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

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6 June 2020

Julia Polansky

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Peter Ebert

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Karl Nordström

8

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Benedikt Brors

19

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Jan G Hengstler

21

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Thomas Lengauer

23

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Philip Rosenstiel

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5

Cristina Cadenas

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25

Jörn Walter

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author name string

Nina Gasparoni

2

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Gilles Gasparoni

3

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Kathrin Gianmoena

4

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Matthias Barann

9

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Anupam Sinha

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Sebastian Fröhler

11

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Jieyi Xiong

12

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Azim Dehghani Amirabad

13

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Fatemeh Behjati Ardakani

14

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Barbara Hutter

15

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Gideon Zipprich

16

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Bärbel Felder

17

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Jürgen Eils

18

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Wei Chen

20

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Marcel H Schulz

26

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Alf Hamann

22

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6 June 2020

language of work or name

English

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publication date

29 November 2016

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21 August 2017

Nucleic Acids Research

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6 June 2020

volume

45

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6 June 2020

issue

1

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6 June 2020

page(s)

54-66

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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

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

21 June 2018

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21 June 2018

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21 June 2018

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

21 June 2018

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

21 June 2018

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

21 June 2018

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21 June 2018

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21 June 2018

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

21 June 2018

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Using DNase digestion data to accurately identify transcription factor binding sites

21 June 2018

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

21 June 2018

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

21 June 2018

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An expansive human regulatory lexicon encoded in transcription factor footprints

21 June 2018

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21 June 2018

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

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

21 June 2018

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21 June 2018

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

21 June 2018

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

21 June 2018

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

21 June 2018

1 reference

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Regularization Paths for Generalized Linear Models via Coordinate Descent

21 June 2018

1 reference

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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

Analysis of computational footprinting methods for DNase sequencing experiments

21 January 2018

1 reference

Telomere shortening and telomere position effect in mild ring 17 syndrome

21 January 2018

1 reference

Predicting transcription factor affinities to DNA from a biophysical model

21 January 2018

1 reference

An integrated encyclopedia of DNA elements in the human genome

21 January 2018

1 reference

JAMM: a peak finder for joint analysis of NGS replicates

21 January 2018

1 reference

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

21 January 2018

1 reference

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 AND SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

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

6 June 2020

PubMed publication ID

27899623

1 reference