Wen-Lian Hsu

Institute of Information Science, Academia Sinica

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2019

Other Publications

Article	Year
HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach. Nucleic acids research\| PubMed ID: 15448186	2004
HYPROSP II--a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. Bioinformatics (Oxford, England)\| PubMed ID: 15932901	2005
GANA--a genetic algorithm for NMR backbone resonance assignment. Nucleic acids research\| PubMed ID: 16093550	2005
A new similarity measure among protein sequences. Proceedings. IEEE Computer Society Bioinformatics Conference\| PubMed ID: 16452810	2003
Various criteria in the evaluation of biomedical named entity recognition. BMC bioinformatics\| PubMed ID: 16504116	2006
Multi-Q: a fully automated tool for multiplexed protein quantitation. Journal of proteome research\| PubMed ID: 16944945	2006
HYPLOSP: a knowledge-based approach to protein local structure prediction. Journal of bioinformatics and computational biology\| PubMed ID: 17245815	2006
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition. BMC bioinformatics\| PubMed ID: 17254295	2006
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC bioinformatics\| PubMed ID: 17326819	2007
Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function. Computational systems bioinformatics. Computational Systems Bioinformatics Conference\| PubMed ID: 17369623	2006
Protein subcellular localization prediction based on compartment-specific biological features. Computational systems bioinformatics. Computational Systems Bioinformatics Conference\| PubMed ID: 17369650	2006
The Multi-Q web server for multiplexed protein quantitation. Nucleic acids research\| PubMed ID: 17553828	2007
BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features. BMC bioinformatics\| PubMed ID: 17764570	2007
Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC bioinformatics\| PubMed ID: 17825110	2007
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. Journal of proteome research\| PubMed ID: 18081245	2008
PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis. Proteins\| PubMed ID: 18260102	2008
Bioinformatics research in the Asia Pacific: a 2007 update. BMC bioinformatics\| PubMed ID: 18315840	2008
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. BMC bioinformatics\| PubMed ID: 18315856	2008
BIOSMILE web search: a web application for annotating biomedical entities and relations. Nucleic acids research\| PubMed ID: 18515840	2008
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. Bioinformatics (Oxford, England)\| PubMed ID: 18974075	2008
Emerging strengths in Asia Pacific bioinformatics. BMC bioinformatics\| PubMed ID: 19091008	2008
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation. BMC bioinformatics\| PubMed ID: 19091017	2008
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC bioinformatics\| PubMed ID: 19091029	2008
Triplet supertree heuristics for the tree of life. BMC bioinformatics\| PubMed ID: 19208181	2009
A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data. Bioinformatics (Oxford, England)\| PubMed ID: 19237446	2009
Predicting helix-helix interactions from residue contacts in membrane proteins. Bioinformatics (Oxford, England)\| PubMed ID: 19244388	2009
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\| PubMed ID: 19528069	2009
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Molecular & cellular proteomics : MCP\| PubMed ID: 19752006	2010
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC bioinformatics\| PubMed ID: 19958518	2009
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features. BMC bioinformatics\| PubMed ID: 19958519	2009
Automated generic analysis tools for protein quantitation using stable isotope labeling. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20013376	2010
An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion. Journal of proteome research\| PubMed ID: 20815410	2010
Improving protein secondary structure prediction based on short subsequences with local structure similarity. BMC genomics\| PubMed ID: 21143813	2010
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. Nucleic acids research\| PubMed ID: 21177659	2011
Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas. PloS one\| PubMed ID: 21637843	2011
Comparative proteomic analysis of proteins involved in the tumorigenic process of seminal vesicle carcinoma in transgenic mice. International journal of proteomics\| PubMed ID: 22084680	2010
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words. PloS one\| PubMed ID: 22163274	2011
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. BMC bioinformatics\| PubMed ID: 22168213	2011
Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PloS one\| PubMed ID: 22457753	2012
Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures. PloS one\| PubMed ID: 22496884	2012
Coreference resolution of medical concepts in discharge summaries by exploiting contextual information. Journal of the American Medical Informatics Association : JAMIA\| PubMed ID: 22556185	2012
Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PloS one\| PubMed ID: 22701576	2012
Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms. PloS one\| PubMed ID: 22848404	2012
Label-free quantitative proteomics of CD133-positive liver cancer stem cells. Proteome science\| PubMed ID: 23170877	2012
Decoding the disease-associated proteins encoded in the human chromosome 4. Journal of proteome research\| PubMed ID: 23256888	2013
Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing. BMC bioinformatics\| PubMed ID: 23282098	2012
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes. Database : the journal of biological databases and curation\| PubMed ID: 23406793	2013
Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications. Journal of proteome research\| PubMed ID: 23560440	2013
Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension. BMC genomics\| PubMed ID: 23879630	2013
TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries. Journal of biomedical informatics\| PubMed ID: 24060600	2013
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices. BMC bioinformatics\| PubMed ID: 24112406	2013
Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations. PloS one\| PubMed ID: 24146760	2013
CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce. PloS one\| PubMed ID: 24897343	2014
LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations. Database : the journal of biological databases and curation\| PubMed ID: 25168057	2014
Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information. Analytical chemistry\| PubMed ID: 25543920	2015
MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS² approach. Analytical chemistry\| PubMed ID: 25629585	2015
A context-aware approach for progression tracking of medical concepts in electronic medical records. Journal of biomedical informatics\| PubMed ID: 26432355	2015
Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics. Journal of proteome research\| PubMed ID: 26549055	2015
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic acids research\| PubMed ID: 26590260	2016
iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination. PloS one\| PubMed ID: 26784691	2016
MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification. Nucleic acids research\| PubMed ID: 27084943	2016
MET network in PubMed: a text-mined network visualization and curation system. Database : the journal of biological databases and curation\| PubMed ID: 27242035	2016
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge. Database : the journal of biological databases and curation\| PubMed ID: 27524807	2016
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database : the journal of biological databases and curation\| PubMed ID: 27589962	2016
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology\| PubMed ID: 27604469	2016
Kart: a divide-and-conquer algorithm for NGS read alignment. Bioinformatics (Oxford, England)\| PubMed ID: 28379292	2017
DART - a fast and accurate RNA-seq mapper with a partitioning strategy. Bioinformatics (Oxford, England)\| PubMed ID: 28968831	2017
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic acids research\| PubMed ID: 29126174	2018
iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Analytical chemistry\| PubMed ID: 29165996	2017
LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task. Database : the journal of biological databases and curation\| PubMed ID: 30346607	2018
Hierarchical and programmable one-pot synthesis of oligosaccharides. Nature communications\| PubMed ID: 30523255	2018
Statistical principle-based approach for gene and protein related object recognition. Journal of cheminformatics\| PubMed ID: 30560325	2018
Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature. Database : the journal of biological databases and curation\| PubMed ID: 30809637	2019
WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline. Analytical chemistry\| PubMed ID: 31305071	2019
Medical knowledge infused convolutional neural networks for cohort selection in clinical trials. Journal of the American Medical Informatics Association : JAMIA\| PubMed ID: 31390470	2019