Published in BMC Bioinformatics on January 18, 2010
Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol (2011) 1.08
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS One (2011) 0.96
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc (2004) 11.50
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res (2003) 1.48
Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model (2005) 1.35
Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa. FEBS J (2007) 0.96
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc (2004) 11.50
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model (2007) 7.70
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units. Eur J Hum Genet (2010) 1.62
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Proportion of de novo cancers among colorectal cancers in Japan. Gastroenterology (2006) 1.43
Selective integration of multiple biological data for supervised network inference. Bioinformatics (2005) 1.28
Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics (2006) 1.16
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models. BMC Syst Biol (2007) 1.15
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics (2006) 1.12
A gram distribution kernel applied to glycan classification and motif extraction. Genome Inform (2006) 1.09
The DICS repository: module-assisted analysis of disease-related gene lists. Bioinformatics (2009) 1.00
Enumeration of condition-dependent dense modules in protein interaction networks. Bioinformatics (2009) 0.98
Proportion of flat- and depressed-type and laterally spreading tumor among advanced colorectal neoplasia. Clin Gastroenterol Hepatol (2011) 0.95
Modeling splicing sites with pairwise correlations. Bioinformatics (2002) 0.92
Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic (2006) 0.92
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach. Bioinformatics (2009) 0.91
PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res (2011) 0.91
Mining complex genotypic features for predicting HIV-1 drug resistance. Bioinformatics (2007) 0.91
Marginalized kernels for RNA sequence data analysis. Genome Inform (2002) 0.89
Statistical significance of combinatorial regulations. Proc Natl Acad Sci U S A (2013) 0.88
PDB-scale analysis of known and putative ligand-binding sites with structural sketches. Proteins (2011) 0.88
SlideSort: all pairs similarity search for short reads. Bioinformatics (2010) 0.88
Analysis of common substructures of metabolic compounds within the different organism groups. Genome Inform (2007) 0.87
Efficient filtering methods for clustering cDNAs with spliced sequence alignment. Bioinformatics (2004) 0.86
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC Bioinformatics (2010) 0.85
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinformatics (2009) 0.83
Mining significant substructure pairs for interpreting polypharmacology in drug-target network. PLoS One (2011) 0.83
ROS-DET: robust detector of switching mechanisms in gene expression. Nucleic Acids Res (2011) 0.82
Prediction of protein-ligand binding affinities using multiple instance learning. J Mol Graph Model (2010) 0.80
Comprehensive genomic analysis of sulfur-relay pathway genes. Genome Inform (2010) 0.78
Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Inform (2008) 0.76
Discovering combinatorial interactions in survival data. Bioinformatics (2013) 0.76
Draft Genome Sequence of Lactobacillus sucicola JCM 15457T, a Motile Lactic Acid Bacterium Isolated from Oak Sap. Genome Announc (2014) 0.75
Health checkup and telemedical intervention program for preventive medicine in developing countries: verification study. J Med Internet Res (2015) 0.75
A therapeutic DNA vaccination strategy for autoimmunity and transplantation. Vaccine (2010) 0.75
Privacy-preserving search for chemical compound databases. BMC Bioinformatics (2015) 0.75
Study of prolonged administration of lanthanum carbonate in dialysis patients. Ther Apher Dial (2013) 0.75
[Clinicopathological features of colorectal villous tumors]. Nihon Rinsho (2003) 0.75
An in silico model for interpreting polypharmacology in drug-target networks. Methods Mol Biol (2013) 0.75
Characterizing common substructures of ligands for GPCR protein subfamilies. Genome Inform (2010) 0.75
On the performance of methods for finding a switching mechanism in gene expression. Genome Inform (2010) 0.75
Cadaveric domino liver transplantation: the first case in Japan. J Hepatobiliary Pancreat Surg (2004) 0.75