(Q31145466)

21 August 2017

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction (English)

1 reference

21 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Julia Polansky

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Peter Ebert

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Karl Nordström

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Benedikt Brors

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Jan G Hengstler

21

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Thomas Lengauer

23

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Philip Rosenstiel

24

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

5

Cristina Cadenas

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

25

Jörn Walter

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

author name string

Nina Gasparoni

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Gilles Gasparoni

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Kathrin Gianmoena

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Matthias Barann

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Anupam Sinha

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Sebastian Fröhler

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Jieyi Xiong

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Azim Dehghani Amirabad

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Fatemeh Behjati Ardakani

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Barbara Hutter

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Gideon Zipprich

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Bärbel Felder

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Jürgen Eils

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Wei Chen

20

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Marcel H Schulz

26

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Alf Hamann

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

language of work or name

English

0 references

publication date

29 November 2016

1 reference

21 August 2017

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

volume

45

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

page(s)

54-66

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

6 June 2020

copyright license

start time

29 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Integrative analysis of 111 reference human epigenomes

21 June 2018

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ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

21 June 2018

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Low affinity binding site clusters confer hox specificity and regulatory robustness.

21 June 2018

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A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

21 June 2018

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Predicting expression: the complementary power of histone modification and transcription factor binding data.

21 June 2018

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UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions

21 June 2018

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Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

21 June 2018

1 reference

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DNase footprint signatures are dictated by factor dynamics and DNA sequence

21 June 2018

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Predictive modelling of gene expression from transcriptional regulatory elements.

21 June 2018

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Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications

21 June 2018

1 reference

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Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

21 June 2018

1 reference

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Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

21 June 2018

1 reference

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Target analysis by integration of transcriptome and ChIP-seq data with BETA.

21 June 2018

1 reference

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Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

21 June 2018

1 reference

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Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme

21 June 2018

1 reference

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CTCF: the protein, the binding partners, the binding sites and their chromatin loops

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Using DNase digestion data to accurately identify transcription factor binding sites

21 June 2018

1 reference

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Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

21 June 2018

1 reference

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Predicting cell-type-specific gene expression from regions of open chromatin

21 June 2018

1 reference

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An expansive human regulatory lexicon encoded in transcription factor footprints

21 June 2018

1 reference

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Genome-wide in silico prediction of gene expression.

21 June 2018

1 reference

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Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

21 June 2018

1 reference

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Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

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Epigenetic priors for identifying active transcription factor binding sites

21 June 2018

1 reference

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Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

21 June 2018

1 reference

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Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

21 June 2018

1 reference

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FIMO: scanning for occurrences of a given motif

21 June 2018

1 reference

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

21 June 2018

1 reference

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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

21 June 2018

1 reference

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Regularization Paths for Generalized Linear Models via Coordinate Descent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

BEDTools: a flexible suite of utilities for comparing genomic features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Genome-wide prediction of transcription factor binding sites using an integrated model.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Predictive chromatin signatures in the mammalian genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

TopHat: discovering splice junctions with RNA-Seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

PASTAA: identifying transcription factors associated with sets of co-regulated genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

The zinc finger transcription factor Zbtb7b represses CD8-lineage gene expression in peripheral CD4+ T cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

The molecular basis of eukaryotic transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Extensive low-affinity transcriptional interactions in the yeast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Liver-specific inactivation of the Nrf1 gene in adult mouse leads to nonalcoholic steatohepatitis and hepatic neoplasia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

The Ets-1 transcription factor is required for complete pre-T cell receptor function and allelic exclusion at the T cell receptor beta locus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Transcription factors in liver development, differentiation, and regeneration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

Peroxisome proliferator-activated receptors, coactivators, and downstream targets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5224477

BLUEPRINT to decode the epigenetic signature written in blood.

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

Analysis of computational footprinting methods for DNase sequencing experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

Telomere shortening and telomere position effect in mild ring 17 syndrome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

Predicting transcription factor affinities to DNA from a biophysical model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

An integrated encyclopedia of DNA elements in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

JAMM: a peak finder for joint analysis of NGS replicates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

IL-12 inhibits glucocorticoid-induced T cell apoptosis by inducing GMEB1 and activating PI3K/Akt pathway.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1061

Roles of CCAAT/enhancer-binding proteins in regulation of liver regenerative growth

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27899623

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

CTCF-binding sites within the H19 ICR differentially regulate local chromatin structures and cis-acting functions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27899623

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKW1061

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899623%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

PubMed publication ID

27899623

1 reference