(Q34350059)

1 August 2017

title

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction (English)

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1 August 2017

2

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1 August 2017

James Galagan

7

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ORCID Public Data File 2021

author name string

Antonio L C Gomes

1

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1 August 2017

Matthew Peterson

3

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1 August 2017

Elham Azizi

4

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1 August 2017

Anna Lyubetskaya

5

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1 August 2017

Luís Carvalho

6

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1 August 2017

publication date

14 July 2014

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1 August 2017

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1 August 2017

volume

24

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1 August 2017

issue

10

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1 August 2017

page(s)

1686-1697

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dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data

1 August 2017

cites work

1 reference

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The Mycobacterium tuberculosis regulatory network and hypoxia

6 July 2018

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Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions.

6 July 2018

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ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

6 July 2018

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

6 July 2018

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High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

6 July 2018

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Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

6 July 2018

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Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

6 July 2018

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Comprehensive insights into Mycobacterium tuberculosis DevR (DosR) regulon activation switch.

6 July 2018

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PeakRanger: a cloud-enabled peak caller for ChIP-seq data

6 July 2018

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The 50th anniversary of the publication of the operon theory in the Journal of Molecular Biology: past, present and future

6 July 2018

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Genome-wide transcription factor binding: beyond direct target regulation

6 July 2018

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Identification of functional elements and regulatory circuits by Drosophila modENCODE

6 July 2018

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A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.

6 July 2018

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Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

6 July 2018

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Discovering homotypic binding events at high spatial resolution.

6 July 2018

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Determining the specificity of protein-DNA interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Evaluation of algorithm performance in ChIP-seq peak detection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Next-generation synthetic gene networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Inferring binding energies from selected binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Computation for ChIP-seq and RNA-seq studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

From DNA sequence to transcriptional behaviour: a quantitative approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

MEME SUITE: tools for motif discovery and searching

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

ChIP-seq accurately predicts tissue-specific activity of enhancers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

The DNA-encoded nucleosome organization of a eukaryotic genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Design and analysis of ChIP-seq experiments for DNA-binding proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

A quantitative model of transcription factor-activated gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Model-based analysis of ChIP-Seq (MACS)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Expression of the Mycobacterium tuberculosis acr-coregulated genes from the DevR (DosR) regulon is controlled by multiple levels of regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: implication in the induction of DevR target genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Genome-wide mapping of in vivo protein-DNA interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

High-resolution profiling of histone methylations in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

A systems approach to measuring the binding energy landscapes of transcription factors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Oxidative stress-activated zinc cluster protein Stb5 has dual activator/repressor functions required for pentose phosphate pathway regulation and NADPH production

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Insulators: exploiting transcriptional and epigenetic mechanisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Extensive low-affinity transcriptional interactions in the yeast genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Global changes in STAT target selection and transcription regulation upon interferon treatments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Switches in bacteriophage lambda development

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

The regulation of bacterial transcription initiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Three NF-kappa B binding sites in the human E-selectin gene required for maximal tumor necrosis factor alpha-induced expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

The Drosophila zeste protein binds cooperatively to sites in many gene regulatory regions: implications for transvection and gene regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

PICS: probabilistic inference for ChIP-seq.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

Computational models for neurogenic gene expression in the Drosophila embryo.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4199365

27 October 2018

Identifiers

DOI

10.1101/GR.161711.113

1 reference

1 August 2017

1 reference

1 August 2017

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