The next generation of transcription factor binding site prediction (Q34987978)

5 August 2017

The next generation of transcription factor binding site prediction (English)

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5 August 2017

2

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Anthony Mathelier

object named as

Anthony Mathelier

series ordinal

1

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publication date

5 September 2013

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PLOS Computational Biology

5 August 2017

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5 August 2017

9

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5 August 2017

9

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5 August 2017

e1003214

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Creative Commons Attribution 4.0 International

5 August 2017

start time

5 September 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Evaluation of methods for modeling transcription factor sequence specificity

8 July 2018

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Sequence and chromatin determinants of cell-type-specific transcription factor binding

8 July 2018

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Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models

8 July 2018

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Improved models for transcription factor binding site identification using nonindependent interactions

8 July 2018

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Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.

8 July 2018

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A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology

8 July 2018

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Evaluation of algorithm performance in ChIP-seq peak detection

8 July 2018

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Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation

8 July 2018

1 reference

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix

8 July 2018

1 reference

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Variation in transcription factor binding among humans

8 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=3764009

Variable structure motifs for transcription factor binding sites

8 July 2018

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JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

8 July 2018

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An ensemble model of competitive multi-factor binding of the genome

8 July 2018

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OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif

8 July 2018

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8 July 2018

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Diversity and complexity in DNA recognition by transcription factors

8 July 2018

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The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes

8 July 2018

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8 July 2018

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Transcription factor binding sites are genetic determinants of retroviral integration in the human genome

8 July 2018

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Discovery of novel tumor suppressor p53 response elements using information theory

8 July 2018

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Discovering sequence motifs with arbitrary insertions and deletions

8 July 2018

1 reference

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Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

8 July 2018

1 reference

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PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Divergence of transcription factor binding sites across related yeast species

8 July 2018

1 reference

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oPOSSUM: integrated tools for analysis of regulatory motif over-representation

8 July 2018

1 reference

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Genome-wide mapping of in vivo protein-DNA interactions

8 July 2018

1 reference

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A systems approach to measuring the binding energy landscapes of transcription factors

8 July 2018

1 reference

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Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

8 July 2018

1 reference

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A genomic code for nucleosome positioning

8 July 2018

1 reference

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Explicit equilibrium modeling of transcription-factor binding and gene regulation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Identification of transcription factor binding sites with variable-order Bayesian networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

The ENCODE (ENCyclopedia Of DNA Elements) Project

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Applied bioinformatics for the identification of regulatory elements

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

HMM Logos for visualization of protein families

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Additivity in protein-DNA interactions: how good an approximation is it?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

SAMIE: statistical algorithm for modeling interaction energies.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

DNA binding site selection of dimeric and tetrameric Stat5 proteins reveals a large repertoire of divergent tetrameric Stat5a binding sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Combining evidence using p-values: application to sequence homology searches

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Computer methods to locate signals in nucleic acid sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Search algorithm for pattern match analysis of nuleic add sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Sequence logos: a new way to display consensus sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3764009

Position dependencies in transcription factor binding sites.

8 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Modeling within-motif dependence for transcription factor binding site predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Prediction of nuclear hormone receptor response elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Individual Comparisons by Ranking Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Probabilistic code for DNA recognition by proteins of the EGR family.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

The Proof and Measurement of Association between Two Things

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Predicting transcription factor affinities to DNA from a biophysical model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003214

Improved detection of motifs with preferential location in promoters

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24039567

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003214

1 reference

journals/ploscb/MathelierW13

5 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

5 August 2017

1 reference

PubMed ID

24039567