Comparative analysis of regulatory information and circuits across distant species (Q34435561)

2 August 2017

Comparative analysis of regulatory information and circuits across distant species (English)

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2 August 2017

31

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37

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2 August 2017

Carlos L Araya

2

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Alan P. Boyle

Alan P Boyle

1

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Anshul Kundaje

Anshul Kundaje

14

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Joel Rozowsky

Joel Rozowsky

19

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Jingyi Jessica Li

Jingyi Jessica Li

15

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Steven E. Brenner

34

Steven E Brenner

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2 August 2017

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Manolis Kellis

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Valerie Reinke

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Michael Snyder

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LaDeana W Hillier

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Robert H Waterston

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Pouya Kheradpour

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2 August 2017

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Philip Cayting

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Matthew Slattery

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Rebecca Spokony

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E Jay Rehm

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Peter J Bickel

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Koon-Kiu Yan

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2 August 2017

9

Judith Janette

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2 August 2017

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Dionne Vafeados

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2 August 2017

Cathleen Brdlik

3

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2 August 2017

Chao Cheng

5

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2 August 2017

Yong Cheng

6

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Kathryn Gardner

7

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Lixia Jiang

10

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2 August 2017

Dionna Kasper

11

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2 August 2017

Trupti Kawli

12

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2 August 2017

Lijia Ma

16

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2 August 2017

Wei Niu

17

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2 August 2017

Robert Terrell

22

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Daifeng Wang

24

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2 August 2017

Peter Weisdepp

25

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2 August 2017

Yi-Chieh Wu

26

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2 August 2017

Dan Xie

27

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Elise A Feingold

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Peter J Good

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Haiyan Huang

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Kevin P White

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language of work or name

English

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publication date

1 August 2014

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2 August 2017

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2 August 2017

512

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7515

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2 August 2017

453-456

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https://scigraph.springernature.com/pub.10.1038/nature13668

2 August 2017

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cites work

Dynamic trans-acting factor colocalization in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated 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=4336544

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor 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=4336544

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

An integrated encyclopedia of DNA elements 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=4336544

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related 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=4336544

Transcription factors: from enhancer binding to developmental control

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

A cis-regulatory map of 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=4336544

Evolution of gene regulatory networks controlling body plan 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=4336544

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Identification of functional elements and regulatory circuits by Drosophila modENCODE

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Comparative epigenomic analysis of murine and human adipogenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Evolutionary tinkering with conserved components of a transcriptional regulatory network

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Divergence of transcription factor binding sites across related yeast species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Network motifs: theory and experimental approaches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Transcriptional repression by REST: recruitment of Sin3A and histone deacetylase to neuronal 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=4336544

Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional 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=4336544

Evolution at two levels in humans and chimpanzees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336544

Comparative analysis of the transcriptome across distant species

27 October 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Model-based analysis of ChIP-Seq (MACS)

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

TreeFix: statistically informed gene tree error correction using species trees

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Unified modeling of gene duplication, loss, and coalescence using a locus tree

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Identification of novel transcripts in annotated genomes using RNA-Seq

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

High-resolution mapping and characterization of open chromatin across the genome

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

An effective statistical evaluation of ChIPseq dataset similarity

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13668

7 January 2021

Identifiers

DOI

10.1038/NATURE13668

1 reference

journals/nature/BoyleABCCCGHJJK14

2 August 2017

1 reference

DBLP Dataset 2021-01-02

release_5qulg5q425ahlbv5qs2i6cfnti

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5qulg5q425ahlbv5qs2i6cfnti

24 November 2022

mapped directly with Wikidata item

PMCID

4336544

1 reference

2 August 2017

1 reference