Published in Nucleic Acids Res on November 20, 2015
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res (2016) 2.58
deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res (2016) 1.07
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res (2016) 1.01
The UCSC Genome Browser database: 2017 update. Nucleic Acids Res (2016) 0.87
Ensembl 2017. Nucleic Acids Res (2016) 0.85
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res (2016) 0.85
CRISPR guide RNA design for research applications. FEBS J (2016) 0.83
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet (2017) 0.82
CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res (2016) 0.82
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res (2016) 0.82
The human-induced pluripotent stem cell initiative-data resources for cellular genetics. Nucleic Acids Res (2016) 0.81
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res (2016) 0.79
Whole-exome sequencing identifies MST1R as a genetic susceptibility gene in nasopharyngeal carcinoma. Proc Natl Acad Sci U S A (2016) 0.79
Role of the Long Non-Coding RNA MAPT-AS1 in Regulation of Microtubule Associated Protein Tau (MAPT) Expression in Parkinson's Disease. PLoS One (2016) 0.79
FANTOM5 CAGE profiles of human and mouse samples. Sci Data (2017) 0.78
Zebrafish Genome Engineering Using the CRISPR-Cas9 System. Trends Genet (2016) 0.78
Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy. Proc Natl Acad Sci U S A (2017) 0.78
LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleic Acids Res (2016) 0.77
Nonhuman primate models for the evaluation of HIV-1 preventive vaccine strategies: model parameter considerations and consequences. Curr Opin HIV AIDS (2016) 0.77
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. Nucleic Acids Res (2016) 0.77
CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. EMBO Rep (2016) 0.77
Unmasking targets of antitumor immunity via high-throughput antigen profiling. Curr Opin Biotechnol (2016) 0.77
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic Acids Res (2016) 0.77
UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics (2016) 0.77
Network Reconstruction Reveals that Valproic Acid Activates Neurogenic Transcriptional Programs in Adult Brain Following Traumatic Injury. Pharm Res (2017) 0.76
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. Nucleic Acids Res (2016) 0.76
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. Database (Oxford) (2017) 0.76
A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies. PLoS Genet (2016) 0.75
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Res (2016) 0.75
Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus. Front Genet (2017) 0.75
Synteny Portal: a web-based application portal for synteny block analysis. Nucleic Acids Res (2016) 0.75
XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies. Int J Endocrinol (2017) 0.75
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PLoS One (2017) 0.75
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. Nucleic Acids Res (2016) 0.75
PEP_scaffolder: using (homologous) proteins to scaffold genomes. Bioinformatics (2016) 0.75
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res (2017) 0.75
DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res (2016) 0.75
Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci. PLoS One (2016) 0.75
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. Database (Oxford) (2016) 0.75
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. BMC Bioinformatics (2016) 0.75
R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Res (2016) 0.75
Protein-Coding Genes' Retrocopies and Their Functions. Viruses (2017) 0.75
Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders. Database (Oxford) (2016) 0.75
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database (Oxford) (2016) 0.75
The Pancreatic Islet Regulome Browser. Front Genet (2017) 0.75
GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms. Nucleic Acids Res (2016) 0.75
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol (2017) 0.75
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res (2016) 0.75
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res (2016) 0.75
RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res (2016) 0.75
Altered Expression of Long Noncoding RNAs in Blood After Ischemic Stroke and Proximity to Putative Stroke Risk Loci. Stroke (2016) 0.75
Genotype Calling from Population-Genomic Sequencing Data. G3 (Bethesda) (2017) 0.75
Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. Genet Med (2016) 0.75
Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis. Genome Med (2017) 0.75
Kinetics of recruitment and allosteric activation of ARHGEF25 isoforms by the heterotrimeric G-protein Gαq. Sci Rep (2016) 0.75
RPAN: rice pan-genome browser for ∼3000 rice genomes. Nucleic Acids Res (2016) 0.75
A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. BMC Genet (2017) 0.75
MathIOmica: An Integrative Platform for Dynamic Omics. Sci Rep (2016) 0.75
iFORM: Incorporating Find Occurrence of Regulatory Motifs. PLoS One (2016) 0.75
No associations of a set of SNPs in the Vascular Endothelial Growth Factor (VEGF) and Matrix Metalloproteinase (MMP) genes with survival of colorectal cancer patients. Cancer Med (2016) 0.75
MicroRNA-206 is differentially expressed in Brca1-deficient mice and regulates epithelial and stromal cell compartments of the mouse mammary gland. Oncogenesis (2016) 0.75
Social and physical environments early in development predict DNA methylation of inflammatory genes in young adulthood. Proc Natl Acad Sci U S A (2017) 0.75
Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. Cell Mol Life Sci (2017) 0.75
Using omics approaches to understand pulmonary diseases. Respir Res (2017) 0.75
Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. BMC Evol Biol (2017) 0.75
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. BMC Bioinformatics (2017) 0.75
Programmed mitophagy is essential for the glycolytic switch during cell differentiation. EMBO J (2017) 0.75
Comparative analysis of miRNAs of two rapeseed genotypes in response to acetohydroxyacid synthase-inhibiting herbicides by high-throughput sequencing. PLoS One (2017) 0.75
"Squirrel" Primer-Based PCR Assay for Direct and Targeted Sanger Sequencing of Short Genomic Segments. J Biomol Tech (2017) 0.75
Poliovirus Receptor: More than a simple viral receptor. Virus Res (2017) 0.75
Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance. Mamm Genome (2016) 0.75
Frequent miRNA-convergent fusion gene events in breast cancer. Nat Commun (2017) 0.75
Impact of Sixteen Established Pancreatic Cancer Susceptibility Loci in American Jews. Cancer Epidemiol Biomarkers Prev (2017) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
dbSNP: the NCBI database of genetic variation. Nucleic Acids Res (2001) 76.97
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 59.82
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2005) 37.39
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
UniProt: a hub for protein information. Nucleic Acids Res (2014) 16.72
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A (2003) 16.58
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (2010) 15.90
Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res (2013) 15.13
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
The UCSC Known Genes. Bioinformatics (2006) 14.67
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res (2013) 14.23
Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58
The Human Gene Mutation Database: 2008 update. Genome Med (2009) 11.72
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol (2009) 11.17
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science (2015) 9.92
ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res (2013) 9.31
BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics (2010) 9.11
Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics (2003) 8.92
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
Ensembl 2015. Nucleic Acids Res (2014) 8.30
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
RefSeq: an update on mammalian reference sequences. Nucleic Acids Res (2013) 7.29
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res (2008) 6.07
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res (2014) 6.00
WindowMasker: window-based masker for sequenced genomes. Bioinformatics (2005) 5.91
LOVD v.2.0: the next generation in gene variant databases. Hum Mutat (2011) 5.53
Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (2008) 5.46
The UCSC Genome Browser database: 2015 update. Nucleic Acids Res (2014) 4.87
ClinGen--the Clinical Genome Resource. N Engl J Med (2015) 4.45
GenBank. Nucleic Acids Res (2014) 3.71
Proteogenomic characterization of human colon and rectal cancer. Nature (2014) 3.61
Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res (2005) 3.59
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res (2014) 3.57
Rfam 12.0: updates to the RNA families database. Nucleic Acids Res (2014) 3.13
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res (2014) 3.12
The Human Epigenome Browser at Washington University. Nat Methods (2011) 2.62
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics (2013) 2.42
Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res (2012) 1.72
Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856. Genetics (2015) 1.04
Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics (2014) 0.94
ENCODE data at the ENCODE portal. Nucleic Acids Res (2015) 1.00
The UCSC Genome Browser database: 2017 update. Nucleic Acids Res (2016) 0.87