Mapping accessible chromatin regions using Sono-Seq

scientific article

Mapping accessible chromatin regions using Sono-Seq is …
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scholarly articleQ13442814

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P819ADS bibcode2009PNAS..10614926A
P356DOI10.1073/PNAS.0905443106
P932PMC publication ID2736440
P698PubMed publication ID19706456
P5875ResearchGate publication ID26766530

P50authorMark Bender GersteinQ6766711
Philippe LefrançoisQ87614441
Michael P. SnyderQ28924918
Joel RozowskyQ37390171
P2093author name stringKevin Struhl
Ghia Euskirchen
Raymond K Auerbach
Zarmik Moqtaderi
Nathan Lamarre-Vincent
P2860cites workChIP-chip: a genomic approach for identifying transcription factor binding sitesQ38287979
Global changes in STAT target selection and transcription regulation upon interferon treatmentsQ38318251
Model-based analysis of ChIP-Seq (MACS)Q21183902
Ensembl 2008Q22065975
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promotersQ24537436
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq dataQ24595121
DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarraysQ24644477
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatinQ24673476
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociQ24673673
NCBI GEO: mining tens of millions of expression profiles--database and tools updateQ24675443
High-resolution profiling of histone methylations in the human genomeQ27860906
Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivoQ28266357
Polycomb gene expression and histone H3 lysine 27 trimethylation changes during bovine preimplantation developmentQ28293525
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controlsQ28305773
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologiesQ28306149
Genome-wide mapping of in vivo protein-DNA interactionsQ29547162
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBFQ29547783
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq dataQ31169616
Cell cycle-specified fluctuation of nucleosome occupancy at gene promotersQ33258473
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatinQ33966079
Chromatin immunoprecipitation and microarray-based analysis of protein locationQ34003310
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencingQ34012676
Open conformation chromatin and pluripotencyQ36987634
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor bindingQ36995336
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAsQ37286495
P433issue35
P407language of work or nameEnglishQ1860
P1104number of pages6
P304page(s)14926-14931
P577publication date2009-08-18
P1433published inProceedings of the National Academy of Sciences of the United States of AmericaQ1146531
P1476titleMapping accessible chromatin regions using Sono-Seq
P478volume106

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cites work (P2860)
Q31007638A Statistical Framework for the Analysis of ChIP-Seq Data
Q51543538A computational pipeline for comparative ChIP-seq analyses.
Q34713637A twin approach to unraveling epigenetics
Q21092716A user's guide to the encyclopedia of DNA elements (ENCODE)
Q35709124Advances in epigenetics and epigenomics for neurodegenerative diseases
Q33522047An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
Q53835008An optimized FAIRE procedure for low cell numbers in yeast.
Q34023095Annotating non-coding regions of the genome
Q30994950BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.
Q34557184Cell context dependent p53 genome-wide binding patterns and enrichment at repeats
Q34561899Centromere-like regions in the budding yeast genome
Q33625340ChIP on Chip: surprising results are often artifacts.
Q33718807ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites
Q33831056ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.
Q51417627ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation.
Q51083207ChIP-seq for the Identification of Functional Elements in the Human Genome.
Q28274448ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Q34012041Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Q29620707Charting histone modifications and the functional organization of mammalian genomes
Q21092435Chromatin landscape dictates HSF binding to target DNA elements
Q36021697Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb
Q33760102Chromatin tandem affinity purification sequencing.
Q30632661Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods.
Q33680184Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution
Q38367824Computational methodology for ChIP-seq analysis
Q47659265Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments
Q35176962DNA methylation status predicts cell type-specific enhancer activity.
Q30625844DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data
Q38807143Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes
Q35621311Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7
Q33967929Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data
Q33847769Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches
Q39321147Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells
Q98945954Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
Q47657203Enzymatic methods for genome-wide profiling of protein binding sites
Q38880734Epigenetic regulation of bone cells
Q40064881Epigenomic annotation of gene regulatory alterations during evolution of the primate brain.
Q35557622Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.
Q37606899Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression
Q21136324Evaluation of algorithm performance in ChIP-seq peak detection
Q33613997Expanded roles of the origin recognition complex in the architecture and function of silenced chromatin in Saccharomyces cerevisiae
Q33823781Extensive variation in chromatin states across humans
Q33631902Genome-wide analysis of histone modifications in human endometrial stromal cells.
Q34215626Genome-wide localization of replication factors
Q34774432Genome-wide profiling of human cap-independent translation-enhancing elements
Q47260307Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes
Q42575672Genomic approaches for the discovery of CFTR regulatory elements
Q41954335Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
Q24628039Genomic views of STAT function in CD4+ T helper cell differentiation
Q35248894Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.
Q29617800Global epigenomic reconfiguration during mammalian brain development
Q34393141H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
Q34729636High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
Q38258264High-resolution digital profiling of the epigenome
Q37593221High-resolution mapping of transcription factor binding sites on native chromatin
Q26823498High-throughput sequencing for biology and medicine
Q33624069Histone modification levels are predictive for gene expression
Q37508182Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays
Q30830996Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
Q39216883Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks
Q92874900JNK1 Induces Notch1 Expression to Regulate Genes Governing Photoreceptor Production
Q30717456Large-scale quality analysis of published ChIP-seq data
Q47861305Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism
Q34484579Limitations and possibilities of low cell number ChIP-seq.
Q21090170MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes
Q38654086Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.
Q37142704Mapping yeast transcriptional networks
Q35860593Metastases suppressor NME2 associates with telomere ends and telomerase and reduces telomerase activity within cells.
Q38166839Modulation of epigenetic regulators and cell fate decisions by miRNAs
Q21090180Most "dark matter" transcripts are associated with known genes
Q33575022Most transcription factor binding sites are in a few mosaic classes of the human genome
Q30826166Motif-based analysis of large nucleotide data sets using MEME-ChIP.
Q38150711Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer
Q34075399Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations
Q42546270Non-canonical protein-DNA interactions identified by ChIP are not artifacts.
Q30440990Non-random DNA fragmentation in next-generation sequencing.
Q34193463Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Q36280311NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data
Q92560338PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription
Q89453270Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells
Q30559360Predictive models of gene regulation from high-throughput epigenomics data
Q33699592Processing and analyzing ChIP-seq data: from short reads to regulatory interactions
Q49790105Proliferation of regulatory DNA elements derived from transposable elements in the maize genome.
Q91833197Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin
Q28477071Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
Q33808041RNA-seq: impact of RNA degradation on transcript quantification
Q38775774Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
Q37696431Recent advances in understanding the molecular mechanisms regulating C. elegans transcription
Q96953990Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation
Q27026725Single molecule and single cell epigenomics.
Q89120341Single-Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility
Q33515789Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
Q38054155Surveying the epigenomic landscape, one base at a time
Q33925015Systematic bias in high-throughput sequencing data and its correction by BEADS.
Q52719687Targeted in situ genome-wide profiling with high efficiency for low cell numbers.
Q93088733The ENCODE Blacklist: Identification of Problematic Regions of the Genome
Q34045599The histone chaperone CAF-1 safeguards somatic cell identity
Q38659363The impact of epigenomic next-generation sequencing approaches on our understanding of neuropsychiatric disorders
Q35191305The intriguing complexities of mammalian gene regulation: how to link enhancers to regulated genes. Are we there yet?
Q34434467The maintenance of chromosome structure: positioning and functioning of SMC complexes.
Q35557755The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
Q33631415Tissue-Specific Expression of Estrogen Receptor 1 Is Regulated by DNA Methylation in a T-DMR.
Q30648765Uniform, optimal signal processing of mapped deep-sequencing data
Q90477312Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data
Q38427027Unraveling the 3D genome: genomics tools for multiscale exploration
Q34947016Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
Q35071005Widespread misinterpretable ChIP-seq bias in yeast
Q37342854Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome.
Q33970447ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

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