Wen-Lian Hsu

HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach.

HYPROSP II--a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.

GANA--a genetic algorithm for NMR backbone resonance assignment.

A new similarity measure among protein sequences.

Various criteria in the evaluation of biomedical named entity recognition.

Multi-Q: a fully automated tool for multiplexed protein quantitation.

HYPLOSP: a knowledge-based approach to protein local structure prediction.

NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition.

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).

Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function.

Protein subcellular localization prediction based on compartment-specific biological features.

The Multi-Q web server for multiplexed protein quantitation.

BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features.

Protein subcellular localization prediction based on compartment-specific features and structure conservation.

Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function.

PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis.

Bioinformatics research in the Asia Pacific: a 2007 update.

Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles.

BIOSMILE web search: a web application for annotating biomedical entities and relations.

Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.

Emerging strengths in Asia Pacific bioinformatics.

Semi-automatic conversion of BioProp semantic annotation to PASBio annotation.

Predicting RNA-binding sites of proteins using support vector machines and evolutionary information.

Triplet supertree heuristics for the tree of life.

A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data.

Predicting helix-helix interactions from residue contacts in membrane proteins.

MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Protein subcellular localization prediction of eukaryotes using a knowledge-based approach.

HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features.

Automated generic analysis tools for protein quantitation using stable isotope labeling.

An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion.

Improving protein secondary structure prediction based on short subsequences with local structure similarity.

TMPad: an integrated structural database for helix-packing folds in transmembrane proteins.

Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas.

Comparative proteomic analysis of proteins involved in the tumorigenic process of seminal vesicle carcinoma in transgenic mice.

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature.

Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.

Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures.

Coreference resolution of medical concepts in discharge summaries by exploiting contextual information.

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.

Label-free quantitative proteomics of CD133-positive liver cancer stem cells.

Decoding the disease-associated proteins encoded in the human chromosome 4.

Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing.

T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes.

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension.

TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries.

Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.

Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations.

Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information.

MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS² approach.

A context-aware approach for progression tracking of medical concepts in electronic medical records.

Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics.

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.

iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination.

MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.

MET network in PubMed: a text-mined network visualization and curation system.

PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Kart: a divide-and-conquer algorithm for NGS read alignment.

DART - a fast and accurate RNA-seq mapper with a partitioning strategy.

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm.

LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task.

Hierarchical and programmable one-pot synthesis of oligosaccharides.

Statistical principle-based approach for gene and protein related object recognition.

Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline.

Medical knowledge infused convolutional neural networks for cohort selection in clinical trials.