Wen-Lian Hsu

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