Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data (Q33967929)

30 July 2017

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data (English)

1 reference

30 July 2017

Dongjun Chung

1

0 references

Colin N Dewey

7

object named as

Colin Dewey

1 reference

30 July 2017

Pei Fen Kuan

2

1 reference

30 July 2017

Bo Li

3

1 reference

30 July 2017

Rajendran Sanalkumar

4

1 reference

30 July 2017

Kun Liang

5

1 reference

30 July 2017

Emery H Bresnick

6

1 reference

30 July 2017

Sündüz Keleş

8

1 reference

30 July 2017

14 July 2011

1 reference

PLOS Computational Biology

30 July 2017

1 reference

30 July 2017

7

1 reference

30 July 2017

7

1 reference

30 July 2017

e1002111

1 reference

Creative Commons Attribution 4.0 International

30 July 2017

start time

14 July 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy

5 July 2018

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Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

5 July 2018

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Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

5 July 2018

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The origins and impact of primate segmental duplications

5 July 2018

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BayesPeak: Bayesian analysis of ChIP-seq data

5 July 2018

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Mapping accessible chromatin regions using Sono-Seq

5 July 2018

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Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.

5 July 2018

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Extracting transcription factor targets from ChIP-Seq data

5 July 2018

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MEME SUITE: tools for motif discovery and searching

5 July 2018

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

5 July 2018

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

5 July 2018

1 reference

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The genomic architecture of segmental duplications and associated copy number variants in dogs

5 July 2018

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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

5 July 2018

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Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

5 July 2018

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

5 July 2018

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

5 July 2018

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Model-based analysis of ChIP-Seq (MACS)

5 July 2018

1 reference

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F-Seq: a feature density estimator for high-throughput sequence tags

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Evolution of the mammalian transcription factor binding repertoire via transposable elements

5 July 2018

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Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

5 July 2018

1 reference

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

5 July 2018

1 reference

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GeneTrack--a genomic data processing and visualization framework.

5 July 2018

1 reference

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Transposable elements and the evolution of regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

5 July 2018

1 reference

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Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.

5 July 2018

1 reference

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

5 July 2018

1 reference

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Genome-wide mapping of in vivo protein-DNA interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

High-resolution profiling of histone methylations in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Primate segmental duplications: crucibles of evolution, diversity and disease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Repbase Update, a database of eukaryotic repetitive elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Genome-scale identification of nucleosome positions in S. cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Bioconductor: open software development for computational biology and bioinformatics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Gene duplication: the genomic trade in spare parts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

DAVID: Database for Annotation, Visualization, and Integrated Discovery

5 July 2018

1 reference

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Segmental duplications: organization and impact within the current human genome project assembly

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Genome-wide location and function of DNA binding proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes

5 July 2018

1 reference

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Mapping global histone acetylation patterns to gene expression

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002111

Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen.

21 January 2018

1 reference

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002111

A new data structure for cumulative frequency tables

21 January 2018

1 reference

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002111

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3136429

10.1371/JOURNAL.PCBI.1002111

29 October 2018

Identifiers

DOI

1 reference

journals/ploscb/ChungKLSLBDK11

30 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

30 July 2017

1 reference