discover-Treat initiative, 246th ACS National Meeting, Indianapolis, Indiana, September 8-12, 2013
  75. Johanna M Jansen, Tseng YJ*, Rommie E Amaro, Teach - Discover - Treat: A COMP initiative to provide high quality computational chemistry tutorials that impact education and drug discovery for neglected diseases, 242nd ACS National Meeting & Exposition, Denver, USA, August 28 - Sept. 1, 2011. (invited talk, Collaborative Drug Discovery for Neglected Diseases session in COMP)
  76. Tseng YJ*, “The symposium of "Cheminformatics aspects of high throughput screening: from robots to models”, (Invited Talk for special symposium), 242nd ACS National Meeting & Exposition, Denver, USA, August 28 - Sept. 1, 2011
  77. Ho TJ, Tseng YJ*, MetaPick, a denoising and peak picking algorithm for extracting single compound from complex mixtures in liquid chromatography/mass spectrometry (LC/MS) metabolomics data, 7th International Conference of the Metabolomics Society, Cairns, Australia, June 27 - 30, 2011. (Best presentation award)
  78. Harn YC, Tseng YJ*, Structure Hunter: Prediction of novel chemical structures in a mixture, 7th International Conference of the Metabolomics Society, Cairns, Australia, June 27 - 30, 2011. (Invited Talk for Technology Innovation Section)
  79. Tian TF, Kuo TC, Tseng YJ*, 3Omics: a web based systems biology visualization tool by integrating transcriptomics, proteomics and metabolomics data in human, 7th International Conference of the Metabolomics Society, Cairns, Australia, June 27 - 30, 2011. (Invited Talk for Systems Biology Section)
  80. Kuo TC, Tian TF, Tseng YJ*, HMO: Human Metabolome Ontology, 7th International Conference of the Metabolomics Society, Cairns, Australia, June 27 - 30, 2011
  81. Wang SY, Tseng YJ*, A fast robust total abundance regression calibration to adjust sever batch effect, 7th International Conference of the Metabolomics Society, Cairns, Australia, June 27 - 30, 2011
  82. Liao HW, Kuo CH, Tseng YJ*, Determination of posaconazole in patient plasma by field amplified sample stacking in capillary electrophoresis, Joint Congress 2011,Berlin, May 1-5, 2011
  83. Lin FY, Tseng YJ*, Lead Optimization with Synthetic Accessibility, 241st ACS National Meeting & Exposition, Anaheim, CA, March 27-31, 2011
  84. Lin SW, Kan WY, Wu FL, Lin DT, Tseng YJ*, A comparison of the clinical outcome toward switching from manual reminders to a cell phone alert system on warfarin therapy (abstract HPS-P-044), World Congress of Pharmacy & Pharmaceutical Sciences 2010, Portugal, August 28-September 2, 2010
  85. Tseng YJ*, Computational hERG Toxicity Classification Model Based on QSAR and Support Vector Machines (Invited talk, Skolnik Award Symposium)”, 240th American Chemical Society National Meeting, Boston, USA, August 24, 2010
  86. Huang YS, Su BH, Tseng YJ*, A fragment-based de-novo design for VEGFR2/3 inhibitors, 240th ACS National Meeting & Exposition, Boston, USA, August 22-26, 2010
  87. Lin FY, Tseng YJ*, Structure-based fragment hopping for lead optimization using pre-docked fragment database, 240th ACS National Meeting & Exposition, Boston, USA, August 22-26, 2010
  88. Tu YS, Su BH, Tseng YJ*, Clustering Based Scaffold Hopping with 4D-Fingerprints, 240th ACS National Meeting & Exposition, Boston, USA, August 22-26, 2010
  89. Wang KC, Wang SY, Tseng YJ*, NMR Deconvolutor: A Robust Deconvolution Algorithm for Quantitative Metabolomics, 6th International Conference of the Metabolomics Society, Amsterdam, June 27 - July 1, 2010
  90. Kuo TC, Tian TF, Tseng YJ*, MetPath: Metabolomics pathway visualization, 5th International Conference of the Metabolomics Society, Alberta, Canada, August 30 - September 2, 2009
  91. Kuo CH, Wang SY, Ho TJ, Tseng YJ*, Chromaligner: a web server for chromatogram alignment, 5th International Conference of the Metabolomics Society, Alberta, Canada, August 30 - September 2, 2009
  92. Kuo CH, Tsai DM, Tseng YJ*, Metabolomics analysis on complex Chinese remedies - Examples from a series of Aristolochic Acid containing remedy induced Nephrotoxicity in Rodents, 5th International Conference of the Metabolomics Society, Alberta, Canada, August 30 - September 2, 2009
  93. Wang KC, Kuo CH, Tseng YJ*, Distribution-based Reconstruction Model for Baseline Correction in Metabolomic NMR Spectrum, 5th International Conference of the Metabolomics Society, Alberta, Canada, August 30 -September 2, 2009
  94. Su BH, Shen MY, Esposito EX, Tseng YJ*, In silico binary QSAR model based on 4D-fingerprints and MOE descriptors for hERG blockage evaluation, 238th ACS National Meeting & Exposition, Washington D.C., August 16-20, 2009
  95. Tsai CC, Chung CH, Chang CH, Huang TF, Tseng YJ*, Structural basis of agonists and antagonists derived from snake venom C-type lectins: Interaction with platelet Glycoprotein VI, 238th ACS National Meeting & Exposition, Washington D.C., August 16-20, 2009
  96. Shen MY, Su BH, Esposito EX, Tseng YJ*, Support vector machine classification model of PubChem hERG Bioassay data with 4D-fingerprint and MOE descriptors, 238th ACS National Meeting & Exposition, Washington D.C., August 16-20, 2009
  97. Kuo CH, Tsai IL, Wang SY, Tseng YJ*, Hypoxia and normoxia metabolomics profiling on MDA 231 Breast Cancer Cells, 4th Metabolomics Society Annual Conference, Boston, USA, September 2-6, 2008
  98. Tseng YJ*, Wang SY, Tsai LL, Kuo CH, Metabolic profiling on breast cancer cell lines in hypoxia, 4th Metabolomics Society Conference, Boston, USA, September 2-6, 2008

Patents

  1. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, CN Patent No. 201580021632.9, November 2020.
  2. 曾宇鳳、孫仲銘、賴文崧、胡海國、劉智民、劉玉麗，「作為 D-胺基酸氧化酶抑制劑之已知化合物之用途」，中華民國專利 I675660 號，2019 年 11 月。
  3. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, AU Patent No. 2015253099, July 2019.
  4. 曾宇鳳、孫仲銘、賴文崧、胡海國、劉智民、劉玉麗，「作為 D-胺基酸氧化酶 (DAAO) 抑制劑之新穎經取代苯并咪唑衍生物」，中華民國專利 I659022 號，2019 年 5 月。
  5. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, US Patent No. 9,868,975, January 2018.
  6. 曾宇鳳、林芳宇，「為先導藥物最適化之以結構為基礎的片段遷越及合成可行性之改良」，中華民國專利 I611053 號，2018 年 1 月。
  7. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, EP Patent No. 17851543.3, September 2017.
  8. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, US Patent No. 16/332,628, September 2017.
  9. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, CN Patent No. 201780056602.0, September 2017.
  10. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, JP Patent No. 2019-513382, September 2017.
  11. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, KR Patent No. 2019-7010035, September 2017.
  12. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, AU Patent No. 2017326359, September 2017.
  13. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, CA Patent No. 3,036,250, September 2017.
  14. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, MX Patent No. MX/a/2019/002726, September 2017.
  15. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, SG Patent No. 11201902053Y, September 2017.
  16. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, IL Patent No. 265108, September 2017.
  17. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, NZ Patent No. 751050, September 2017.
  18. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Novel substituted benzimidazole derivatives as D-amino acid oxidase (DAAO) inhibitors”, HK Patent No. unassigned as of the CV, September 2017.
  19. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, EP Patent No. 15786611.2, April 2015.
  20. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, EP Patent No. 19150604.7, April 2015.
  21. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, JP Patent No. 2017-510438, April 2015.
  22. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, JP Patent No. 2020-035496, April 2015.
  23. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, KR Patent No. 10-2016-7032409, April 2015.
  24. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, CA Patent No. 2,946,153, April 2015.
  25. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, MX Patent No. MX/a/2016/011551, April 2015.
  26. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, SG Patent No. 11201607166X, April 2015.
  27. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, IL Patent No. 248567, April 2015.
  28. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, NZ Patent No. 723652, April 2015.
  29. Yufeng Jane Tseng, Chung-Ming Sun, Wen-Sung Lai, Hai-Gwo Hwu, Chih-Min Liu, Yu-Li Liu, “Use of known compounds as D-amino acid oxidase inhibitors”, HK Patent No. 17106840.0, April 2015.
  30. Tseng, Y. J., Lin, F. Y., Structure-Based Fragment Hopping For Lead Optimization And Improvement In Synthetic Accessibility, U.S. Patent No. 13778858, February 27, 2013.
  31. Fu, W. M., Kang, K. H., Liou, H. H., Liou, H. C., Tseng, Y. J., Quinazolinone and quinazoline compounds and their pharmaceutical uses, U.S. Provisional Patent No. 61/649425, May 21, 2012.
  32. Tseng, Y. J., Ho, T. J., Kuo, C. H., True ion pick (TIPick): a denoising and peak picking algorithm to extract ion signals from liquid chromatography/mass spectrometry data, U.S. Provisional Patent No. 61/861544, August, 2013.
  33. Tseng, Y. J., Wang, K. C., A Distribution-based Classification Method for Baseline Correction of Metabolomic 1D Proton Nuclear Magnetic Resonance Spectra, U.S. Provisional Patent No. 16/137,048, June, 2013.
  34. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., use of known compounds as d-amino acid oxidase inhibitors, U.S. Provisional Patent No. 61/986480, April, 2014.
  35. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., compounds for use as d-amino acid oxidase inhibitors, U.S. Provisional Patent No. 62/056917, September, 2014.
  36. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., use of known compounds as d-amino acid oxidase inhibitors, U.S. PCT Patent No. PCT/US2015/028385, April, 2015.
  37. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., use of known compounds as d-amino acid oxidase inhibitors, TW Patent No. 104114104, April, 2015.
  38. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., new formulation for stabilize acid unstable compound, U.S. Provisional Patent No. 62/312279, March, 2016.
  39. Tseng, Y. J., Liu, Y.L., Sun, C.M., Lai, W.S., Liu, C.M., Hwu, H.G., new formulation for neuropsychiatric disorders, U.S. Provisional Patent No. 62/3401135, May, 2016.
  40. Chen, Huei-Wen; Lee, Jen-Yi; Yang, Pan-Chyr; Yu, Sung-Liang; Chen, Jian-Wei; Yang, Chih-Hsin; Ho, Chao-Chi; Lee, Kuo-Hsiung; Tseng, Yufeng Jane; Chang, Gee-Chen; Use of curcumin or its analogues in cancer therapy utilizing epidermal growth factor receptor tyrosine kinase inhibitor, U.S. Patent 20110224205A1, February 11,2011
  41. Sun, Chung-ming; Kuo, Ming-liang; Tseng, Yufeng, "Bicyclic Heteroaryl Compounds", U.S. Patent 20110082143, October 1, 2010
  42. Fu, Wen-Mei; Kang, Kai-Hsiang; Liou, Horng Huei; Liou, Horng Chi; Tseng, Yufeng; Quinazolinone and quinazoline compounds and their pharmaceutical uses, U.S. Provisional Patent No. 61/649425, May 21, 2012
  43. Tseng, Yufeng; Lin, Fang-yu; Structure-Based Fragment Hopping For Lead Optimization And Improvement In Synthetic Accessibility, U.S. Provisional Patent No. 61/603,501, February 27, 2012
  44. Tseng, Yufeng; Ho, Tsung-Jung; Kuo, Ching-hua; True ion pick (TIPick): a denoising and peak picking algorithm to extract ion signals from liquid chromatography/mass spectrometry data, February, 2013, Patent Pending
  45. Tseng, Yufeng; Wang Kuo-Ching, A Distribution-based Classification Method for Baseline Correction of Metabolomic 1D Proton Nuclear Magnetic Resonance Spectra, February, 2013, Patent Pending

Books

  1. 曾宇鳳（民 112 年）。電腦模擬評估苯乙胺類物質藥毒理作用之研究。衛生福利部食品藥物管理署管制藥品簡訊，95，1-3。
  2. 曾宇鳳（譯）（2022）。學界藥品開發實用指南：SPARK 方法論（原作者：Daria Mochly-Rosen）。臺北市：國立臺灣大學。
  3. 曾宇鳳（民 111 年 4 月）。以電腦模擬方式建置資料庫與評估類大麻活性物質。衛生福利部食品藥物管理署管制藥品簡訊，91，1-3。
  4. 曾宇鳳（民 110 年 4 月）。以電腦模擬方式建置資料庫與評估新興影響精神物質之應用。衛生福利部食品藥物管理署管制藥品簡訊，87，1-3。
  5. 曾宇鳳*（2019）。人工智慧藥物開發。載於許毓真（主編），醫藥產業年鑑 2019（頁 288-292）。臺北市：財團法人生物技術開發中心。
  6. YJ Tseng*, BH Su, MT Hsu, OA Lin. Steps Toward a Virtual Rat: Predictive Absorption, Distribution, Metabolism, and Toxicity Models. Frontiers in Molecular Design and Chemical Information Science - Herman Skolnik Award Symposium 2015: Jürgen Bajorath (ISBN: 9780841231412). Oct, 2016: ACS Symposium Series, Vol. 1222. Chapter 14, pp 283–329.
  7. YJ Tseng*, Essential Algorithms in Cheminformatics. In: Molecular Conceptor. Israel. 2008: 13.1-13.10.