Published in Mol Biol Evol on October 20, 2004
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44
Why do hubs tend to be essential in protein networks? PLoS Genet (2006) 3.29
Evolutionary and physiological importance of hub proteins. PLoS Comput Biol (2006) 2.34
The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci (2006) 1.71
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47
The conservation and evolutionary modularity of metabolism. Genome Biol (2009) 1.24
Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci U S A (2009) 1.16
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. BMC Syst Biol (2012) 1.01
Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics (2005) 0.91
The dichotomy in degree correlation of biological networks. PLoS One (2011) 0.91
The protein interaction network of the epithelial junctional complex: a system-level analysis. Mol Biol Cell (2008) 0.88
The yeast kinome displays scale free topology with functional hub clusters. BMC Bioinformatics (2005) 0.81
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PLoS One (2014) 0.77
The role of protein interactions in mediating essentiality and synthetic lethality. PLoS One (2013) 0.76
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. BMC Syst Biol (2009) 0.76
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
Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett (2005) 2.68
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
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res (2010) 2.37
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
Human gene organization driven by the coordination of replication and transcription. Genome Res (2007) 1.71
Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci U S A (2005) 1.64
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
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics (2009) 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
A novel strategy of transcription regulation by intragenic nucleosome ordering. Genome Res (2009) 1.21
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput Biol (2011) 1.20
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
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput Biol (2012) 1.12
Nucleosome positioning by genomic excluding-energy barriers. Proc Natl Acad Sci U S A (2009) 1.09
Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (2004) 1.07
Beyond 100 genomes. Genome Biol (2003) 1.06
Replication-associated mutational asymmetry in the human genome. Mol Biol Evol (2011) 1.02
Human genome replication proceeds through four chromatin states. PLoS Comput Biol (2013) 1.01
Genetic variation between Helicobacter pylori strains: gene acquisition or loss? Trends Microbiol (2002) 0.98
3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res (2012) 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
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
Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments. J Phys Chem B (2010) 0.84
From simple bacterial and archaeal replicons to replication N/U-domains. J Mol Biol (2013) 0.84
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
Ubiquitous human 'master' origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers. J Phys Condens Matter (2015) 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
Science communication media for scientists and the public. EMBO Rep (2007) 0.75
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
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