Probabilistic inference of transcription factor binding from multiple data sources (Q31150555)

13 November 2017

Probabilistic inference of transcription factor binding from multiple data sources (English)

1 reference

13 November 2017

2

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13 November 2017

3

Ilya Shmulevich

1 reference

PMC publication ID

2268002

13 November 2017

language of work or name

English

0 references

publication date

26 March 2008

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13 November 2017

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13 November 2017

3

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13 November 2017

3

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13 November 2017

e1820

1 reference

Creative Commons Attribution 4.0 International

13 November 2017

start time

26 March 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Integrated assessment and prediction of transcription factor binding

21 June 2018

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Defining the sequence-recognition profile of DNA-binding molecules

21 June 2018

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Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

21 June 2018

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A regularized discriminative model for the prediction of protein-peptide interactions

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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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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21 June 2018

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Applied bioinformatics for the identification of regulatory elements

21 June 2018

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Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

21 June 2018

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Inferring cellular networks using probabilistic graphical models

21 June 2018

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Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites

21 June 2018

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JASPAR: an open-access database for eukaryotic transcription factor binding profiles

21 June 2018

1 reference

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Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Transcription regulation and animal diversity

21 June 2018

1 reference

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Sequencing and comparison of yeast species to identify genes and regulatory elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Transcriptional regulatory networks in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

The human genome browser at UCSC

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

TRANSCompel: a database on composite regulatory elements in eukaryotic 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=2268002

Detection of cis-element clusters in higher eukaryotic DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed 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=2268002

Genome-wide location and function of DNA binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

TRANSFAC: an integrated system for gene expression regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Modeling gene expression with differential equations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence 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=2268002

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Computer methods to locate signals in nucleic acid sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Finding motifs in promoter regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Modeling within-motif dependence for transcription factor binding site predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

A probabilistic method to detect regulatory modules

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Predicting gene expression from sequence

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Clustering of genes into regulons using integrated modeling-COGRIM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

An introduction to ROC analysis

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

Genome-wide discovery of transcriptional modules from DNA sequence and gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001820

The statistical significance of nucleotide position-weight matrix matches.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2268002

Fast probabilistic analysis of sequence function using scoring matrices

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18364997

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0001820

1 reference

13 November 2017

0 references

1 reference

PMC publication ID

2268002

13 November 2017

PubMed publication ID

18364997

1 reference

PMC publication ID

2268002