PubRank

Minoru Kanehisa

Author PubWeight™ 248.93‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007 29.46
2 Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc 2003 15.30
3 LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 2002 13.61
4 Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc 2004 11.50
5 KEGG as a glycome informatics resource. Glycobiology 2005 11.05
6 Network-based analysis and characterization of adverse drug-drug interactions. J Chem Inf Model 2011 7.92
7 Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model 2007 7.70
8 Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004 7.17
9 Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol 2007 6.59
10 Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 2005 5.76
11 The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics 2007 5.63
12 AAindex: amino acid index database, progress report 2008. Nucleic Acids Res 2007 4.21
13 KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 2008 4.14
14 iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci 2008 4.03
15 Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J Chem Inf Model 2013 3.58
16 Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 2008 2.96
17 E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 2009 2.88
18 The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res 2007 2.65
19 iPath2.0: interactive pathway explorer. Nucleic Acids Res 2011 2.50
20 Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 2003 2.45
21 Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res 2009 2.40
22 Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model 2009 2.28
23 Towards zoomable multidimensional maps of the cell. Nat Biotechnol 2007 2.20
24 VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res 2007 2.17
25 Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics 2010 2.14
26 Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell 2003 2.11
27 Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007 2.09
28 Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2005 1.80
29 EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 2006 1.75
30 The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 2005 1.75
31 Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin Cancer Res 2005 1.64
32 ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res 2006 1.58
33 PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res 2010 1.49
34 DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2003 1.46
35 KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 2004 1.43
36 Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor sigE. J Biol Chem 2005 1.40
37 KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res 2012 1.36
38 The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol 2012 1.33
39 Extracting active pathways from gene expression data. Bioinformatics 2003 1.31
40 Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics 2005 1.28
41 Using the KEGG database resource. Curr Protoc Bioinformatics 2005 1.25
42 Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics 2006 1.23
43 Using the KEGG database resource. Curr Protoc Bioinformatics 2012 1.19
44 Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 2006 1.18
45 Domain shuffling and the evolution of vertebrates. Genome Res 2009 1.18
46 Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res 2005 1.17
47 SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res 2010 1.16
48 Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosyst 2009 1.15
49 Observing metabolic functions at the genome scale. Genome Biol 2007 1.10
50 MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 2006 1.09
51 Heuristics for chemical compound matching. Genome Inform 2003 1.09
52 Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol 2007 1.09
53 Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosynth Res 2007 1.08
54 t4 workshop report: Pathways of Toxicity. ALTEX 2013 1.06
55 Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol 2004 1.06
56 Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics 2007 1.05
57 Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics 2006 1.03
58 A two-component Mn2+-sensing system negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell 2002 1.03
59 New amino acid indices based on residue network topology. Genome Inform 2007 1.00
60 KEGG bioinformatics resource for plant genomics research. Methods Mol Biol 2007 0.98
61 Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform 2003 0.97
62 ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 2006 0.97
63 Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform 2004 0.97
64 Screening for the target gene of cyanobacterial cAMP receptor protein SYCRP1. Mol Microbiol 2002 0.97
65 Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol Biol Evol 2008 0.96
66 KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res 2010 0.96
67 Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics 2012 0.96
68 Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa. FEBS J 2007 0.96
69 A score matrix to reveal the hidden links in glycans. Bioinformatics 2004 0.96
70 A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Inform 2005 0.95
71 GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res 2012 0.95
72 Network analysis of adverse drug interactions. Genome Inform 2008 0.94
73 Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics 2007 0.94
74 EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG. Plant Physiol 2007 0.94
75 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
76 Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic 2006 0.92
77 Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform 2004 0.91
78 A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 2005 0.91
79 Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res 2002 0.90
80 Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. MBio 2012 0.89
81 Analysis of common substructures of metabolic compounds within the different organism groups. Genome Inform 2007 0.87
82 An improved scoring scheme for predicting glycan structures from gene expression data. Genome Inform 2007 0.87
83 Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics 2008 0.87
84 KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol 2013 0.86
85 Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 2004 0.86
86 Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics 2007 0.85
87 Characterization and classification of adverse drug interactions. Genome Inform 2010 0.84
88 Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes. Gene 2008 0.83
89 Predicting B cell epitope residues with network topology based amino acid indices. Genome Inform 2007 0.83
90 Extraction of species-specific glycan substructures. Genome Inform 2004 0.83
91 varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics 2008 0.83
92 Bioinformatics approaches in glycomics and drug discovery. Curr Opin Mol Ther 2006 0.82
93 Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Inform 2004 0.82
94 Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Inform 2010 0.81
95 Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics 2004 0.81
96 Analysis of a lipid biosynthesis protein family and phospholipid structural variations. Genome Inform 2010 0.80
97 PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. J Bioinform Comput Biol 2014 0.80
98 Extraction of organism groups from phylogenetic profiles using independent component analysis. Genome Inform 2002 0.79
99 MRP1 mutated in the L0 region transports SN-38 but not leukotriene C4 or estradiol-17 (beta-D-glucuronate). Biochem Pharmacol 2005 0.79
100 Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis. Proteomics 2007 0.79
101 Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J Bioinform Comput Biol 2005 0.79
102 MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. BMC Bioinformatics 2011 0.78
103 New kernel methods for phenotype prediction from genotype data. Genome Inform 2010 0.78
104 Glycomic analysis using KEGG GLYCAN. Methods Mol Biol 2015 0.78
105 Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. Genome Inform 2005 0.78
106 Comprehensive genomic analysis of sulfur-relay pathway genes. Genome Inform 2010 0.78
107 Metabolite antigens and pathway incompatibility. Genome Inform 2006 0.78
108 The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. Genome Inform 2006 0.77
109 Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics 2004 0.77
110 Comparative analysis of DNA-binding proteins between thermophilic and mesophilic bacteria. Genome Inform 2005 0.77
111 Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Inform 2007 0.77
112 Genome-wide analysis of plant UGT family based on sequence and substrate information. Genome Inform 2010 0.77
113 Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Inform 2006 0.76
114 Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Inform 2008 0.76
115 Phylogenetic analysis of lipid mediator GPCRs. Genome Inform 2010 0.75
116 [KEGG GLYCAN and glycome informatics]. Tanpakushitsu Kakusan Koso 2008 0.75
117 Characterization of alpha-phosphoglucomutase isozymes from Toxoplasma gondii. Parasitol Int 2010 0.75
118 Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis. Environ Sci Technol 2007 0.75
119 Autoimmune diseases and peptide variations. Genome Inform 2005 0.75
120 Identification of metabolic units induced by environmental signals. Bioinformatics 2006 0.75
121 varDB: a database of antigenic variant sequences--current status and future prospects. Acta Trop 2009 0.75
122 Characterizing common substructures of ligands for GPCR protein subfamilies. Genome Inform 2010 0.75
123 Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Inform 2005 0.75
124 Tools for investigating mechanisms of antigenic variation: new extensions to varDB. Genome Inform 2009 0.75
125 Population model-based inter-diplotype similarity measure for accurate diplotype clustering. J Comput Biol 2011 0.75
126 [Bioinformatics, systems biology and KEGG]. Seikagaku 2008 0.75