Predicting the human epigenome from DNA motifs (Q34439703)

2 August 2017

title

Predicting the human epigenome from DNA motifs (English)

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2 August 2017

1

John W Whitaker

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2 August 2017

3

Wei Wang

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2 August 2017

Zhao Chen

2

1 reference

2 August 2017

publication date

21 September 2014

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2 August 2017

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2 August 2017

volume

12

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2 August 2017

issue

3

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2 August 2017

page(s)

265-72, 7 p following 272

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Identification of genetic variants that affect histone modifications in human cells

2 August 2017

cites work

1 reference

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Extensive variation in chromatin states across humans

6 July 2018

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Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription

6 July 2018

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Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters

6 July 2018

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Epigenomic analysis of multilineage differentiation of human embryonic stem cells

6 July 2018

1 reference

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Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Emerging roles for chromatin as a signal integration and storage platform

6 July 2018

1 reference

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Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Determinants of nucleosome positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

6 July 2018

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Braveheart, a long noncoding RNA required for cardiovascular lineage commitment

6 July 2018

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DNA-binding specificities of human 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=4344378

RNA-guided human genome engineering via Cas9

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Sequence features and chromatin structure around the genomic regions bound by 119 human 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=4344378

Functional analysis of transcription factor binding sites in human 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=4344378

Dynamics and memory of heterochromatin in living 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=4344378

Genome regulation by long noncoding RNAs.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Spatial partitioning of the regulatory landscape of the X-inactivation centre

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Topological domains in mammalian genomes identified by analysis of chromatin 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=4344378

Linking genome to epigenome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Summarizing and correcting the GC content bias in high-throughput 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=4344378

The Hippo pathway in organ size control, tissue regeneration and stem cell self-renewal

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Systematic bias in high-throughput sequencing data and its correction by BEADS.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

The nuclear orphan receptor Nr4a2 induces Foxp3 and regulates differentiation of CD4+ T 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=4344378

A TALE nuclease architecture for efficient genome editing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

GC-rich sequence elements recruit PRC2 in mammalian ES 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=4344378

Histone H3K27ac separates active from poised enhancers and predicts developmental state

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Regularization Paths for Generalized Linear Models via Coordinate Descent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Nucleosome sequence preferences influence in vivo nucleosome organization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Long noncoding RNA as modular scaffold of histone modification complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Origins of specificity in protein-DNA recognition.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Nucleosome dynamics define transcriptional 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=4344378

Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast 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=4344378

PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Herding Hippos: regulating growth in flies and man.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Loss of YY1 impacts the heterochromatic state and meiotic double-strand breaks during mouse spermatogenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Histone modifications at human enhancers reflect global cell-type-specific 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=4344378

Poly(dA:dT) tracts: major determinants of nucleosome organization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

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=4344378

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Genomic sequence is highly predictive of local nucleosome depletion

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Predicting gene expression from sequence: a reexamination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Chromatin modifications and their function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

A genomic code for nucleosome positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

SOX2 functions to maintain neural progenitor identity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Structure and function of Nurr1 identifies a class of ligand-independent nuclear receptors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Coordinated histone modifications mediated by a CtBP co-repressor 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=4344378

Subnuclear targeting of Runx/Cbfa/AML factors is essential for tissue-specific differentiation during embryonic 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=4344378

Close encounters of many kinds: Fos-Jun interactions that mediate transcription regulatory specificity.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Induction of AP-2alpha expression by adenoviral infection involves inactivation of the AP-2rep transcriptional corepressor CtBP1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

GATA-5: a transcriptional activator expressed in a novel temporally and spatially-restricted pattern during embryonic 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=4344378

Transcription enhancer factor-1 (TEF-1) DNA binding sites can specifically enhance gene expression at the beginning of mouse 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=4344378

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

6 July 2018

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Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

21 January 2018

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The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution.

21 January 2018

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The transcription factor c-Maf controls the production of interleukin-4 but not other Th2 cytokines

21 January 2018

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STAR: an integrated solution to management and visualization of sequencing data

21 January 2018

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Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

21 January 2018

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The UCSC Genome Browser database: 2014 update

21 January 2018

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RefSeq: an update on mammalian reference sequences

21 January 2018

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BEDTools: a flexible suite of utilities for comparing genomic features

21 January 2018

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The uniqueome: a mappability resource for short-tag sequencing

21 January 2018

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DREME: motif discovery in transcription factor ChIP-seq data

21 January 2018

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Transcriptional regulatory code of a eukaryotic genome

21 January 2018

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Quantifying similarity between motifs

21 January 2018

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21 January 2018

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TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 January 2018

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JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

21 January 2018

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UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

21 January 2018

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hPDI: a database of experimental human protein-DNA interactions

21 January 2018

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Hierarchical Grouping to Optimize an Objective Function

21 January 2018

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DNA-binding factors shape the mouse methylome at distal regulatory regions

21 January 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Predicting gene expression from sequence

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

Regulation of gene expression at the beginning of mammalian development and the TEAD family of transcription factors

27 October 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4344378

TEA regulates local TCR-Jalpha accessibility through histone acetylation

27 October 2018

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12 December 2020

A preoccupied position on nucleosomes

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12 December 2020

Rewriting the Epigenome

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12 December 2020

A transcription factor–based mechanism for mouse heterochromatin formation

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12 December 2020

The WEKA data mining software: an update

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7 January 2021

inferred from DOI database lookup

Amylases in the Human Vagina

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3065

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NMETH.3065

1 reference

Dimensions Publication ID

2 August 2017

1029002309

0 references

Fatcat ID

release_6tnzbhotdjcrdmz6mkisl4gas4

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/6tnzbhotdjcrdmz6mkisl4gas4

24 November 2022

mapped directly with Wikidata item

PMC publication ID

4344378

1 reference

2 August 2017

1 reference