Published in Bioinformatics on January 19, 2007
Network enrichment analysis in complex experiments. Stat Appl Genet Mol Biol (2010) 1.44
Alignment and classification of time series gene expression in clinical studies. Bioinformatics (2008) 1.22
Reverse engineering dynamic temporal models of biological processes and their relationships. Proc Natl Acad Sci U S A (2010) 1.09
Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. BMC Syst Biol (2010) 0.82
A temporal switch model for estimating transcriptional activity in gene expression. Bioinformatics (2013) 0.79
Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models. BMC Bioinformatics (2015) 0.75
Application of dynamic topic models to toxicogenomics data. BMC Bioinformatics (2016) 0.75
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinformatics (2009) 1.33
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Brief Bioinform (2011) 1.26
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules. PLoS One (2012) 1.18
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. Bioinformatics (2005) 1.11
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics (2006) 1.09
Calpain cleavage prediction using multiple kernel learning. PLoS One (2011) 1.09
Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Brief Bioinform (2013) 1.08
PURE: a PubMed article recommendation system based on content-based filtering. Genome Inform (2007) 1.03
CaMPDB: a resource for calpain and modulatory proteolysis. Genome Inform (2010) 1.01
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics (2006) 0.97
Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform (2003) 0.97
A score matrix to reveal the hidden links in glycans. Bioinformatics (2004) 0.96
The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes. Mol Biol Evol (2004) 0.94
Annotating gene function by combining expression data with a modular gene network. Bioinformatics (2007) 0.93
Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints. IEEE Trans Cybern (2013) 0.88
Detecting Differentially Coexpressed Genes from Labeled Expression Data: A Brief Review. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.87
Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics (2008) 0.87
MetaMHC: a meta approach to predict peptides binding to MHC molecules. Nucleic Acids Res (2010) 0.86
Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides. J Immunol (2002) 0.86
Prediction of MHC class I binding peptides by a query learning algorithm based on hidden markov models. J Biol Phys (2002) 0.86
Mining metabolic pathways through gene expression. Bioinformatics (2010) 0.86
Identifying neighborhoods of coordinated gene expression and metabolite profiles. PLoS One (2012) 0.86
Understanding the substrate specificity of conventional calpains. Biol Chem (2012) 0.85
A review of statistical methods for prediction of proteolytic cleavage. Brief Bioinform (2011) 0.84
Latent feature kernels for link prediction on sparse graphs. IEEE Trans Neural Netw Learn Syst (2012) 0.84
Ensemble approaches for improving HLA class I-peptide binding prediction. J Immunol Methods (2010) 0.83
Mining significant substructure pairs for interpreting polypharmacology in drug-target network. PLoS One (2011) 0.83
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinformatics (2009) 0.83
ROS-DET: robust detector of switching mechanisms in gene expression. Nucleic Acids Res (2011) 0.82
Genome-wide integration on transcription factors, histone acetylation and gene expression reveals genes co-regulated by histone modification patterns. PLoS One (2011) 0.82
Multiple graph label propagation by sparse integration. IEEE Trans Neural Netw Learn Syst (2013) 0.81
Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics (2004) 0.81
Graph mining: procedure, application to drug discovery and recent advances. Drug Discov Today (2012) 0.81
Application of a new probabilistic model for mining implicit associated cancer genes from OMIM and medline. Cancer Inform (2007) 0.79
Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. Bioinformatics (2007) 0.79
Computational intelligence in solving bioinformatics problems. Artif Intell Med (2005) 0.78
TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence. Immunome Res (2010) 0.77
In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure-Property Relationship Models. Pharm Res (2015) 0.77
Computational recognition for long non-coding RNA (lncRNA): Software and databases. Brief Bioinform (2016) 0.77
Integrated view of the human chromosome X-centric proteome project. J Proteome Res (2012) 0.77
A markov classification model for metabolic pathways. Algorithms Mol Biol (2010) 0.76
Active pathway identification and classification with probabilistic ensembles. Genome Inform (2010) 0.76
HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. Source Code Biol Med (2009) 0.75
Current status and prospects of computational resources for natural product dereplication: a review. Brief Bioinform (2015) 0.75
A framework for determining outlying microarray experiments. Genome Inform (2008) 0.75
Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Inform (2005) 0.75
Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis. Environ Sci Technol (2007) 0.75
Generalized Sparse Learning of Linear Models Over the Complete Subgraph Feature Set. IEEE Trans Pattern Anal Mach Intell (2016) 0.75
Identifying pathways of coordinated gene expression. Methods Mol Biol (2013) 0.75
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Boosted network classifiers for local feature selection. IEEE Trans Neural Netw Learn Syst (2012) 0.75
On the performance of methods for finding a switching mechanism in gene expression. Genome Inform (2010) 0.75
Semi-supervised graph partitioning with decision trees. Genome Inform (2008) 0.75
Introduction to the special issue on GIW 2016. J Bioinform Comput Biol (2016) 0.75
Annotating gene functions with integrative spectral clustering on microarray expressions and sequences. Genome Inform (2010) 0.75
An in silico model for interpreting polypharmacology in drug-target networks. Methods Mol Biol (2013) 0.75
Discriminative graph embedding for label propagation. IEEE Trans Neural Netw (2011) 0.75