Published in Nucleic Acids Res on November 27, 2012
miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res (2013) 13.41
STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res (2014) 10.79
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2012) 8.41
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2013) 5.25
The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res (2013) 4.42
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res (2013) 4.33
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2014) 3.55
A blood RNA signature for tuberculosis disease risk: a prospective cohort study. Lancet (2016) 3.16
Bcl-6 directly represses the gene program of the glycolysis pathway. Nat Immunol (2014) 2.47
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2015) 2.44
ArrayExpress update--simplifying data submissions. Nucleic Acids Res (2014) 2.34
Biological interpretation of genome-wide association studies using predicted gene functions. Nat Commun (2015) 2.16
Understanding multicellular function and disease with human tissue-specific networks. Nat Genet (2015) 2.04
DAPIT Over-Expression Modulates Glucose Metabolism and Cell Behaviour in HEK293T Cells. PLoS One (2015) 2.02
Data integration in the era of omics: current and future challenges. BMC Syst Biol (2014) 1.82
The mouse Gene Expression Database (GXD): 2014 update. Nucleic Acids Res (2013) 1.78
Computational solutions for omics data. Nat Rev Genet (2013) 1.58
Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res (2015) 1.53
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res (2016) 1.52
Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab (2015) 1.52
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PLoS One (2015) 1.50
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. Stand Genomic Sci (2014) 1.48
Transcriptome analysis reveals differential splicing events in IPF lung tissue. PLoS One (2014) 1.45
Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer. BMC Genomics (2015) 1.44
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PLoS One (2015) 1.41
Identification of differentially expressed genes in pituitary adenomas by integrating analysis of microarray data. Int J Endocrinol (2015) 1.41
Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog (2016) 1.39
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol (2014) 1.37
Gene name errors are widespread in the scientific literature. Genome Biol (2016) 1.36
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res (2013) 1.35
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol (2015) 1.35
Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity. Nat Med (2016) 1.32
g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res (2016) 1.31
SEEK: a systems biology data and model management platform. BMC Syst Biol (2015) 1.30
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform (2015) 1.29
GeneMANIA: Fast gene network construction and function prediction for Cytoscape. F1000Res (2014) 1.27
linkedISA: semantic representation of ISA-Tab experimental metadata. BMC Bioinformatics (2014) 1.25
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. Nucleic Acids Res (2014) 1.25
Evidence for the biogenesis of more than 1,000 novel human microRNAs. Genome Biol (2014) 1.23
Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat Struct Mol Biol (2013) 1.20
Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods (2015) 1.19
A quality control system for profiles obtained by ChIP sequencing. Nucleic Acids Res (2013) 1.18
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB. EMBO Mol Med (2014) 1.17
The Gene Expression Omnibus Database. Methods Mol Biol (2016) 1.14
Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PLoS Biol (2014) 1.14
Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics (2014) 1.12
Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS One (2013) 1.10
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. OMICS (2014) 1.09
Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics (2014) 1.08
Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med (2014) 1.05
Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol Sci (2014) 1.05
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res (2015) 1.05
Identification of a BRCA1-mRNA splicing complex required for efficient DNA repair and maintenance of genomic stability. Mol Cell (2014) 1.04
Mouse Tumor Biology (MTB): a database of mouse models for human cancer. Nucleic Acids Res (2014) 1.04
Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PLoS One (2014) 1.04
A second trigeminal CGRP receptor: function and expression of the AMY1 receptor. Ann Clin Transl Neurol (2015) 1.03
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics (2015) 1.03
BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells. Nucleic Acids Res (2013) 1.03
Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. BMC Genomics (2014) 1.03
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res (2013) 1.02
The future of whole-cell modeling. Curr Opin Biotechnol (2014) 1.01
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. Plant Cell Physiol (2015) 1.00
Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes. Dev Cell (2014) 0.99
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Res (2014) 0.99
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn (2014) 0.99
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Res (2014) 0.98
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Database (Oxford) (2015) 0.97
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. Nucleic Acids Res (2013) 0.97
SLC25A1, or CIC, is a novel transcriptional target of mutant p53 and a negative tumor prognostic marker. Oncotarget (2014) 0.97
Characterizing and controlling the inflammatory network during influenza A virus infection. Sci Rep (2014) 0.97
GXD: a community resource of mouse Gene Expression Data. Mamm Genome (2015) 0.96
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. Mol Microbiol (2014) 0.95
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res (2015) 0.95
Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data. BMC Med Genet (2014) 0.95
Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Res (2015) 0.95
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford) (2016) 0.95
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res (2014) 0.95
The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol (2014) 0.94
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genomics (2014) 0.94
The immunology of host defence peptides: beyond antimicrobial activity. Nat Rev Immunol (2016) 0.94
Constitutive patterns of gene expression regulated by RNA-binding proteins. Genome Biol (2014) 0.94
Downregulation of long noncoding RNA MALAT1 induces epithelial-to-mesenchymal transition via the PI3K-AKT pathway in breast cancer. Int J Clin Exp Pathol (2015) 0.94
Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance. Genome Med (2015) 0.93
Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res (2015) 0.93
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. BMC Genomics (2015) 0.93
Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks. Nucleic Acids Res (2016) 0.93
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res (2013) 0.93
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. BMC Bioinformatics (2014) 0.93
Pharmacological characterisation of ligand- and voltage-gated ion channels expressed in human iPSC-derived forebrain neurons. Psychopharmacology (Berl) (2014) 0.93
Structural bioinformatics of the interactome. Annu Rev Biophys (2014) 0.93
Personalized identification of altered pathways in cancer using accumulated normal tissue data. Bioinformatics (2014) 0.93
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Mol Psychiatry (2015) 0.93
PRAME as an Independent Biomarker for Metastasis in Uveal Melanoma. Clin Cancer Res (2016) 0.93
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Front Genet (2014) 0.92
Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res (2014) 0.92
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. BMC Bioinformatics (2015) 0.92
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
Archiving next generation sequencing data. Nucleic Acids Res (2009) 6.98
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res (2011) 6.69
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics (2007) 6.67
PubMed related articles: a probabilistic topic-based model for content similarity. BMC Bioinformatics (2007) 5.30
The NCBI BioSystems database. Nucleic Acids Res (2009) 4.80
Data archiving is a good investment. Nature (2011) 3.53
NCBI Epigenomics: a new public resource for exploring epigenomic data sets. Nucleic Acids Res (2010) 3.27
Microarray standards at last. Nature (2002) 2.96
Gene data to hit milestone. Nature (2012) 2.27
Microarray analysis of spaceflown murine thymus tissue reveals changes in gene expression regulating stress and glucocorticoid receptors. J Cell Biochem (2010) 1.57
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (2008) 20.68
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res (2010) 19.07
NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res (2005) 17.61
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
Multiple-laboratory comparison of microarray platforms. Nat Methods (2005) 11.74
CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res (2008) 10.73
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
Activation of the interferon system by short-interfering RNAs. Nat Cell Biol (2003) 8.63
MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res (2006) 7.57
Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet (2011) 7.31
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods (2006) 6.25
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71
Annotating the human genome with Disease Ontology. BMC Genomics (2009) 4.71
A single IGF1 allele is a major determinant of small size in dogs. Science (2007) 4.68
Interferon-γ links ultraviolet radiation to melanomagenesis in mice. Nature (2011) 3.56
Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol (2006) 3.53
Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res (2005) 2.64
Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet (2006) 2.62
Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma. Nat Genet (2009) 2.58
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (2009) 2.37
LEAFY COTYLEDON1-LIKE defines a class of regulators essential for embryo development. Plant Cell (2003) 2.36
Database of mRNA gene expression profiles of multiple human organs. Genome Res (2005) 2.11
Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity. Proc Natl Acad Sci U S A (2004) 2.04
Cryptococcus neoformans overcomes stress of azole drugs by formation of disomy in specific multiple chromosomes. PLoS Pathog (2010) 2.04
Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma. Cancer Cell (2011) 1.96
RCircos: an R package for Circos 2D track plots. BMC Bioinformatics (2013) 1.95
Sre1p, a regulator of oxygen sensing and sterol homeostasis, is required for virulence in Cryptococcus neoformans. Mol Microbiol (2007) 1.93
MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes Dev (2011) 1.85
A molecular function map of Ewing's sarcoma. PLoS One (2009) 1.69
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics (2008) 1.68
Large-scale profiling of archival lymph nodes reveals pervasive remodeling of the follicular lymphoma methylome. Cancer Res (2009) 1.58
Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression. BMC Genomics (2009) 1.57
Identification of an inhibitor of the EWS-FLI1 oncogenic transcription factor by high-throughput screening. J Natl Cancer Inst (2011) 1.55
Vorinostat inhibits brain metastatic colonization in a model of triple-negative breast cancer and induces DNA double-strand breaks. Clin Cancer Res (2009) 1.40
NCBI Peptidome: a new repository for mass spectrometry proteomics data. Nucleic Acids Res (2009) 1.38
Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis. Mol Cancer Res (2009) 1.36
Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A (2013) 1.35
Suppressor role of activating transcription factor 2 (ATF2) in skin cancer. Proc Natl Acad Sci U S A (2008) 1.26
Assessment of automated image analysis of breast cancer tissue microarrays for epidemiologic studies. Cancer Epidemiol Biomarkers Prev (2010) 1.25
Promyelocytic leukemia zinc finger protein regulates interferon-mediated innate immunity. Immunity (2009) 1.22
Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer. Genome Res (2013) 1.11
Molecular grading of ductal carcinoma in situ of the breast. Clin Cancer Res (2008) 1.09
Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. Cancer Res (2012) 1.05
Importance of mitochondria in survival of Cryptococcus neoformans under low oxygen conditions and tolerance to cobalt chloride. PLoS Pathog (2008) 1.04
Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS One (2011) 1.04
Chemical analysis of four capsules containing the controlled substance analogues 4-methylmethcathinone, 2-fluoromethamphetamine, alpha-phthalimidopropiophenone and N-ethylcathinone. Forensic Sci Int (2010) 0.99
Constitutive Fms-like tyrosine kinase 3 activation results in specific changes in gene expression in myeloid leukaemic cells. Br J Haematol (2007) 0.99
One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors. Genetics (2004) 0.96
Cytogenetic characterization and gene expression profiling in the rat reflux-induced esophageal tumor model. J Thorac Cardiovasc Surg (2007) 0.96
Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes. J Med Genet (2006) 0.95
Inhibition of HIV-1 virus replication using small soluble Tat peptides. Virology (2005) 0.92
In defense against pathogens. Both plant sentinels and foot soldiers need to know the enemy. Plant Physiol (2003) 0.92
Overexpression of a cell wall glycoprotein in Fusarium oxysporum increases virulence and resistance to a plant PR-5 protein. Plant J (2003) 0.90
Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype. J Clin Endocrinol Metab (2013) 0.90
Novel polymorphic form of adefovir dipivoxil derived from polymer-directed crystallization. Pharmazie (2011) 0.90
Expression of IFITM1 in chronic myeloid leukemia patients. Leuk Res (2005) 0.89
Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics (2012) 0.88
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem (2008) 0.88
Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling. J Mol Diagn (2010) 0.87
A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology. Am J Pathol (2011) 0.87
In vivo role of alternative splicing and serine phosphorylation of the microphthalmia-associated transcription factor. Genetics (2012) 0.83
A novel binding pocket of cyclin-dependent kinase 2. Proteins (2009) 0.83
Advanced bone formation in mice with a dominant-negative mutation in the thyroid hormone receptor β gene due to activation of Wnt/β-catenin protein signaling. J Biol Chem (2012) 0.82
Photodestructible vesicles. Langmuir (2006) 0.81
Whole genome and transcriptome sequencing of a B3 thymoma. PLoS One (2013) 0.81
Nursing documentation usage analysis. AMIA Annu Symp Proc (2008) 0.81
Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform (2015) 0.80
Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. PLoS One (2007) 0.79
Lipid metabolism genes in contralateral unaffected breast and estrogen receptor status of breast cancer. Cancer Prev Res (Phila) (2013) 0.78
Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples. Methods Mol Biol (2012) 0.77