Big Browser Extensible Data Format
Names
More detailed information about this field from each metasource.
Big Browser Extensible Data Format
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
BigBed
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Big Browser Extensible Data Format
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
BigBed
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Big Browser Extensible Data Format
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
BigBed
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as BED files do. BigBed files are created initially from BED type files, using the program bedToBigBed. The resulting bigBed files are in an indexed binary format. The main advantage of the bigBed files is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets bigBed is considerably faster than regular BED files.
Description
More detailed information about this field from each metasource.
The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as BED files do. BigBed files are created initially from BED type files, using the program bedToBigBed. The resulting bigBed files are in an indexed binary format. The main advantage of the bigBed files is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets bigBed is considerably faster than regular BED files.
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Webpage:
http://genome.ucsc.edu/goldenPath/help/bigBed.htmlWebpage
More detailed information about this field from each metasource.
http://genome.ucsc.edu/goldenPath/help/bigBed.html
metasource: Fairsharing.orgversion: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
BigWig and BigBed: enabling browsing of large distributed datasets
PMID: 20639541
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
PMID: 24227676
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
BigWig and BigBed: enabling browsing of large distributed datasets
PMID: 20639541
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
PMID: 24227676
metasource: Fairsharing.org
version: FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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BigWig and BigBed: enabling browsing of large distributed datasets
PubMed citations: 457.
457 articles citing: BigWig and BigBed: enabling browsing of large distributed datasets
A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project. PMID:35883178
Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes. PMID:35806206
Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA. PMID:35800774
Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding. PMID:35799193
Limitations of mouse models for sickle cell disease conferred by their human globin transgene configurations. PMID:35793591
Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing. PMID:35787786
Bioinformatics Methods for ChIP-seq Histone Analysis. PMID:35733020
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
TSABL: Trait Specific Annotation Based Locus predictor. PMID:35705896
RNA-Seq Analysis of the Growth Hormone Transgenic Female Triploid Atlantic Salmon (Salmo salar) Hepatic Transcriptome Reveals Broad Temperature-Mediated Effects on Metabolism and Other Biological Processes. PMID:35677560
Sorghum root epigenetic landscape during limiting phosphorus conditions. PMID:35600998
Localization of a TORC1-eIF4F translation complex during CD8+ T cell activation drives divergent cell fate. PMID:35597236
Immune disease variants modulate gene expression in regulatory CD4+ T cells. PMID:35591976
DNA-PK promotes DNA end resection at DNA double strand breaks in G0 cells. PMID:35575473
Assessing and assuring interoperability of a genomics file format. PMID:35575355
Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. PMID:35551737
Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation. PMID:35550614
Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. PMID:35523900
A Stage-Specific OTX2 Regulatory Network and Maturation-Associated Gene Programs Are Inherent Barriers to RPE Neural Competency. PMID:35517508
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells. PMID:35513721
Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription. PMID:35486737
The nuclear lamina binds the EBV genome during latency and regulates viral gene expression. PMID:35421198
Non-coding RNA LEVER sequestration of PRC2 can mediate long range gene regulation. PMID:35411071
Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. PMID:35383280
Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells. PMID:35383166
An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis. PMID:35382117
Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs. PMID:35328433
Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. PMID:35314780
A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. PMID:35302162
EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. PMID:35182476
Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. PMID:35173350
Whole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2:eGFP line. PMID:35171990
SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. PMID:35115713
Heat shock induces premature transcript termination and reconfigures the human transcriptome. PMID:35114099
Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq. PMID:35103973
Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling. PMID:35103963
Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II. PMID:35102600
Genomic patterns of transcription-replication interactions in mouse primary B cells. PMID:35100392
Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. PMID:35075135
KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. PMID:35042549
A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data. PMID:35022082
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. PMID:35017527
Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos. PMID:34982026
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. PMID:34928370
Prioritising positively selected variants in whole-genome sequencing data using FineMAV. PMID:34922440
Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila. PMID:34887421
A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. PMID:34880227
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events. PMID:34871444
Physiologically relevant miRNAs in mammalian oocytes are rare and highly abundant. PMID:34866300
Glutathione Metabolism Is a Regulator of the Acute Inflammatory Response of Monocytes to (1→3)-β-D-Glucan. PMID:34858388
Histone variant H2A.Z regulates zygotic genome activation. PMID:34853314
recount3: summaries and queries for large-scale RNA-seq expression and splicing. PMID:34844637
WEE1 inhibition induces anti-tumor immunity by activating ERV and the dsRNA pathway. PMID:34825915
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. PMID:34815310
Transcriptional profile and chromatin accessibility in zebrafish melanocytes and melanoma tumors. PMID:34791221
Thyroid hormone signaling promotes hepatic lipogenesis through the transcription factor ChREBP. PMID:34784250
CHD4 Conceals Aberrant CTCF-Binding Sites at TAD Interiors by Regulating Chromatin Accessibility in Mouse Embryonic Stem Cells. PMID:34764232
Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors. PMID:34731634
The UCSC Genome Browser database: 2022 update. PMID:34718705
Intrinsic and acquired drug resistance to LSD1 inhibitors in small cell lung cancer occurs through a TEAD4-driven transcriptional state. PMID:34669238
Transcription and splicing dynamics during early Drosophila development. PMID:34667107
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. PMID:34663447
The chromatin remodeler Ino80 mediates RNAPII pausing site determination. PMID:34663418
Multiomic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals novel markers of almost all major cell types. PMID:34643097
CoolBox: a flexible toolkit for visual analysis of genomics data. PMID:34629071
Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. PMID:34599234
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism. PMID:34565452
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. PMID:34548076
Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. PMID:34529940
Identifying transcript 5' capped ends in Plasmodium falciparum. PMID:34527439
Role of 53BP1 in end protection and DNA synthesis at DNA breaks. PMID:34503990
Targeting the IRE1α/XBP1s pathway suppresses CARM1-expressing ovarian cancer. PMID:34493732
Formation of spermatogonia and fertile oocytes in golden hamsters requires piRNAs. PMID:34489573
Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. PMID:34469576
ASCL1, NKX2-1, and PROX1 co-regulate subtype-specific genes in small-cell lung cancer. PMID:34466783
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. PMID:34446581
TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes. PMID:34433064
Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters. PMID:34383744
HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data. PMID:34360892
Genome-wide variability in recombination activity is associated with meiotic chromatin organization. PMID:34301629
Isolation and Characterization of Barley (Hordeum vulgare) Extracellular Vesicles to Assess Their Role in RNA Spray-Based Crop Protection. PMID:34281265
HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing. PMID:34274995
Binary pan-cancer classes with distinct vulnerabilities defined by pro- or anti-cancer YAP/TEAD activity. PMID:34270926
Recommendations for the FAIRification of genomic track metadata. PMID:34249331
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome. PMID:34187599
Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation. PMID:34187555
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. PMID:34183853
An Analysis of Methylome Evolution in Primates. PMID:34175932
Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. PMID:34157120
The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. PMID:34155658
A role for condensin in mediating transcriptional adaptation to environmental stimuli. PMID:34083394
CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase. PMID:34074795
DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A. PMID:34037658
PEPPRO: quality control and processing of nascent RNA profiling data. PMID:33992117
Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia. PMID:33980539
Functional mapping of androgen receptor enhancer activity. PMID:33975627
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. PMID:33932985
Checkpoint-mediated DNA polymerase ε exonuclease activity curbing counteracts resection-driven fork collapse. PMID:33932350
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. PMID:33931649
Identification of candidate PAX2-regulated genes implicated in human kidney development. PMID:33907292
Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. PMID:33903675
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes. PMID:33888511
Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. PMID:33886094
A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance. PMID:33838102
Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. PMID:33826921
PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives. PMID:33822034
m6A-independent genome-wide METTL3 and METTL14 redistribution drives the senescence-associated secretory phenotype. PMID:33795874
Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. PMID:33789109
Neuronal enhancers are hotspots for DNA single-strand break repair. PMID:33767446
Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites. PMID:33751115
Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function. PMID:33717143
Megadepth: efficient coverage quantification for BigWigs and BAMs. PMID:33693500
The epigenetic pioneer EGR2 initiates DNA demethylation in differentiating monocytes at both stable and transient binding sites. PMID:33692344
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. PMID:33681991
ATAC-seq on Sorted Adult Mouse Neurons. PMID:33654878
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. PMID:33632298
Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants. PMID:33631116
Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq. PMID:33606259
Base-resolution models of transcription-factor binding reveal soft motif syntax. PMID:33603233
Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. PMID:33597535
Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region. PMID:33556624
Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. PMID:33504799
CAGE-seq reveals that HIV-1 latent infection does not trigger unique cellular responses in a Jurkat T cell model. PMID:33504604
A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism. PMID:33497421
Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. PMID:33472063
InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PMID:33465132
Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. PMID:33460557
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. PMID:33446241
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PMID:33428615
Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis. PMID:33406971
MEF2 (Myocyte Enhancer Factor 2) Is Essential for Endothelial Homeostasis and the Atheroprotective Gene Expression Program. PMID:33406884
Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression. PMID:33406418
Novel Biological Functions of the NsdC Transcription Factor in Aspergillus fumigatus. PMID:33402536
Order and stochasticity in the folding of individual Drosophila genomes. PMID:33397980
RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions. PMID:33357438
Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency. PMID:33352108
Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in flies and mice. PMID:33334823
SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome. PMID:33293552
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). PMID:33239395
GTRD: an integrated view of transcription regulation. PMID:33231677
Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences. PMID:33225957
Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). PMID:33193703
LSH mediates gene repression through macroH2A deposition. PMID:33159050
Broad genic repression domains signify enhanced silencing of oncogenes. PMID:33144558
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PMID:33137082
Preparation and Analysis of GLOE-Seq Libraries for Genome-Wide Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions. PMID:33111111
Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken. PMID:33111104
Regulation of single-cell genome organization into TADs and chromatin nanodomains. PMID:33077913
RASP: an atlas of transcriptome-wide RNA secondary structure probing data. PMID:33068412
Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing. PMID:33048927
Adipocytes fail to maintain cellular identity during obesity due to reduced PPARγ activity and elevated TGFβ-SMAD signaling. PMID:32992037
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Genome-wide methylation data from R1 (wild-type) and the transgenic Dnmt1Tet/Tet mouse embryonic stem cells overexpressing DNA methyltransferase 1 (DNMT1). PMID:32944600
The qBED track: a novel genome browser visualization for point processes. PMID:32941613
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. PMID:32933554
Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1. PMID:32923585
lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. PMID:32895492
Altered 3D chromatin structure permits inversional recombination at the IgH locus. PMID:32851160
The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription. PMID:32845241
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin. PMID:32822575
Robust partitioning of microRNA targets from downstream regulatory changes. PMID:32821933
Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes. PMID:32747824
ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair. PMID:32744506
The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PMID:32667960
Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression. PMID:32620123
Epiviz File Server: Query, transform and interactively explore data from indexed genomic files. PMID:32618995
Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection. PMID:32511266
High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. PMID:32497496
MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. PMID:32471342
YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells. PMID:32452550
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. PMID:32424275
Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis. PMID:32424070
Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. PMID:32408516
TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. PMID:32324215
Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq. PMID:32320643
Hotspots of Aberrant Enhancer Activity in Fibrolamellar Carcinoma Reveal Candidate Oncogenic Pathways and Therapeutic Vulnerabilities. PMID:32294439
Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos. PMID:32286279
Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment. PMID:32277910
DNA punch cards for storing data on native DNA sequences via enzymatic nicking. PMID:32269230
Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. PMID:32221288
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. PMID:32213349
Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk. PMID:32203495
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. PMID:32192535
An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. PMID:32188783
Regulation of the RNAPII Pool Is Integral to the DNA Damage Response. PMID:32142654
TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. PMID:32067044
ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis. PMID:32051414
GsmPlot: a web server to visualize epigenome data in NCBI. PMID:32050905
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. PMID:32033573
Combined burden and functional impact tests for cancer driver discovery using DriverPower. PMID:32024818
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs. PMID:32001327
CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions. PMID:31996894
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PMID:31978041
Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. PMID:31964861
The most abundant maternal lncRNA Sirena1 acts post-transcriptionally and impacts mitochondrial distribution. PMID:31956907
Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping. PMID:31950077
Influenza-induced monocyte-derived alveolar macrophages confer prolonged antibacterial protection. PMID:31932810
The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation. PMID:31901448
Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing. PMID:31901446
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. PMID:31875554
Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. PMID:31851922
Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus. PMID:31850067
Gastrointestinal transcription factors drive lineage-specific developmental programs in organ specification and cancer. PMID:31844668
Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors. PMID:31815011
A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2. PMID:31722198
Free circular introns with an unusual branchpoint in neuronal projections. PMID:31697236
Lactate Efflux From Intervertebral Disc Cells Is Required for Maintenance of Spine Health. PMID:31692093
MoMI-G: modular multi-scale integrated genome graph browser. PMID:31690272
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. PMID:31653198
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. PMID:31640799
Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. PMID:31602465
Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State. PMID:31588023
Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms. PMID:31533980
Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability. PMID:31519522
A Method to Study de novo Formation of Chromatin Domains. PMID:31498316
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. PMID:31477927
An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. PMID:31467088
BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer. PMID:31462713
Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. PMID:31445886
ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data. PMID:31404415
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. PMID:31391082
The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. PMID:31384064
Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2. PMID:31375664
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. PMID:31362726
JMJD6 is a tumorigenic factor and therapeutic target in neuroblastoma. PMID:31346162
Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors. PMID:31320637
Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene. PMID:31287004
Mutual editing of alternative splicing between breast cancer cells and macrophages. PMID:31233192
Atlas of Subcellular RNA Localization Revealed by APEX-Seq. PMID:31230715
Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. PMID:31221665
GR and LSD1/KDM1A-Targeted Gene Activation Requires Selective H3K4me2 Demethylation at Enhancers. PMID:31216473
Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. PMID:31202577
Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. PMID:31174959
A machine-learning approach for accurate detection of copy number variants from exome sequencing. PMID:31171634
ARID1A spatially partitions interphase chromosomes. PMID:31131328
Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping. PMID:31127282
Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome. PMID:31114899
Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. PMID:31110351
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. PMID:31106365
SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. PMID:31104839
YeasTSS: an integrative web database of yeast transcription start sites. PMID:31032841
TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. PMID:31005419
Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. PMID:30970245
N6-Methylation of Adenosine of FZD10 mRNA Contributes to PARP Inhibitor Resistance. PMID:30967398
A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. PMID:30923056
FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. PMID:30922998
Repression of Germline Genes in Caenorhabditis elegans Somatic Tissues by H3K9 Dimethylation of Their Promoters. PMID:30910798
Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations. PMID:30898439
Drosophila p53 directs nonapoptotic programs in postmitotic tissue. PMID:30892991
UniProt genomic mapping for deciphering functional effects of missense variants. PMID:30840782
The CagRS Two-Component System Regulates Clavulanic Acid Metabolism via Multiple Pathways in Streptomyces clavuligerus F613-1. PMID:30837970
Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum. PMID:30833341
MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin. PMID:30819107
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution. PMID:30642251
Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. PMID:30577869
Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor. PMID:30576656
Variation in proviral content among human genomes mediated by LTR recombination. PMID:30568734
The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans. PMID:30567997
Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction. PMID:30566871
Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal. PMID:30514857
HDAC stimulates gene expression through BRD4 availability in response to IFN and in interferonopathies. PMID:30463877
Role of Cnot6l in maternal mRNA turnover. PMID:30456367
The evolutionary dynamics of microRNAs in domestic mammals. PMID:30451897
TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4+CD8+ thymocytes. PMID:30420627
Genome-wide chromatin accessibility and transcriptome profiling show minimal epigenome changes and coordinated transcriptional dysregulation of hedgehog signaling in Danforth's short tail mice. PMID:30380057
Chromatin accessibility dynamics across C. elegans development and ageing. PMID:30362940
Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. PMID:30341288
Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis. PMID:30333496
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. PMID:30286773
Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. PMID:30244833
Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes in Saccharomyces cerevisiae. PMID:30237209
The RNA exosome contributes to gene expression regulation during stem cell differentiation. PMID:30212902
Refined RIP-seq protocol for epitranscriptome analysis with low input materials. PMID:30212448
Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3' End RNA-Seq. PMID:30157438
Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells. PMID:30143598
HiGlass: web-based visual exploration and analysis of genome interaction maps. PMID:30143029
Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances. PMID:30134820
Non-redundant ISGF3 Components Promote NK Cell Survival in an Auto-regulatory Manner during Viral Infection. PMID:30134157
Revealing a human p53 universe. PMID:30107566
Transcription factor Etv6 regulates functional differentiation of cross-presenting classical dendritic cells. PMID:30087163
Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. PMID:30075113
ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference. PMID:30064353
The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets. PMID:30052804
Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PMID:30028832
GIVE: portable genome browsers for personal websites. PMID:30016975
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans. PMID:29979962
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes. PMID:29889196
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
Transcription Factor IRF8 Orchestrates the Adaptive Natural Killer Cell Response. PMID:29858012
Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. PMID:29808028
Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras. PMID:29766023
Enhanced JBrowse plugins for epigenomics data visualization. PMID:29699480
Cstf2t Regulates expression of histones and histone-like proteins in male germ cells. PMID:29673127
Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity. PMID:29657031
Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress. PMID:29636001
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. PMID:29621972
Gon4l regulates notochord boundary formation and cell polarity underlying axis extension by repressing adhesion genes. PMID:29615614
Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo. PMID:29572359
Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. PMID:29500235
Distinct histone modifications denote early stress-induced drug tolerance in cancer. PMID:29492189
High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets. PMID:29432475
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. PMID:29420797
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. PMID:29386051
Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. PMID:29337142
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. PMID:29233090
Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation. PMID:29176792
An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies. PMID:29106447
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data. PMID:29087447
OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. PMID:29069459
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development. PMID:29044125
Mfd translocase is necessary and sufficient for transcription-coupled repair in Escherichia coli. PMID:28986449
The IRF4 Gene Regulatory Module Functions as a Read-Write Integrator to Dynamically Coordinate T Helper Cell Fate. PMID:28930660
Six Highly Conserved Targets of RNAi Revealed in HIV-1-Infected Patients from Russia Are Also Present in Many HIV-1 Strains Worldwide. PMID:28918033
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. PMID:28912564
5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells. PMID:28863138
First-generation annotations for the fathead minnow (Pimephales promelas) genome. PMID:28853170
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. PMID:28837811
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. PMID:28750606
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. PMID:28732548
Platelet function is modified by common sequence variation in megakaryocyte super enhancers. PMID:28703137
Convergent roles of ATF3 and CSL in chromatin control of cancer-associated fibroblast activation. PMID:28684431
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. PMID:28673540
McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. PMID:28637810
The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells. PMID:28623086
Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge. PMID:28614293
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. PMID:28482034
A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. PMID:28472346
Automated multiplex genome-scale engineering in yeast. PMID:28469255
Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. PMID:28445466
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. PMID:28402545
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer. PMID:28344039
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. PMID:28336542
Genome-wide chromatin accessibility, DNA methylation and gene expression analysis of histone deacetylase inhibition in triple-negative breast cancer. PMID:28239551
iHMS: a database integrating human histone modification data across developmental stages and tissues. PMID:28187703
Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. PMID:28111014
Tissue resolved, gene structure refined equine transcriptome. PMID:28107812
PBrowse: a web-based platform for real-time collaborative exploration of genomic data. PMID:28100700
Chromatin dynamics regulate mesenchymal stem cell lineage specification and differentiation to osteogenesis. PMID:28077316
Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. PMID:28056764
Scalable Genomics with R and Bioconductor. PMID:28018047
SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics. PMID:27918597
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. PMID:27876760
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. PMID:27797775
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. PMID:27716038
Flexible expressed region analysis for RNA-seq with derfinder. PMID:27694310
Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels. PMID:27656675
Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. PMID:27622383
HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines. PMID:27605307
Rail-RNA: scalable analysis of RNA-seq splicing and coverage. PMID:27592709
LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer. PMID:27485121
Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-Protein Kinase Catalytic Subunit. PMID:27470713
Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. PMID:27353328
Boiler: lossy compression of RNA-seq alignments using coverage vectors. PMID:27298258
The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. PMID:27226635
GeNemo: a search engine for web-based functional genomic data. PMID:27098038
Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. PMID:27036967
Chromas from chromatin: sonification of the epigenome. PMID:27019695
Effects of Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome. PMID:26976640
The Universal 3D3 Antibody of Human PODXL Is Pluripotent Cytotoxic, and Identifies a Residual Population After Extended Differentiation of Pluripotent Stem Cells. PMID:26886504
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators. PMID:26868127
Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes. PMID:26783963
Repression of p53-target gene Bbc3/PUMA by MYSM1 is essential for the survival of hematopoietic multipotent progenitors and contributes to stem cell maintenance. PMID:26768662
Expression of Ribosomal RNA and Protein Genes in Human Embryonic Stem Cells Is Associated With the Activating H3K4me3 Histone Mark. PMID:26755341
Comprehensive nucleosome mapping of the human genome in cancer progression. PMID:26735342
Standardizing chromatin research: a simple and universal method for ChIP-seq. PMID:26704968
Ensembl 2016. PMID:26687719
MethylAction: detecting differentially methylated regions that distinguish biological subtypes. PMID:26673711
The UCSC Genome Browser database: 2016 update. PMID:26590259
The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling. PMID:26584623
Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. PMID:26562774
ENCODE data at the ENCODE portal. PMID:26527727
Transcription factor trapping by RNA in gene regulatory elements. PMID:26516199
Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain. PMID:26511496
smallWig: parallel compression of RNA-seq WIG files. PMID:26424856
Cell type-selective disease-association of genes under high regulatory load. PMID:26338775
An interactive genome browser of association results from the UK10K cohorts project. PMID:26315906
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. PMID:26167643
Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism. PMID:26156244
Chromatin Signature Identifies Monoallelic Gene Expression Across Mammalian Cell Types. PMID:26092837
Sepsis induces specific changes in histone modification patterns in human monocytes. PMID:25793379
Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment. PMID:25753668
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. PMID:25740935
The DREAM complex promotes gene body H2A.Z for target repression. PMID:25737279
A genomic data viewer for iPad. PMID:25723152
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PMID:25679813
Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq. PMID:25652644
MYC regulates the non-coding transcriptome. PMID:25587025
Quantitative bacterial transcriptomics with RNA-seq. PMID:25483350
The UCSC Genome Browser database: 2015 update. PMID:25428374
piRBase: a web resource assisting piRNA functional study. PMID:25425034
Epidaurus: aggregation and integration analysis of prostate cancer epigenome. PMID:25378314
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
Ensembl 2015. PMID:25352552
Navigating protected genomics data with UCSC Genome Browser in a Box. PMID:25348212
Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. PMID:25343476
Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype. PMID:25250711
Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. PMID:25248638
BEDTools: The Swiss-Army Tool for Genome Feature Analysis. PMID:25199790
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. PMID:25063299
ChIPseek, a web-based analysis tool for ChIP data. PMID:24974934
Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. PMID:24922322
The personal genome browser: visualizing functions of genetic variants. PMID:24799434
Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARγ-driven enhancers. PMID:24788520
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. PMID:24735413
G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD. PMID:24609361
bwtool: a tool for bigWig files. PMID:24489365
Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties. PMID:24373287
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. PMID:24363377
CrossMap: a versatile tool for coordinate conversion between genome assemblies. PMID:24351709
Processing genome scale tabular data with wormtable. PMID:24308302
The UCSC Genome Browser database: 2014 update. PMID:24270787
mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis. PMID:24267917
Practical guidelines for the comprehensive analysis of ChIP-seq data. PMID:24244136
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. PMID:24227676
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. PMID:24214966
GWIPS-viz: development of a ribo-seq genome browser. PMID:24185699
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. PMID:23812591
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. PMID:23735015
PLncDB: plant long non-coding RNA database. PMID:23476021
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. PMID:23393188
Using the Wash U Epigenome Browser to examine genome-wide sequencing data. PMID:23255151
ChromoZoom: a flexible, fluid, web-based genome browser. PMID:23220575
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. PMID:23193273
The Ruby UCSC API: accessing the UCSC genome database using Ruby. PMID:22994508
Analysing and interpreting DNA methylation data. PMID:22986265
Modeling gene expression using chromatin features in various cellular contexts. PMID:22950368
The UCSC genome browser and associated tools. PMID:22908213
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. PMID:22517427
Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database. PMID:22438815
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors. PMID:22232429
Identifying elemental genomic track types and representing them uniformly. PMID:22208806
The Human Epigenome Browser at Washington University. PMID:22127213
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME. PMID:21984761
Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PMID:21980304
The UCSC Genome Browser. PMID:21975940
Developing and implementing an institute-wide data sharing policy. PMID:21955348
Cistrome: an integrative platform for transcriptional regulation studies. PMID:21859476
ReadDB provides efficient storage for mapped short reads. PMID:21736741
Next generation sequencing based approaches to epigenomics. PMID:21266347
Dalliance: interactive genome viewing on the web. PMID:21252075
Tabix: fast retrieval of sequence features from generic TAB-delimited files. PMID:21208982
ENCODE whole-genome data in the UCSC genome browser (2011 update). PMID:21037257
The UCSC Genome Browser database: update 2011. PMID:20959295
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630 -
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
PubMed citations: 203.
203 articles citing: Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
Long-Read Nanopore Sequencing Identifies Mismatch Repair-Deficient Related Genes with Alternative Splicing in Colorectal Cancer. PMID:35909892
Drosophila eugracilis - Akt. PMID:35856017
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development-New Insights From Technical Advances. PMID:35615697
Genome-wide promoter methylation profiling in a cellular model of melanoma progression reveals markers of malignancy and metastasis that predict melanoma survival. PMID:35606887
Global DNA Methylation Profiles in Peripheral Blood of WTC-Exposed Community Members with Breast Cancer. PMID:35564499
Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed. PMID:35530816
An Association between EMX2 Variations and Mayer-Rokitansky-Küster-Hauser Syndrome: A Case-Control Study of Chinese Women. PMID:35463657
Non-coding RNA LEVER sequestration of PRC2 can mediate long range gene regulation. PMID:35411071
Complete genomic and epigenetic maps of human centromeres. PMID:35357911
Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. PMID:35179489
Small RNA pathways in the nematode Ascaris in the absence of piRNAs. PMID:35149688
Identification of differentially methylated genes in first-trimester placentas with trisomy 16. PMID:35064135
A comparison on predicting functional impact of genomic variants. PMID:35047814
Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN. PMID:34965941
The Genome of the "Sea Vomit" Didemnum vexillum. PMID:34947908
Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila. PMID:34887421
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. PMID:34751401
MVIP: multi-omics portal of viral infection. PMID:34718748
The UCSC Genome Browser database: 2022 update. PMID:34718705
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. PMID:34649537
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. PMID:34594038
TGF-β/activin signaling promotes CDK7 inhibitor resistance in triple-negative breast cancer cells through upregulation of multidrug transporters. PMID:34481843
ASCL1, NKX2-1, and PROX1 co-regulate subtype-specific genes in small-cell lung cancer. PMID:34466783
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Multi-omics integration in the age of million single-cell data. PMID:34417589
Conservation of Zebrafish MicroRNA-145 and Its Role during Neural Crest Cell Development. PMID:34209401
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Inducible expression quantitative trait locus analysis of the MUC5AC gene in asthma in urban populations of children. PMID:34019912
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:33976134
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways. PMID:33941243
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. PMID:33836575
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PMID:33826604
Genomics of the Parasitic Nematode Ascaris and Its Relatives. PMID:33800545
Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. PMID:33789109
MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. PMID:33677108
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition. PMID:33522899
Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2. PMID:33413422
bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage. PMID:33370262
GENCODE 2021. PMID:33270111
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). PMID:33239395
GTRD: an integrated view of transcription regulation. PMID:33231677
Broad genic repression domains signify enhanced silencing of oncogenes. PMID:33144558
Ensembl 2021. PMID:33137190
MicroRNA-488 inhibits proliferation and motility of tumor cells via downregulating FSCN1, modulated by Notch3 in breast carcinomas. PMID:33099573
Emergent Coordination of the CHKB and CPT1B Genes in Eutherian Mammals: Implications for the Origin of Brown Adipose Tissue. PMID:33058877
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:33024961
Patient-specific genomics and cross-species functional analysis implicate LRP2 in hypoplastic left heart syndrome. PMID:33006316
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. PMID:32976578
The UCSC SARS-CoV-2 Genome Browser. PMID:32908258
Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms. PMID:32868490
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PMID:32760067
Genome-Wide DNA Methylation Profiles in Community Members Exposed to the World Trade Center Disaster. PMID:32751422
Optical mapping of the 22q11.2DS region reveals complex repeat structures and preferred locations for non-allelic homologous recombination (NAHR). PMID:32699385
Epiviz File Server: Query, transform and interactively explore data from indexed genomic files. PMID:32618995
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:32577641
An Erg-driven transcriptional program controls B cell lymphopoiesis. PMID:32541654
Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. PMID:32533862
Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats. PMID:32511223
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation. PMID:32497138
Machine learning uncovers cell identity regulator by histone code. PMID:32483223
CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. PMID:32481589
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments. PMID:32463100
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. PMID:32383760
PCNA-associated factor KIAA0101 transcriptionally induced by ELK1 controls cell proliferation and apoptosis in nasopharyngeal carcinoma: an integrated bioinformatics and experimental study. PMID:32275642
A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/- rats. PMID:32252027
Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II. PMID:32251483
The Paralogous Krüppel-like Factors 9 and 13 Regulate the Mammalian Cellular Circadian Clock Output Gene Dbp. PMID:32241200
Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies. PMID:32238901
The African Swine Fever Virus Transcriptome. PMID:32075923
An atlas of transposable element-derived alternative splicing in cancer. PMID:32075558
Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. PMID:32075554
Epigenetic loss of heterozygosity of Apc and an inflammation-associated mutational signature detected in Lrig1+/--driven murine colonic adenomas. PMID:32059662
Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. PMID:32013076
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs. PMID:32001327
Accurate quantification of circular RNAs identifies extensive circular isoform switching events. PMID:31900416
A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers. PMID:31899510
Clinical Implications of Sub-grouping HER2 Positive Tumors by Amplicon Structure and Co-amplified Genes. PMID:31827209
Genetic Variant Associated With Survival of Patients With Stage II-III Colon Cancer. PMID:31811950
The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. PMID:31717504
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. PMID:31665499
Novel Neonatal Variants of the Carbamoyl Phosphate Synthetase 1 Deficiency: Two Case Reports and Review of Literature. PMID:31507628
HTLV-1 basic leucine zipper factor protects cells from oxidative stress by upregulating expression of Heme Oxygenase I. PMID:31251786
Functional characterization of CNOT3 variants identified in familial adenomatous polyposis adenomas. PMID:31231471
Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. PMID:31213516
BarkBase: Epigenomic Annotation of Canine Genomes. PMID:31181663
CORR® ORS Richard A. Brand Award: Disruption in Peroxisome Proliferator-Activated Receptor-γ (PPARG) Increases Osteonecrosis Risk Through Genetic Variance and Pharmacologic Modulation. PMID:31135556
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes. PMID:31070714
Genetic Variations and Precision Medicine. PMID:31019429
LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data. PMID:31014252
A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. PMID:30923056
UniProt genomic mapping for deciphering functional effects of missense variants. PMID:30840782
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. PMID:30760546
Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements. PMID:30755505
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
TogoGenome/TogoStanza: modularized Semantic Web genome database. PMID:30624651
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1. PMID:30557369
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. PMID:30481262
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. PMID:30462313
ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. PMID:30413482
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. PMID:30407557
The UCSC Genome Browser database: 2019 update. PMID:30407534
Ensembl 2019. PMID:30407521
Database resources of the National Center for Biotechnology Information. PMID:30395293
LNCipedia 5: towards a reference set of human long non-coding RNAs. PMID:30371849
X-Chromosome Inactivation and Escape from X Inactivation in Mouse. PMID:30218369
Revealing a human p53 universe. PMID:30107566
Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. PMID:30097472
Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer. PMID:30038405
miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. PMID:29997117
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). PMID:29907088
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. PMID:29809150
Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. PMID:29761462
miR-181a regulates erythroid enucleation via the regulation of Xpo7 expression. PMID:29567782
Maternal 5mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. PMID:29545821
BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis. PMID:29434197
DNA Methylation-Based Classifier for Accurate Molecular Diagnosis of Bone Sarcomas. PMID:29354796
Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. PMID:29259021
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. PMID:29258433
Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function. PMID:29177109
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285
The Encyclopedia of DNA elements (ENCODE): data portal update. PMID:29126249
The UCSC Genome Browser database: 2018 update. PMID:29106570
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
Genome-wide prediction of DNase I hypersensitivity using gene expression. PMID:29051481
Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development. PMID:29044125
miRNA-122 Protects Mice and Human Hepatocytes from Acetaminophen Toxicity by Regulating Cytochrome P450 Family 1 Subfamily A Member 2 and Family 2 Subfamily E Member 1 Expression. PMID:28963035
Loss of β-catenin in resident cardiac fibroblasts attenuates fibrosis induced by pressure overload in mice. PMID:28959037
C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. PMID:28915724
Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. PMID:28905132
FANTOM5 CAGE profiles of human and mouse samples. PMID:28850106
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. PMID:28850105
A heterochromatin-dependent transcription machinery drives piRNA expression. PMID:28847004
Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells. PMID:28818098
Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. PMID:28645144
A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. PMID:28575488
Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. PMID:28572566
Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PMID:28453575
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
Clinical Features, Molecular Heterogeneity, and Prognostic Implications in YARS2-Related Mitochondrial Myopathy. PMID:28395030
INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. PMID:28344988
Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. PMID:28341547
Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium. PMID:28327113
A Golden Age for Working with Public Proteomics Data. PMID:28118949
Tissue resolved, gene structure refined equine transcriptome. PMID:28107812
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. PMID:27899657
The UCSC Genome Browser database: 2017 update. PMID:27899642
Ensembl 2017. PMID:27899575
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
SORL1 mutations in early- and late-onset Alzheimer disease. PMID:27822510
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
NGSmethDB 2017: enhanced methylomes and differential methylation. PMID:27794041
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. PMID:27786492
The human-induced pluripotent stem cell initiative-data resources for cellular genetics. PMID:27733501
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. PMID:27638885
PGD: a pangolin genome hub for the research community. PMID:27616775
A scientist's guide for submitting data to ZFIN. PMID:27443940
Defining the identity of mouse embryonic dermal fibroblasts. PMID:27265328
A systematic, large-scale comparison of transcription factor binding site models. PMID:27209209
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PMID:27100087
Cistrome-based Cooperation between Airway Epithelial Glucocorticoid Receptor and NF-κB Orchestrates Anti-inflammatory Effects. PMID:27076634
A protocadherin gene cluster regulatory variant is associated with nicotine withdrawal and the urge to smoke. PMID:27067016
The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PMID:27019336
Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? PMID:26906613
UCSC Data Integrator and Variant Annotation Integrator. PMID:26740527
Ensembl 2016. PMID:26687719
ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. PMID:26666652
The UCSC Genome Browser database: 2016 update. PMID:26590259
Ensembl Genomes 2016: more genomes, more complexity. PMID:26578574
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
ENCODE data at the ENCODE portal. PMID:26527727
Dataset of transcriptional landscape of B cell early activation. PMID:26484262
An interactive genome browser of association results from the UK10K cohorts project. PMID:26315906
A New Noncoding RNA Arranges Bacterial Chromosome Organization. PMID:26307168
Compound heterozygous NOTCH1 mutations underlie impaired cardiogenesis in a patient with hypoplastic left heart syndrome. PMID:26164125
Divergence of transcriptional landscape occurs early in B cell activation. PMID:25987903
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. PMID:25865119
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. PMID:25690853
The Genome 10K Project: a way forward. PMID:25689317
The UCSC Ebola Genome Portal. PMID:25685613
Extending reference assembly models. PMID:25651527
DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. PMID:25556833
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. PMID:25504731
Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. PMID:25501035
The UCSC Genome Browser database: 2015 update. PMID:25428374
DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. PMID:25416797
Navigating protected genomics data with UCSC Genome Browser in a Box. PMID:25348212
Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. PMID:25343476
Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. PMID:25248638
Comparative assembly hubs: web-accessible browsers for comparative genomics. PMID:25138168
The UCSC Genome Browser: What Every Molecular Biologist Should Know. PMID:24984850
ChIPseek, a web-based analysis tool for ChIP data. PMID:24974934
The UCSC Genome Browser database: 2014 update. PMID:24270787
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