Published in J Mol Biol on September 19, 2003
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS Comput Biol (2006) 1.25
Codon usage domains over bacterial chromosomes. PLoS Comput Biol (2006) 1.09
Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data. BMC Genomics (2005) 1.07
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci U S A (2010) 1.02
Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy. Biophys J (2007) 0.98
Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola. BMC Genomics (2007) 0.96
Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Proc Natl Acad Sci U S A (2006) 0.90
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat Protoc (2012) 0.89
Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics (2007) 0.88
Stem-loop structures in prokaryotic genomes. BMC Genomics (2006) 0.87
Novel algorithms reveal streptococcal transcriptomes and clues about undefined genes. PLoS Comput Biol (2007) 0.83
Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria. J Bacteriol (2011) 0.81
Systematic identification of stem-loop containing sequence families in bacterial genomes. BMC Genomics (2008) 0.76
SigWinR; the SigWin-detector updated and ported to R. BMC Res Notes (2009) 0.75
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
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23
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
Clustering the annotation space of proteins. BMC Bioinformatics (2005) 0.91
Metabolic database systems for the analysis of genome-wide function. Biotechnol Bioeng (2003) 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
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
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
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics (2009) 0.78
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
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
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
Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families. Proteins (2005) 0.75
BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics (2015) 0.75