Wen-Lian Hsu Institute of Information Science Academia Sinica Biography Publications Institution JoVE Articles Wen-Lian Hsu has not added a biography. If you are Wen-Lian Hsu and would like to personalize this page please email our Author Liaison for assistance. Publications Medical Knowledge Infused Convolutional Neural Networks for Cohort Selection in Clinical Trials Journal of the American Medical Informatics Association : JAMIA. Aug, 2019 | Pubmed ID: 31390470 WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline Analytical Chemistry. Aug, 2019 | Pubmed ID: 31305071 Statistical Principle-based Approach for Recognizing and Normalizing MicroRNAs Described in Scientific Literature Database : the Journal of Biological Databases and Curation. 01, 2019 | Pubmed ID: 30809637 Statistical Principle-based Approach for Gene and Protein Related Object Recognition Journal of Cheminformatics. Dec, 2018 | Pubmed ID: 30560325 Hierarchical and Programmable One-pot Synthesis of Oligosaccharides Nature Communications. 12, 2018 | Pubmed ID: 30523255 LPTK: a Linguistic Pattern-aware Dependency Tree Kernel Approach for the BioCreative VI CHEMPROT Task Database : the Journal of Biological Databases and Curation. 01, 2018 | Pubmed ID: 30346607 MiRTarBase Update 2018: a Resource for Experimentally Validated MicroRNA-target Interactions Nucleic Acids Research. Jan, 2018 | Pubmed ID: 29126174 ITop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm Analytical Chemistry. 12, 2017 | Pubmed ID: 29165996 DART - a Fast and Accurate RNA-seq Mapper with a Partitioning Strategy Bioinformatics (Oxford, England). 09, 2017 | Pubmed ID: 28968831 Kart: a Divide-and-conquer Algorithm for NGS Read Alignment Bioinformatics (Oxford, England). Aug, 2017 | Pubmed ID: 28379292 An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement in Accuracy Genome Biology. 09, 2016 | Pubmed ID: 27604469 BioCreative V BioC Track Overview: Collaborative Biocurator Assistant Task for BioGRID Database : the Journal of Biological Databases and Curation. 2016 | Pubmed ID: 27589962 PIPE: a Protein-protein Interaction Passage Extraction Module for BioCreative Challenge Database : the Journal of Biological Databases and Curation. 2016 | Pubmed ID: 27524807 MET Network in PubMed: a Text-mined Network Visualization and Curation System Database : the Journal of Biological Databases and Curation. 2016 | Pubmed ID: 27242035 MAGIC-web: a Platform for Untargeted and Targeted N-linked Glycoprotein Identification Nucleic Acids Research. Jul, 2016 | Pubmed ID: 27084943 IMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination PloS One. 2016 | Pubmed ID: 26784691 MiRTarBase 2016: Updates to the Experimentally Validated MiRNA-target Interactions Database Nucleic Acids Research. Jan, 2016 | Pubmed ID: 26590260 Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics Journal of Proteome Research. Dec, 2015 | Pubmed ID: 26549055 A Context-aware Approach for Progression Tracking of Medical Concepts in Electronic Medical Records Journal of Biomedical Informatics. Dec, 2015 | Pubmed ID: 26432355 MAGIC: an Automated N-linked Glycoprotein Identification Tool Using a Y1-ion Pattern Matching Algorithm and in Silico MS² Approach Analytical Chemistry. Feb, 2015 | Pubmed ID: 25629585 Metabolite Identification for Mass Spectrometry-based Metabolomics Using Multiple Types of Correlated Ion Information Analytical Chemistry. Feb, 2015 | Pubmed ID: 25543920 LiverCancerMarkerRIF: a Liver Cancer Biomarker Interactive Curation System Combining Text Mining and Expert Annotations Database : the Journal of Biological Databases and Curation. 2014 | Pubmed ID: 25168057 CloudDOE: a User-friendly Tool for Deploying Hadoop Clouds and Analyzing High-throughput Sequencing Data with MapReduce PloS One. 2014 | Pubmed ID: 24897343 Efficient and Interpretable Prediction of Protein Functional Classes by Correspondence Analysis and Compact Set Relations PloS One. 2013 | Pubmed ID: 24146760 Lipid Exposure Prediction Enhances the Inference of Rotational Angles of Transmembrane Helices BMC Bioinformatics. Oct, 2013 | Pubmed ID: 24112406 TEMPTING System: a Hybrid Method of Rule and Machine Learning for Temporal Relation Extraction in Patient Discharge Summaries Journal of Biomedical Informatics. Dec, 2013 | Pubmed ID: 24060600 Construction of Gene Clusters Resembling Genetic Causal Mechanisms for Common Complex Disease with an Application to Young-onset Hypertension BMC Genomics. Jul, 2013 | Pubmed ID: 23879630 Spectrum-based Method to Generate Good Decoy Libraries for Spectral Library Searching in Peptide Identifications Journal of Proteome Research. May, 2013 | Pubmed ID: 23560440 T-HOD: a Literature-based Candidate Gene Database for Hypertension, Obesity and Diabetes Database : the Journal of Biological Databases and Curation. 2013 | Pubmed ID: 23406793 Decoding the Disease-associated Proteins Encoded in the Human Chromosome 4 Journal of Proteome Research. Jan, 2013 | Pubmed ID: 23256888 Prediction of Nuclear Proteins Using Nuclear Translocation Signals Proposed by Probabilistic Latent Semantic Indexing BMC Bioinformatics. 2012 | Pubmed ID: 23282098 Label-free Quantitative Proteomics of CD133-positive Liver Cancer Stem Cells Proteome Science. Nov, 2012 | Pubmed ID: 23170877 Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-dimensional Probability Density Distributions of Interacting Atoms PloS One. 2012 | Pubmed ID: 22848404 Protein-protein Interaction Site Predictions with Three-dimensional Probability Distributions of Interacting Atoms on Protein Surfaces PloS One. 2012 | Pubmed ID: 22701576 Coreference Resolution of Medical Concepts in Discharge Summaries by Exploiting Contextual Information Journal of the American Medical Informatics Association : JAMIA. Sep-Oct, 2012 | Pubmed ID: 22556185 Computational Comparative Study of Tuberculosis Proteomes Using a Model Learned from Signal Peptide Structures PloS One. 2012 | Pubmed ID: 22496884 Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-antigen Recognition Interface PloS One. 2012 | Pubmed ID: 22457753 MeInfoText 2.0: Gene Methylation and Cancer Relation Extraction from Biomedical Literature BMC Bioinformatics. Dec, 2011 | Pubmed ID: 22168213 Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words PloS One. 2011 | Pubmed ID: 22163274 Phosphoproteomics Identifies Oncogenic Ras Signaling Targets and Their Involvement in Lung Adenocarcinomas PloS One. 2011 | Pubmed ID: 21637843 TMPad: an Integrated Structural Database for Helix-packing Folds in Transmembrane Proteins Nucleic Acids Research. Jan, 2011 | Pubmed ID: 21177659 Comparative Proteomic Analysis of Proteins Involved in the Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice International Journal of Proteomics. 2010 | Pubmed ID: 22084680 Improving Protein Secondary Structure Prediction Based on Short Subsequences with Local Structure Similarity BMC Genomics. Dec, 2010 | Pubmed ID: 21143813 An Informatics-assisted Label-free Quantitation Strategy That Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion Journal of Proteome Research. Nov, 2010 | Pubmed ID: 20815410 Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling Methods in Molecular Biology (Clifton, N.J.). 2010 | Pubmed ID: 20013376 IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation Molecular & Cellular Proteomics : MCP. Jan, 2010 | Pubmed ID: 19752006 HypertenGene: Extracting Key Hypertension Genes from Biomedical Literature with Position and Automatically-generated Template Features BMC Bioinformatics. Dec, 2009 | Pubmed ID: 19958519 Protein Subcellular Localization Prediction of Eukaryotes Using a Knowledge-based Approach BMC Bioinformatics. Dec, 2009 | Pubmed ID: 19958518 MaXIC-Q Web: a Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS Nucleic Acids Research. Jul, 2009 | Pubmed ID: 19528069 Predicting Helix-helix Interactions from Residue Contacts in Membrane Proteins Bioinformatics (Oxford, England). Apr, 2009 | Pubmed ID: 19244388 A Neural Network Model for Constructing Endophenotypes of Common Complex Diseases: an Application to Male Young-onset Hypertension Microarray Data Bioinformatics (Oxford, England). Apr, 2009 | Pubmed ID: 19237446 Triplet Supertree Heuristics for the Tree of Life BMC Bioinformatics. Jan, 2009 | Pubmed ID: 19208181 Predicting RNA-binding Sites of Proteins Using Support Vector Machines and Evolutionary Information BMC Bioinformatics. Dec, 2008 | Pubmed ID: 19091029 Semi-automatic Conversion of BioProp Semantic Annotation to PASBio Annotation BMC Bioinformatics. Dec, 2008 | Pubmed ID: 19091017 Emerging Strengths in Asia Pacific Bioinformatics BMC Bioinformatics. Dec, 2008 | Pubmed ID: 19091008 Protease Substrate Site Predictors Derived from Machine Learning on Multilevel Substrate Phage Display Data Bioinformatics (Oxford, England). Dec, 2008 | Pubmed ID: 18974075 BIOSMILE Web Search: a Web Application for Annotating Biomedical Entities and Relations Nucleic Acids Research. Jul, 2008 | Pubmed ID: 18515840 Exploiting Likely-positive and Unlabeled Data to Improve the Identification of Protein-protein Interaction Articles BMC Bioinformatics. 2008 | Pubmed ID: 18315856 Bioinformatics Research in the Asia Pacific: a 2007 Update BMC Bioinformatics. 2008 | Pubmed ID: 18315840 PSLDoc: Protein Subcellular Localization Prediction Based on Gapped-dipeptides and Probabilistic Latent Semantic Analysis Proteins. Aug, 2008 | Pubmed ID: 18260102 Enhanced Membrane Protein Topology Prediction Using a Hierarchical Classification Method and a New Scoring Function Journal of Proteome Research. Feb, 2008 | Pubmed ID: 18081245 Protein Subcellular Localization Prediction Based on Compartment-specific Features and Structure Conservation BMC Bioinformatics. Sep, 2007 | Pubmed ID: 17825110 BIOSMILE: a Semantic Role Labeling System for Biomedical Verbs Using a Maximum-entropy Model with Automatically Generated Template Features BMC Bioinformatics. Sep, 2007 | Pubmed ID: 17764570 The Multi-Q Web Server for Multiplexed Protein Quantitation Nucleic Acids Research. Jul, 2007 | Pubmed ID: 17553828 Detection of the Inferred Interaction Network in Hepatocellular Carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma Genes Online) BMC Bioinformatics. Feb, 2007 | Pubmed ID: 17326819 Protein Subcellular Localization Prediction Based on Compartment-specific Biological Features Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 2006 | Pubmed ID: 17369650 Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 2006 | Pubmed ID: 17369623 NERBio: Using Selected Word Conjunctions, Term Normalization, and Global Patterns to Improve Biomedical Named Entity Recognition BMC Bioinformatics. Dec, 2006 | Pubmed ID: 17254295 HYPLOSP: a Knowledge-based Approach to Protein Local Structure Prediction Journal of Bioinformatics and Computational Biology. Dec, 2006 | Pubmed ID: 17245815 Multi-Q: a Fully Automated Tool for Multiplexed Protein Quantitation Journal of Proteome Research. Sep, 2006 | Pubmed ID: 16944945 Various Criteria in the Evaluation of Biomedical Named Entity Recognition BMC Bioinformatics. Feb, 2006 | Pubmed ID: 16504116 GANA--a Genetic Algorithm for NMR Backbone Resonance Assignment Nucleic Acids Research. 2005 | Pubmed ID: 16093550 HYPROSP II--a Knowledge-based Hybrid Method for Protein Secondary Structure Prediction Based on Local Prediction Confidence Bioinformatics (Oxford, England). Aug, 2005 | Pubmed ID: 15932901 HYPROSP: a Hybrid Protein Secondary Structure Prediction Algorithm--a Knowledge-based Approach Nucleic Acids Research. 2004 | Pubmed ID: 15448186 A New Similarity Measure Among Protein Sequences Proceedings. IEEE Computer Society Bioinformatics Conference. 2003 | Pubmed ID: 16452810 Hierarkisk og programmerbar One-Pot Oligosaccharide syntese Cheng-Wei Cheng1, Yixuan Zhou1, Wen-Harn Pan2, Supriya Dey3, Chung-Yi Wu1, Wen-Lian Hsu4, Chi-Huey Wong1,3 1Genomics Research Center, Academia Sinica, 2Institute of Biomedical Sciences, Academia Sinica, 3Department of Chemistry, Scripps Research Institute, 4Institute of Information Science, Academia Sinica JoVE 59987 Química
Hierarkisk og programmerbar One-Pot Oligosaccharide syntese Cheng-Wei Cheng1, Yixuan Zhou1, Wen-Harn Pan2, Supriya Dey3, Chung-Yi Wu1, Wen-Lian Hsu4, Chi-Huey Wong1,3 1Genomics Research Center, Academia Sinica, 2Institute of Biomedical Sciences, Academia Sinica, 3Department of Chemistry, Scripps Research Institute, 4Institute of Information Science, Academia Sinica JoVE 59987 Química