Published in Bioinformatics on June 16, 2005
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics (2012) 1.61
Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned. Chem Biodivers (2010) 0.94
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics (2015) 0.87
Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One (2013) 0.80
CATH FunFHMMer web server: protein functional annotations using functional family assignments. Nucleic Acids Res (2015) 0.80
The chlamydiales pangenome revisited: structural stability and functional coherence. Genes (Basel) (2012) 0.77
Computational approaches to selecting and optimising targets for structural biology. Methods (2011) 0.77
Matching curated genome databases: a non trivial task. BMC Genomics (2008) 0.75
The Booly aliasing resource: a database of grouped biological identifiers. Bioinformation (2011) 0.75
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
Human MicroRNA targets. PLoS Biol (2004) 34.51
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14
Requirement of bic/microRNA-155 for normal immune function. Science (2007) 16.24
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
Identification of virus-encoded microRNAs. Science (2004) 12.56
MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16
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
microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity (2007) 6.72
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev (2007) 4.69
RNA editing of human microRNAs. Genome Biol (2006) 4.16
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
Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods (2008) 3.41
Detection of functional modules from protein interaction networks. Proteins (2004) 3.08
An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet (2009) 3.05
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
Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc (2009) 2.66
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
The miR-144/451 locus is required for erythroid homeostasis. J Exp Med (2010) 2.54
Prediction of microRNA targets. Drug Discov Today (2007) 2.46
The balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39
Computational prediction of protein-protein interactions. Mol Biotechnol (2007) 2.35
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
Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction. Circulation (2012) 2.14
Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08
Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods (2013) 1.92
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
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev (2009) 1.84
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One (2009) 1.83
The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature (2011) 1.77
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
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
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
Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets. Cancer Res (2010) 1.59
Annotation of mammalian primary microRNAs. BMC Genomics (2008) 1.53
Classification schemes for protein structure and function. Nat Rev Genet (2003) 1.52
A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst Biol (2008) 1.49
MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells. J Biol Chem (2012) 1.43
Efficient inhibition of miR-155 function in vivo by peptide nucleic acids. Nucleic Acids Res (2010) 1.41
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
Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol Cell (2013) 1.29
Structural and functional properties of genes involved in human cancer. BMC Genomics (2006) 1.29
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet (2012) 1.28
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
Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs. Proc Natl Acad Sci U S A (2010) 1.20
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis. BMC Genomics (2010) 1.20
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective. Res Microbiol (2005) 1.18
MapMi: automated mapping of microRNA loci. BMC Bioinformatics (2010) 1.15
From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J Mol Biol (2003) 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
Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (2004) 1.07
SylArray: a web server for automated detection of miRNA effects from expression data. Bioinformatics (2010) 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
MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs. PLoS One (2012) 0.99
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
Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Mol Cancer (2014) 0.98
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation. BMC Genomics (2009) 0.96
MiR-221 influences effector functions and actin cytoskeleton in mast cells. PLoS One (2011) 0.95