Published in EMBO Rep on May 01, 2005
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol (2007) 11.03
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80
Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol (2005) 1.82
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol (2008) 1.81
The automatic annotation of bacterial genomes. Brief Bioinform (2012) 1.50
New metrics for comparative genomics. Curr Opin Biotechnol (2006) 1.08
Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One (2012) 0.96
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol (2014) 0.95
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PLoS Comput Biol (2013) 0.95
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics (2010) 0.83
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol (2012) 0.82
Systems biology perspectives on minimal and simpler cells. Microbiol Mol Biol Rev (2014) 0.78
Matching curated genome databases: a non trivial task. BMC Genomics (2008) 0.75
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res (2001) 7.11
Protein function in the post-genomic era. Nature (2000) 7.00
The past, present and future of genome-wide re-annotation. Genome Biol (2002) 2.77
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77
The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol (2001) 1.74
Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res (2005) 1.61
Beyond 100 genomes. Genome Biol (2003) 1.06
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol (2008) 8.91
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
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
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
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
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16
Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. Blood (2012) 2.14
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
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol (2004) 1.88
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One (2009) 1.83
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
Classification schemes for protein structure and function. Nat Rev Genet (2003) 1.52
Is there a role for antigen selection in mantle cell lymphoma? Immunogenetic support from a series of 807 cases. Blood (2011) 1.49
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
Functional evolution of the yeast protein interaction network. Mol Biol Evol (2004) 1.25
Molecular subsets of mantle cell lymphoma defined by the IGHV mutational status and SOX11 expression have distinct biologic and clinical features. Cancer Res (2012) 1.24
GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics (2003) 1.23
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective. Res Microbiol (2005) 1.18
Antigen selection in B-cell lymphomas--tracing the evidence. Semin Cancer Biol (2013) 1.16
From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J Mol Biol (2003) 1.15
The normal IGHV1-69-derived B-cell repertoire contains stereotypic patterns characteristic of unmutated CLL. Blood (2009) 1.15
Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. BMC Evol Biol (2009) 1.14
Probabilistic annotation of protein sequences based on functional classifications. BMC Bioinformatics (2005) 1.12
Evidence for the significant role of immunoglobulin light chains in antigen recognition and selection in chronic lymphocytic leukemia. Blood (2008) 1.09
Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (2004) 1.07
Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ Microbiol (2010) 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
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics (2007) 0.98
Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper. BMC Plant Biol (2011) 0.97
Robustness of metabolic map reconstruction. J Bioinform Comput Biol (2004) 0.91
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biol (2006) 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
Analysis of xyloglucan endotransglycosylase/hydrolase (XTH) genes from allotetraploid (Gossypium hirsutum) cotton and its diploid progenitors expressed during fiber elongation. J Plant Physiol (2008) 0.90
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
The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J (2011) 0.87
Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? BMC Genomics (2010) 0.87
Transcriptome classification reveals molecular subtypes in psoriasis. BMC Genomics (2012) 0.87
Effects of OTU clustering and PCR artifacts on microbial diversity estimates. Microb Ecol (2012) 0.86
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
IgG-switched CLL has a distinct immunogenetic signature from the common MD variant: ontogenetic implications. Clin Cancer Res (2013) 0.84
Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia. Immunogenetics (2014) 0.83
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform (2012) 0.83
MASiVEdb: the Sirevirus Plant Retrotransposon Database. BMC Genomics (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
The study of a SPATULA-like bHLH transcription factor expressed during peach (Prunus persica) fruit development. Plant Physiol Biochem (2011) 0.80