Published in Bioinformatics on April 12, 2003
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69
BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res (2005) 13.30
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol (2009) 7.95
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol (2009) 1.40
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. Nucleic Acids Res (2005) 1.32
Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands. Proc Natl Acad Sci U S A (2011) 1.21
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PLoS One (2009) 1.10
Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics (2008) 0.90
Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics (2007) 0.90
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) (2010) 0.85
Automatic detection of false annotations via binary property clustering. BMC Bioinformatics (2005) 0.82
Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics Proteomics Bioinformatics (2007) 0.82
A semi-automated genome annotation comparison and integration scheme. BMC Bioinformatics (2013) 0.80
Pathway analysis software: annotation errors and solutions. Mol Genet Metab (2010) 0.79
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. BMC Bioinformatics (2006) 0.78
The chlamydiales pangenome revisited: structural stability and functional coherence. Genes (Basel) (2012) 0.77
Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors. PLoS One (2015) 0.76
Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Stand Genomic Sci (2015) 0.75
Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
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
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
Requirement of bic/microRNA-155 for normal immune function. Science (2007) 16.24
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics (2005) 14.50
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
MicroRNAs regulate brain morphogenesis in zebrafish. Science (2005) 11.16
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (2002) 11.11
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
A mitochondria-K+ channel axis is suppressed in cancer and its normalization promotes apoptosis and inhibits cancer growth. Cancer Cell (2007) 9.20
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Humid tropical forest clearing from 2000 to 2005 quantified by using multitemporal and multiresolution remotely sensed data. Proc Natl Acad Sci U S A (2008) 8.46
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell (2011) 7.02
Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet (2012) 6.97
The molecular architecture of the nuclear pore complex. Nature (2007) 6.93
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity (2007) 6.72
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet (2011) 6.43
A gene network for navigating the literature. Nat Genet (2004) 6.43
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics (2005) 6.02
Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet (2009) 5.31
Determining the architectures of macromolecular assemblies. Nature (2007) 4.94
MicroRNA profiling of the murine hematopoietic system. Genome Biol (2005) 4.94
Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (2003) 4.88
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev (2007) 4.69
Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev (2009) 4.43
Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Res (2003) 4.42
Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol (2008) 4.36
Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun (2013) 4.35
The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci (2008) 4.28
Functional copy-number alterations in cancer. PLoS One (2008) 4.27
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
RNA editing of human microRNAs. Genome Biol (2006) 4.16
Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics (2002) 4.12
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics (2005) 3.85
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol (2003) 3.80
Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins (2013) 3.78
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64