(Q48232838)

9 February 2018

http://europepmc.org/abstract/MED/26901649

title

Analysis of computational footprinting methods for DNase sequencing experiments (English)

1 reference

9 February 2018

http://europepmc.org/abstract/MED/26901649

author

Eduardo G Gusmao

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

author name string

Manuel Allhoff

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Martin Zenke

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Ivan G Costa

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

publication date

22 February 2016

1 reference

9 February 2018

http://europepmc.org/abstract/MED/26901649

published in

Nature Methods

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

303-309

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/nmeth.3772

31 May 2020

exact match

0 references

cites work

An integrated encyclopedia of DNA elements in the human genome

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

An expansive human regulatory lexicon encoded in transcription factor footprints

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

DNase footprint signatures are dictated by factor dynamics and DNA sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Epigenetic priors for identifying active transcription factor binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Conservation of trans-acting circuitry during mammalian regulatory evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

ChIP-seq: advantages and challenges of a maturing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

The glucocorticoid receptor: rapid exchange with regulatory sites in living cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Heterodimerization with different Jun proteins controls c-Fos intranuclear dynamics and distribution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

A genome-wide map of CTCF multivalency redefines the CTCF code

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Probing DNA shape and methylation state on a genomic scale with DNase I.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Model-based analysis of ChIP-Seq (MACS)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Discovery of functional noncoding elements by digital analysis of chromatin structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

The Ensembl genome database project

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

FIMO: scanning for occurrences of a given motif

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

DNA binding sites: representation and discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Biopython: freely available Python tools for computational molecular biology and bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

MOODS: fast search for position weight matrix matches in DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

An introduction to ROC analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

limma powers differential expression analyses for RNA-sequencing and microarray studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

The difficulty of a fair comparison

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26901649

12 December 2020

inferred from PubMed ID database lookup

Estrogen-receptor-alpha exchange and chromatin dynamics are ligand- and domain-dependent

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26901649

12 December 2020

inferred from PubMed ID database lookup

The relationship between Precision-Recall and ROC curves

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

7 January 2021

inferred from DOI database lookup

Comments on the Savitzky-Golay convolution method for least-squares-fit smoothing and differentiation of digital data

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3772

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NMETH.3772

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json

release_3nzz6iy4wzdurdlu6er42zeh7q

31 May 2020

Fatcat ID

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26901649%20AND%20SRC:MED&resulttype=core&format=json