Published in Nucleic Acids Res on December 04, 2013
limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res (2015) 14.81
Ensembl 2016. Nucleic Acids Res (2015) 3.61
ArrayExpress update--simplifying data submissions. Nucleic Acids Res (2014) 2.34
The Ensembl Variant Effect Predictor. Genome Biol (2016) 1.80
Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res (2015) 1.53
Enhancer evolution across 20 mammalian species. Cell (2015) 1.48
Growth and hormone profiling in children with congenital melanocytic naevi. Br J Dermatol (2015) 1.40
WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res (2015) 1.35
BioJS: an open source standard for biological visualisation - its status in 2014. F1000Res (2014) 1.18
The extracellular matrix: Tools and insights for the "omics" era. Matrix Biol (2015) 1.08
Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res (2015) 1.05
Distribution of miRNA expression across human tissues. Nucleic Acids Res (2016) 1.04
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn (2014) 0.99
GXD: a community resource of mouse Gene Expression Data. Mamm Genome (2015) 0.96
Biological databases for human research. Genomics Proteomics Bioinformatics (2015) 0.96
BioModels linked dataset. BMC Syst Biol (2014) 0.94
Anatomy of BioJS, an open source community for the life sciences. Elife (2015) 0.93
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res (2015) 0.93
Triticeae resources in Ensembl Plants. Plant Cell Physiol (2014) 0.92
arrayMap 2014: an updated cancer genome resource. Nucleic Acids Res (2014) 0.91
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res (2015) 0.91
Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. Gene (2016) 0.89
The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell (2016) 0.87
Long non-coding RNA Databases in Cardiovascular Research. Genomics Proteomics Bioinformatics (2016) 0.87
"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. Microarrays (Basel) (2015) 0.87
Unique Features of Human Protein Arginine Methyltransferase 9 (PRMT9) and Its Substrate RNA Splicing Factor SF3B2. J Biol Chem (2015) 0.86
A Precision Medicine Approach to the Rescue of Function on Malignant Calmodulinopathic Long QT Syndrome. Circ Res (2016) 0.85
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. Mol Biol Cell (2014) 0.84
piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals. PLoS One (2015) 0.84
miTALOS v2: Analyzing Tissue Specific microRNA Function. PLoS One (2016) 0.84
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. Sci Rep (2015) 0.83
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Nucleic Acids Res (2015) 0.83
Systems medicine: evolution of systems biology from bench to bedside. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med (2014) 0.83
FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications. PLoS One (2014) 0.83
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. Physiol Genomics (2014) 0.82
Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine. PLoS One (2015) 0.82
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet (2015) 0.81
A bioinformatic and computational study of myosin phosphatase subunit diversity. Am J Physiol Regul Integr Comp Physiol (2014) 0.81
CTNNA3 and SEMA3D: Promising loci for asthma exacerbation identified through multiple genome-wide association studies. J Allergy Clin Immunol (2015) 0.81
Regulatory insight into the European human pluripotent stem cell registry. Stem Cells Dev (2014) 0.81
Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments. Mol Biol Evol (2016) 0.80
miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs. Nucleic Acids Res (2014) 0.80
Homozygous loss-of-function variants in European cosmopolitan and isolate populations. Hum Mol Genet (2015) 0.80
A Human "eFP" Browser for Generating Gene Expression Anatograms. PLoS One (2016) 0.78
Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes. EBioMedicine (2015) 0.78
Are Human Translated Pseudogenes Functional? Mol Biol Evol (2015) 0.78
RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles. BMC Genomics (2015) 0.78
MERAV: a tool for comparing gene expression across human tissues and cell types. Nucleic Acids Res (2015) 0.78
Cyclic thrombospondin-1 mimetics: grafting of a thrombospondin sequence into circular disulfide-rich frameworks to inhibit endothelial cell migration. Biosci Rep (2015) 0.78
Small Maf proteins (MafF, MafG, MafK): History, structure and function. Gene (2016) 0.78
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. BMC Syst Biol (2014) 0.78
RPdb: a database of experimentally verified cellular reprogramming records. Bioinformatics (2015) 0.78
Myosin 1e promotes breast cancer malignancy by enhancing tumor cell proliferation and stimulating tumor cell de-differentiation. Oncotarget (2016) 0.78
dbCPG: A web resource for cancer predisposition genes. Oncotarget (2016) 0.77
Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. Genome Res (2016) 0.77
MTD: a mammalian transcriptomic database to explore gene expression and regulation. Brief Bioinform (2016) 0.77
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res (2015) 0.77
DDMGD: the database of text-mined associations between genes methylated in diseases from different species. Nucleic Acids Res (2014) 0.77
Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins. Proc Biol Sci (2015) 0.77
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell (2017) 0.76
Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics. Front Bioeng Biotechnol (2016) 0.76
PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool. Sci Rep (2015) 0.76
Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression. BMC Genomics (2015) 0.76
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. Bioinformatics (2015) 0.76
Turning publicly available gene expression data into discoveries using gene set context analysis. Nucleic Acids Res (2015) 0.76
Assignment of Functional Relevance to Genes at Type 2 Diabetes-Associated Loci Through Investigation of β-Cell Mass Deficits. Mol Endocrinol (2016) 0.76
A genome wide association study identifies a lncRna as risk factor for pathological inflammatory responses in leprosy. PLoS Genet (2017) 0.75
Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PLoS One (2016) 0.75
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). Sci Rep (2017) 0.75
A novel binary T-vector with the GFP reporter gene for promoter characterization. PLoS One (2014) 0.75
Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level. BMC Plant Biol (2014) 0.75
Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics. Sci Rep (2016) 0.75
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PLoS One (2016) 0.75
Inverse Association of Plasma Level of Glutathione Peroxidase with Liver Fibrosis in Chronic Hepatitis B: Potential Role of Iron. Middle East J Dig Dis (2016) 0.75
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. Database (Oxford) (2016) 0.75
Pluralistic and stochastic gene regulation: examples, models and consistent theory. Nucleic Acids Res (2016) 0.75
Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Res (2016) 0.75
NABIC Microarray: an integrated database of high throughput data for gene expression profiles. Bioinformation (2015) 0.75
FHF2 isoforms differentially regulate Nav1.6-mediated resurgent sodium currents in dorsal root ganglion neurons. Pflugers Arch (2016) 0.75
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. F1000Res (2016) 0.75
Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. BMC Genomics (2016) 0.75
Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease. Sci Rep (2015) 0.75
Genetics and Genomics of Longitudinal Lung Function Patterns in Asthmatics. Am J Respir Crit Care Med (2016) 0.75
Meta-Analysis of Tourette Syndrome and Attention Deficit Hyperactivity Disorder Provides Support for a Shared Genetic Basis. Front Neurosci (2016) 0.75
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Res (2017) 0.75
Mg2+ effect on argonaute and RNA duplex by molecular dynamics and bioinformatics implications. PLoS One (2014) 0.75
Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. Hum Mol Genet (2017) 0.75
TRANS PROF DB: A new resource for sharing translational profiles. Translation (Austin) (2014) 0.75
Roles of solvent accessibility and gene expression in modeling protein sequence evolution. Evol Bioinform Online (2015) 0.75
The transcriptomic and proteomic landscapes of bone marrow and secondary lymphoid tissues. PLoS One (2014) 0.75
EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. Pac Symp Biocomput (2016) 0.75
Separating the wheat from the chaff: systematic identification of functionally relevant noncoding variants in ADHD. Mol Psychiatry (2016) 0.75
HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. Front Neuroanat (2016) 0.75
Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes. Int J Mol Sci (2016) 0.75
UPF0586 Protein C9orf41 Homolog Is Anserine-producing Methyltransferase. J Biol Chem (2015) 0.75
SNP array and FISH analysis of a proband with a 22q13.2- 22qter duplication shed light on the molecular origin of the rearrangement. BMC Med Genet (2015) 0.75
Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57. BMC Med Genet (2016) 0.75
CSmiRTar: Condition-Specific microRNA targets database. PLoS One (2017) 0.75
Evaluating biomarkers to model cancer risk post cosmic ray exposure. Life Sci Space Res (Amst) (2016) 0.75
miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res (2010) 25.85
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Modeling sample variables with an Experimental Factor Ontology. Bioinformatics (2010) 6.27
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res (2011) 3.61
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
Enterotypes of the human gut microbiome. Nature (2011) 24.36
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
International network of cancer genome projects. Nature (2010) 20.35
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol (2002) 16.75
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res (2013) 14.23
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome. N Engl J Med (2003) 11.17
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
Variation in transcription factor binding among humans. Science (2010) 9.33
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Software for computing and annotating genomic ranges. PLoS Comput Biol (2013) 8.20
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
Modeling sample variables with an Experimental Factor Ontology. Bioinformatics (2010) 6.27
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature (2008) 6.10
Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell (2003) 6.04
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics (2008) 5.95
Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci U S A (2013) 5.68
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (2009) 5.62
Periodic gene expression program of the fission yeast cell cycle. Nat Genet (2004) 5.60
Modeling biomedical experimental processes with OBI. J Biomed Semantics (2010) 5.36
A global map of human gene expression. Nat Biotechnol (2010) 5.32
Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A (2010) 5.21
Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res (2009) 4.99
ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70
Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev (2003) 4.68
Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Res (2004) 4.21
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS (2008) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Standards for microarray data. Science (2002) 4.11
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc (2013) 4.00
Analysis of cell-based RNAi screens. Genome Biol (2006) 3.99
Submission of microarray data to public repositories. PLoS Biol (2004) 3.83
The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) (2013) 3.82
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc (2009) 3.77
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res (2008) 3.73
ArrayExpress service for reviewers/editors of DNA microarray papers. Nat Biotechnol (2006) 3.61
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res (2011) 3.61
Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 3.61
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2003) 3.34
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics (2003) 3.30
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Standards for microarray data: an open letter. Environ Health Perspect (2004) 3.15
Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics (2010) 3.10
Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell (2002) 3.07
The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res (2011) 3.05
VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res (2006) 2.94
A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nat Med (2010) 2.88
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res (2011) 2.87
Reuse of public genome-wide gene expression data. Nat Rev Genet (2012) 2.79
The underlying principles of scientific publication. Bioinformatics (2002) 2.79
Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics (2006) 2.60
The EBI RDF platform: linked open data for the life sciences. Bioinformatics (2014) 2.55
Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics (2007) 2.50
Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods (2011) 2.47
Tools for mapping high-throughput sequencing data. Bioinformatics (2012) 2.46