(Q34017882)

30 July 2017

title

Tree-based position weight matrix approach to model transcription factor binding site profiles (English)

1 reference

30 July 2017

Yingtao Bi

1

1 reference

30 July 2017

Hyunsoo Kim

series ordinal

2

1 reference

30 July 2017

Ravi Gupta

series ordinal

3

1 reference

30 July 2017

Ramana V Davuluri

series ordinal

4

1 reference

30 July 2017

language of work or name

English

0 references

publication date

2 September 2011

1 reference

30 July 2017

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30 July 2017

volume

6

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30 July 2017

issue

9

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30 July 2017

page(s)

e24210

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Creative Commons Attribution 4.0 International

30 July 2017

copyright license

start time

2 September 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Deep and wide digging for binding motifs in ChIP-Seq data.

5 July 2018

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Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction

5 July 2018

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Analyzing 'omics data using hierarchical models

5 July 2018

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Variable structure motifs for transcription factor binding sites

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

5 July 2018

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DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

5 July 2018

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ChIP-seq: advantages and challenges of a maturing technology

5 July 2018

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Identifying regulatory elements in eukaryotic genomes

5 July 2018

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Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

5 July 2018

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A feature-based approach to modeling protein-DNA interactions

5 July 2018

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Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

5 July 2018

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The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

5 July 2018

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Eukaryotic transcription factor binding sites--modeling and integrative search methods

5 July 2018

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JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

5 July 2018

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Genome-wide mapping of in vivo protein-DNA interactions

5 July 2018

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High-resolution profiling of histone methylations in the human genome

5 July 2018

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A survey of motif discovery methods in an integrated framework

5 July 2018

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MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

5 July 2018

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Assessing computational tools for the discovery of transcription factor binding sites

5 July 2018

1 reference

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Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

5 July 2018

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5 July 2018

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A global view of the selection forces in the evolution of yeast cis-regulation

5 July 2018

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A non-parametric model for transcription factor binding sites

5 July 2018

1 reference

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An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

5 July 2018

1 reference

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Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

Repressor element silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) can act as an enhancer as well as a repressor of corticotropin-releasing hormone gene transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

5 July 2018

1 reference

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Prediction of complete gene structures in human genomic DNA

5 July 2018

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Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

Sequence logos: a new way to display consensus sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3166302

Combining frequency and positional information to predict transcription factor binding sites

5 July 2018

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DNA motif representation with nucleotide dependency.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Position dependencies in transcription factor binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Identifying transcription factor binding sites through Markov chain optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Finding short DNA motifs using permuted Markov models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Modeling within-motif dependence for transcription factor binding site predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Enhanced position weight matrices using mixture models

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

Context-specific independence mixture modeling for positional weight matrices

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0024210

10.1371/JOURNAL.PONE.0024210

21 January 2018

Identifiers

DOI

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference