Published in Bioinformatics on July 22, 2003
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
The balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39
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
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol (2004) 1.88
Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One (2011) 1.25
Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PLoS Genet (2011) 1.20
Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci (2009) 1.08
The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol (2011) 1.00
Lineage-specific expansion of DNA-binding transcription factor families. Trends Genet (2010) 0.90
Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages. PLoS Genet (2009) 0.90
Inferring gene family histories in yeast identifies lineage specific expansions. PLoS One (2014) 0.85
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. BMC Evol Biol (2011) 0.80
The chlamydiales pangenome revisited: structural stability and functional coherence. Genes (Basel) (2012) 0.77
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 balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39
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
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
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks. BMC Res Notes (2011) 0.85
Metabolic innovations towards the human lineage. BMC Evol Biol (2008) 0.85
Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. PLoS One (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
Lineage-specific partitions in archaeal transcription. Archaea (2007) 0.79
Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species. PLoS Comput Biol (2010) 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
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics (2009) 0.78
BioTextQuest: a web-based biomedical text mining suite for concept discovery. Bioinformatics (2011) 0.78
The comparative genomics of protein interactions. Genome Inform (2007) 0.76
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. BMC Evol Biol (2011) 0.76
Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis. Comp Funct Genomics (2003) 0.75
Science communication media for scientists and the public. EMBO Rep (2007) 0.75
Biological information extraction and co-occurrence analysis. Methods Mol Biol (2014) 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