(Q36228906)

12 August 2017

title

DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter (English)

1 reference

12 August 2017

Bryan Quach

1

0 references

Terrence S. Furey

object named as

Terrence S Furey

series ordinal

2

0 references

language of work or name

English

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publication date

19 December 2016

1 reference

12 August 2017

1 reference

12 August 2017

volume

33

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12 August 2017

issue

7

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12 August 2017

page(s)

956-963

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Analysis of computational footprinting methods for DNase sequencing experiments

12 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

DNase footprint signatures are dictated by factor dynamics and DNA sequence

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Protein-DNA binding: complexities and multi-protein codes

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Using DNase digestion data to accurately identify transcription factor binding sites

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

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An expansive human regulatory lexicon encoded in transcription factor footprints

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Epigenetic priors for identifying active transcription factor binding sites

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

22 September 2018

1 reference

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Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

22 September 2018

1 reference

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FIMO: scanning for occurrences of a given motif

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Altering the chromatin landscape for nucleotide excision repair

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

Genome-wide mapping of in vivo protein-DNA interactions

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

ROCR: visualizing classifier performance in R

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

The ENCODE (ENCyclopedia Of DNA Elements) Project

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6075477

A training algorithm for optimal margin classifiers

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW740

Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW740

10.1093/BIOINFORMATICS/BTW740

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/QuachF17

12 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

6075477

0 references

1 reference