Published in Nucleic Acids Res on September 07, 2004
Functional organization of the transcriptome in human brain. Nat Neurosci (2008) 7.02
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics (2006) 1.65
A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59
Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res (2006) 1.12
Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinform (2011) 1.07
Genomes, phylogeny, and evolutionary systems biology. Proc Natl Acad Sci U S A (2005) 1.07
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics (2006) 1.02
Analysis of gene expression in operons of Streptomyces coelicolor. Genome Biol (2006) 0.98
Modularity of stress response evolution. Proc Natl Acad Sci U S A (2008) 0.97
Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells. PLoS Comput Biol (2010) 0.96
COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. Nucleic Acids Res (2010) 0.91
Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol (2007) 0.87
A new systematic computational approach to predicting target genes of transcription factors. Nucleic Acids Res (2007) 0.85
Promoter-sharing by different genes in human genome--CPNE1 and RBM12 gene pair as an example. BMC Genomics (2008) 0.84
Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms. PLoS One (2008) 0.83
The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. Nucleic Acids Res (2012) 0.80
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions. Genome Biol (2007) 0.78
Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5' regulatory regions that are potentially involved in nucleosome formation. BMC Genomics (2008) 0.77
Sequential metabolic phases as a means to optimize cellular output in a constant environment. PLoS One (2015) 0.76
Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses. Sci Rep (2016) 0.76
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
Functional discovery via a compendium of expression profiles. Cell (2000) 31.39
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
A gene-coexpression network for global discovery of conserved genetic modules. Science (2003) 18.75
The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A (1999) 16.35
A gene expression map for Caenorhabditis elegans. Science (2001) 9.74
Transcription regulation and animal diversity. Nature (2003) 9.22
The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol (2003) 7.72
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Measuring genome evolution. Proc Natl Acad Sci U S A (1998) 6.97
SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics (1999) 6.79
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2004) 6.72
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res (2001) 6.31
Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat Genet (2004) 4.77
Similarities and differences in genome-wide expression data of six organisms. PLoS Biol (2003) 4.75
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol (2001) 3.86
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res (2003) 3.29
Use of contiguity on the chromosome to predict functional coupling. In Silico Biol (1999) 3.25
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A (2003) 3.14
Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc Biol Sci (1999) 3.04
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 2.68
Predicting gene function by conserved co-expression. Trends Genet (2003) 2.56
Gene order is not conserved in bacterial evolution. Trends Genet (1996) 2.44
Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol (1997) 2.39
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol (1997) 2.29
Genetics and the making of Homo sapiens. Nature (2003) 2.20
Universality and flexibility in gene expression from bacteria to human. Proc Natl Acad Sci U S A (2004) 2.03
Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res (2000) 1.88
Reconstruction of the proto-mitochondrial metabolism. Science (2003) 1.83
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc Natl Acad Sci U S A (2000) 1.77
Quantifying modularity in the evolution of biomolecular systems. Genome Res (2004) 1.67
Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol (2002) 1.55
Protein families in multicellular organisms. Curr Opin Struct Biol (1999) 1.53
Adaptive evolution after gene duplication. Trends Genet (2002) 1.02
Optimized design and assessment of whole genome tiling arrays. Bioinformatics (2007) 11.38
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
Repeatability of published microarray gene expression analyses. Nat Genet (2008) 8.24
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Benchmarking ortholog identification methods using functional genomics data. Genome Biol (2006) 3.54
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
SHOT: a web server for the construction of genome phylogenies. Trends Genet (2002) 2.79
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep (2004) 2.75
The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci U S A (2002) 2.59
Predicting gene function by conserved co-expression. Trends Genet (2003) 2.56
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell (2011) 2.46
Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics (2007) 2.29
Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). J Mol Biol (2005) 2.16
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. PLoS Genet (2010) 2.14
Genome trees and the nature of genome evolution. Annu Rev Microbiol (2005) 2.12
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity. PLoS Pathog (2008) 1.98
Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol (2012) 1.86
Phenome connections. Trends Genet (2008) 1.84
Reconstruction of the proto-mitochondrial metabolism. Science (2003) 1.83
Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res (2007) 1.79
A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. EMBO J (2010) 1.74
Quantifying modularity in the evolution of biomolecular systems. Genome Res (2004) 1.67
Drug-induced regulation of target expression. PLoS Comput Biol (2010) 1.65
An anaerobic mitochondrion that produces hydrogen. Nature (2005) 1.64
Origin and evolution of the peroxisomal proteome. Biol Direct (2006) 1.55
Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol (2011) 1.51
The iron-sulphur protein Ind1 is required for effective complex I assembly. EMBO J (2008) 1.42
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics (2009) 1.42
Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease. Am J Hum Genet (2009) 1.39
Shaping the mitochondrial proteome. Biochim Biophys Acta (2004) 1.38
TEFM (c17orf42) is necessary for transcription of human mtDNA. Nucleic Acids Res (2011) 1.38
The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium. Cilia (2013) 1.31
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. J Bacteriol (2004) 1.30
Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol (2013) 1.30
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol (2004) 1.29
Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics (2006) 1.27
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol (2013) 1.22
Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing. PLoS One (2012) 1.22
Combinatorial gene regulation in Plasmodium falciparum. Trends Genet (2005) 1.22
TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance. Trends Biochem Sci (2003) 1.21
Evolutionary diversity of vertebrate small heat shock proteins. J Mol Evol (2004) 1.20
Network neighbors of drug targets contribute to drug side-effect similarity. PLoS One (2011) 1.17
The alpha-kinase family: an exceptional branch on the protein kinase tree. Cell Mol Life Sci (2009) 1.16
Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics (2008) 1.15
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform (2011) 1.15
Signature genes as a phylogenomic tool. Mol Biol Evol (2008) 1.13
From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. PLoS Comput Biol (2007) 1.13
Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci U S A (2013) 1.11
Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays. J Biol Chem (2007) 1.10
The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. Mol Biol Evol (2011) 1.09
Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Curr Opin Biotechnol (2011) 1.07
The biological coherence of human phenome databases. Am J Hum Genet (2009) 1.07
Comparative genomics of the Rab protein family in Apicomplexan parasites. Microbes Infect (2008) 1.06
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet (2009) 1.03
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. Genome Biol (2012) 1.03
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics (2006) 1.02
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics (2005) 1.01
C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation. Nucleic Acids Res (2012) 1.01
Conservation of divergent transcription in fungi. Trends Genet (2008) 0.99
Molecular characterization of phosphoglycerate mutase in archaea. FEMS Microbiol Lett (2002) 0.99
Mosaic origin of the mitochondrial proteome. Proteomics (2010) 0.98
Human monogenic disease genes have frequently functionally redundant paralogs. PLoS Comput Biol (2013) 0.97
Comparative genomics for reliable protein-function prediction from genomic data. Trends Genet (2004) 0.96
A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy. Am J Hum Genet (2011) 0.95
Complex fate of paralogs. BMC Evol Biol (2008) 0.95
Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PLoS One (2012) 0.95
Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Res (2008) 0.95
Asymmetric relationships between proteins shape genome evolution. Genome Biol (2009) 0.94
Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Immunogenetics (2003) 0.93
The properties of protein family space depend on experimental design. Bioinformatics (2005) 0.91
A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy. Brain (2013) 0.91
The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. BMC Genomics (2009) 0.90
Inferring metabolic states in uncharacterized environments using gene-expression measurements. PLoS Comput Biol (2013) 0.89
Human intellectual disability genes form conserved functional modules in Drosophila. PLoS Genet (2013) 0.89
Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level. J Proteome Res (2010) 0.89
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. BMC Genomics (2007) 0.89
A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia. Hum Mol Genet (2012) 0.88
NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I. FEBS Lett (2011) 0.87
FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (2011) 0.87
Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics (2008) 0.87
Evolution of closely linked gene pairs in vertebrate genomes. Mol Biol Evol (2008) 0.86
Measuring the physical cohesiveness of proteins using physical interaction enrichment. Bioinformatics (2010) 0.85
BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion. Antioxid Redox Signal (2012) 0.85
Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology. Mitochondrion (2011) 0.85
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. BMC Genomics (2011) 0.84
Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity. Pflugers Arch (2008) 0.84
The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin. BMC Evol Biol (2007) 0.83
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication. Genome Biol (2009) 0.83
Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells. Mol Immunol (2011) 0.83
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. Nat Commun (2013) 0.82
CEP89 is required for mitochondrial metabolism and neuronal function in man and fly. Hum Mol Genet (2013) 0.82
Spike-in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload. Proteomics (2014) 0.81