Published in Genome Res on July 01, 2003
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
The energetics of genome complexity. Nature (2010) 4.58
Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev (2007) 4.13
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Evolutionary origins of genomic repertoires in bacteria. PLoS Biol (2005) 3.43
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol (2007) 3.10
Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet (2009) 3.03
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet (2011) 2.54
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53
Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A (2005) 2.37
Rapid evolutionary innovation during an Archaean genetic expansion. Nature (2010) 2.34
The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31
Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res (2004) 2.14
Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol (2005) 2.10
Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics (2006) 2.01
The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comput Biol (2006) 1.98
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A (2007) 1.96
Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci U S A (2009) 1.95
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res (2006) 1.66
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct (2012) 1.66
Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol (2007) 1.58
Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biol (2006) 1.55
Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res (2006) 1.48
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol (2008) 1.40
Energetics and genetics across the prokaryote-eukaryote divide. Biol Direct (2011) 1.36
Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Comput Biol (2007) 1.33
Comparative genomics of gene-family size in closely related bacteria. Genome Biol (2004) 1.31
Bacterial genome instability. Microbiol Mol Biol Rev (2014) 1.31
Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci (2009) 1.29
On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci (2009) 1.29
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24
Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci U S A (2005) 1.22
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol (2014) 1.21
Preferential attachment in the evolution of metabolic networks. BMC Genomics (2005) 1.20
The role of laterally transferred genes in adaptive evolution. BMC Evol Biol (2007) 1.18
Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol Evol (2009) 1.16
Essential bacterial functions encoded by gene pairs. J Bacteriol (2006) 1.12
Evolution of divergent life history strategies in marine alphaproteobacteria. MBio (2013) 1.04
ε/ζ systems: their role in resistance, virulence, and their potential for antibiotic development. J Mol Med (Berl) (2011) 1.04
Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics (2010) 1.01
Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol (2005) 1.01
Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome. Proc Natl Acad Sci U S A (2007) 0.99
Uncovering rate variation of lateral gene transfer during bacterial genome evolution. BMC Genomics (2008) 0.96
Gene frequency distributions reject a neutral model of genome evolution. Genome Biol Evol (2013) 0.94
Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species. Infect Genet Evol (2012) 0.94
Ancestral genes can control the ability of horizontally acquired loci to confer new traits. PLoS Genet (2011) 0.92
Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions. F1000Res (2016) 0.90
Automatic selection of representative proteins for bacterial phylogeny. BMC Evol Biol (2005) 0.89
Modelling prokaryote gene content. Evol Bioinform Online (2007) 0.88
Does gene translocation accelerate the evolution of laterally transferred genes? Genetics (2009) 0.86
Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. Mol Biol Evol (2013) 0.85
Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biol (2007) 0.85
Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) encoding a putative manganese-oxidizing enzyme in Bacillus species. Appl Environ Microbiol (2008) 0.83
Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Res (2008) 0.83
Phylogenetic signal and functional categories in Proteobacteria genomes. BMC Evol Biol (2007) 0.82
Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One (2013) 0.80
Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition. Genomics Proteomics Bioinformatics (2012) 0.80
Inferring bacterial genome flux while considering truncated genes. Genetics (2010) 0.80
Genetic studies on the virus-like regions in the genome of hyperthermophilic archaeon, Thermococcus kodakarensis. Extremophiles (2012) 0.80
The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life. J Mol Evol (2015) 0.80
Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. PLoS Comput Biol (2014) 0.79
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics (2009) 0.78
Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. Genome Biol Evol (2012) 0.77
Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme. BMC Evol Biol (2013) 0.76
The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res (2017) 0.76
Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes. Sci Rep (2016) 0.75
A de novo protein confers copper resistance in Escherichia coli. Protein Sci (2016) 0.75
Genetic Characteristics and Multiple-PCR Development for Capsular Identification of Specific Serotypes of Campylobacter jejuni. PLoS One (2016) 0.75
Gene-Family Extension Measures and Correlations. Life (Basel) (2016) 0.75
Inferring gene duplications, transfers and losses can be done in a discrete framework. J Math Biol (2015) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature (1997) 34.00
The RDP-II (Ribosomal Database Project). Nucleic Acids Res (2001) 27.07
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
Lateral gene transfer and the nature of bacterial innovation. Nature (2000) 20.98
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature (1999) 19.34
Molecular evidence for an ancient duplication of the entire yeast genome. Nature (1997) 13.86
Massive gene decay in the leprosy bacillus. Nature (2001) 11.98
Genome phylogeny based on gene content. Nat Genet (1999) 8.12
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res (2001) 7.11
Deletional bias and the evolution of bacterial genomes. Trends Genet (2001) 5.81
The closest BLAST hit is often not the nearest neighbor. J Mol Evol (2001) 5.55
Microbial minimalism: genome reduction in bacterial pathogens. Cell (2002) 5.17
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res (2000) 3.95
Genome size and evolution. Chromosoma (1973) 2.93
Evolutionary dynamics of full genome content in Escherichia coli. EMBO J (2000) 2.86
Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev (1999) 2.25
Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev (2000) 2.22
Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev (2001) 1.95
The emergence of major cellular processes in evolution. FEBS Lett (1996) 1.59
Proposal concerning mechanism of evolution of the genome of Escherichia coli. Proc Natl Acad Sci U S A (1975) 1.58
Strain-specific genes of Helicobacter pylori: distribution, function and dynamics. Nucleic Acids Res (2001) 1.50
Biodiversity: microbial genomes multiply. Nature (2002) 1.33
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23
Orthology: another terminology muddle. Trends Genet (1999) 1.10
Evolutionary genomics: is Buchnera a bacterium or an organelle? Curr Biol (2000) 1.05
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics (2002) 4.12
Detection of functional modules from protein interaction networks. Proteins (2004) 3.08
Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res (2004) 2.86
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res (2004) 2.66
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31
Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27
BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics (2005) 2.26
Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08
The phylogenetic extent of metabolic enzymes and pathways. Genome Res (2003) 1.92
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77
Myriads of protein families, and still counting. Genome Biol (2003) 1.75
Transcription regulation and environmental adaptation in bacteria. Trends Microbiol (2003) 1.63
Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res (2005) 1.61
MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (2005) 1.34
Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics (2005) 1.33
An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol (2004) 1.31
Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 1.29
The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res (2003) 1.28
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
Percolation of annotation errors through hierarchically structured protein sequence databases. Math Biosci (2005) 1.27
Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep (2005) 1.25
Functional evolution of the yeast protein interaction network. Mol Biol Evol (2004) 1.25
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23
From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J Mol Biol (2003) 1.15
Probabilistic annotation of protein sequences based on functional classifications. BMC Bioinformatics (2005) 1.12
Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (2004) 1.07
Beyond 100 genomes. Genome Biol (2003) 1.06
Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends Microbiol (2002) 0.98
Robustness of metabolic map reconstruction. J Bioinform Comput Biol (2004) 0.91
The properties of protein family space depend on experimental design. Bioinformatics (2005) 0.91
Metabolic database systems for the analysis of genome-wide function. Biotechnol Bioeng (2003) 0.91
Clustering the annotation space of proteins. BMC Bioinformatics (2005) 0.91
Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics (2007) 0.90
Genome-wide expression patterns in physiological cardiac hypertrophy. BMC Genomics (2010) 0.89
CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics (2005) 0.89
CORRIE: enzyme sequence annotation with confidence estimates. BMC Bioinformatics (2007) 0.87
Transcriptome classification reveals molecular subtypes in psoriasis. BMC Genomics (2012) 0.87
Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. PLoS One (2011) 0.85
Metabolic innovations towards the human lineage. BMC Evol Biol (2008) 0.85
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks. BMC Res Notes (2011) 0.85
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform (2012) 0.83
Gene network and proteomic analyses of cardiac responses to pathological and physiological stress. Circ Cardiovasc Genet (2013) 0.81
Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One (2013) 0.80
Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species. PLoS Comput Biol (2010) 0.79
Lineage-specific partitions in archaeal transcription. Archaea (2007) 0.79
Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics (2003) 0.79
Genome-wide detection and family clustering of ion channels. FEBS Lett (2002) 0.78
BioTextQuest: a web-based biomedical text mining suite for concept discovery. Bioinformatics (2011) 0.78
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics (2009) 0.78
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. BMC Evol Biol (2011) 0.76
The comparative genomics of protein interactions. Genome Inform (2007) 0.76
Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis. Comp Funct Genomics (2003) 0.75
Biological information extraction and co-occurrence analysis. Methods Mol Biol (2014) 0.75
Science communication media for scientists and the public. EMBO Rep (2007) 0.75
BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics (2015) 0.75
Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families. Proteins (2005) 0.75