(Q34121728)

31 July 2017

title

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information (English)

1 reference

31 July 2017

Xiaotu Ma

1

1 reference

31 July 2017

Ashwinikumar Kulkarni

2

1 reference

31 July 2017

Zhihua Zhang

3

1 reference

31 July 2017

Zhenyu Xuan

4

1 reference

31 July 2017

Robert Serfling

5

1 reference

31 July 2017

Michael Q Zhang

6

1 reference

31 July 2017

language of work or name

English

0 references

publication date

6 January 2012

1 reference

31 July 2017

published in

Nucleic Acids Research

1 reference

31 July 2017

volume

40

1 reference

31 July 2017

issue

7

1 reference

31 July 2017

page(s)

e50

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

31 July 2017

copyright license

start time

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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DREME: motif discovery in transcription factor ChIP-seq data

28 July 2018

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De-novo discovery of differentially abundant transcription factor binding sites including their positional preference

28 July 2018

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Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Deep and wide digging for binding motifs in ChIP-Seq data.

28 July 2018

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CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

28 July 2018

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Evaluation of algorithm performance in ChIP-seq peak detection

28 July 2018

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MER41 repeat sequences contain inducible STAT1 binding sites

28 July 2018

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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

28 July 2018

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Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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

28 July 2018

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An integrated software system for analyzing ChIP-chip and ChIP-seq data

28 July 2018

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Model-based analysis of ChIP-Seq (MACS)

28 July 2018

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

28 July 2018

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Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

28 July 2018

1 reference

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Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

28 July 2018

1 reference

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Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets

28 July 2018

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Genome-wide mapping of in vivo protein-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Normal uniform mixture differential gene expression detection for cDNA microarrays

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Identifying tissue-selective transcription factor binding sites in vertebrate promoters

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Assessing computational tools for the discovery of transcription factor binding sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Finding motifs using random projections

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Localized motif discovery in gene regulatory sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

A census of human transcription factors: function, expression and evolution

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

High-resolution profiling of histone methylations in the human genome

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

MotifCut: regulatory motifs finding with maximum density subgraphs

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

DWE: discriminating word enumerator

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3326300

Finding composite regulatory patterns in DNA sequences

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22228832

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR1135

1 reference

31 July 2017

1 reference

31 July 2017

1 reference