BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors (Q33512623)

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English	BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors	scientific article

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scholarly article

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Europe PubMed Central

PubMed publication ID

27 July 2017

BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors (English)

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Europe PubMed Central

PubMed publication ID

27 July 2017

author name string

Junbai Wang

1

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Europe PubMed Central

PubMed publication ID

27 July 2017

Morigen

2

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Europe PubMed Central

PubMed publication ID

27 July 2017

publication date

20 October 2009

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Europe PubMed Central

PubMed publication ID

27 July 2017

BMC Bioinformatics

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Europe PubMed Central

PubMed publication ID

27 July 2017

10

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Europe PubMed Central

PubMed publication ID

27 July 2017

345

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Europe PubMed Central

PubMed publication ID

27 July 2017

copyright license

Creative Commons Attribution 2.0 Generic

20 October 2009

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April 2022 Public Data File from Crossref

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April 2022 Public Data File from Crossref

describes a project that uses

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Europe PubMed Central

18 June 2022

https://europepmc.org/article/PMC/2771022

based on heuristic

inferred from PubMed Central ID database lookup

Computational biology of genome expression and regulation--a review of microarray bioinformatics

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Extracting sequence features to predict protein-DNA interactions: a comparative study

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Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

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CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data

1 reference

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21 June 2018

Nucleosome organization in the Drosophila genome.

1 reference

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21 June 2018

Discovering gapped binding sites of yeast transcription factors

1 reference

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A nucleosome-guided map of transcription factor binding sites in yeast

1 reference

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21 June 2018

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors

1 reference

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21 June 2018

A high-resolution atlas of nucleosome occupancy in yeast

1 reference

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21 June 2018

Divergence of transcription factor binding sites across related yeast species

1 reference

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21 June 2018

Predictive models of gene regulation: application of regression methods to microarray data

1 reference

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21 June 2018

Precise physical models of protein-DNA interaction from high-throughput data

1 reference

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Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

1 reference

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21 June 2018

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

1 reference

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21 June 2018

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

1 reference

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21 June 2018

Extensive low-affinity transcriptional interactions in the yeast genome

1 reference

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Adaptively inferring human transcriptional subnetworks

1 reference

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21 June 2018

Method for identifying transcription factor binding sites in yeast

1 reference

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Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae

1 reference

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Global nucleosome occupancy in yeast

1 reference

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1 reference

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1 reference

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ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

1 reference

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A biophysical approach to transcription factor binding site discovery

1 reference

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Global analysis of protein expression in yeast

1 reference

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Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae

1 reference

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Getting into chromatin: how do transcription factors get past the histones?

1 reference

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Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

1 reference

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

1 reference

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21 June 2018

Physical constraints and functional characteristics of transcription factor-DNA interaction.

1 reference

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

1 reference

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

1 reference

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Regulatory element detection using correlation with expression.

1 reference

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H2O2 sensing through oxidation of the Yap1 transcription factor

1 reference

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Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling

1 reference

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The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress

1 reference

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Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene

1 reference

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21 June 2018

TRANSFAC: an integrated system for gene expression regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

21 June 2018

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1 reference

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1 reference

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21 June 2018

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1 reference

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21 June 2018

SGD: Saccharomyces Genome Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

21 June 2018

Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

21 June 2018

Quantitative specificity of the Mnt repressor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

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1 reference

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21 June 2018

Multiple elements and auto-repression regulate Rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

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1 reference

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Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae.

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31 October 2018

Nucleotide variation of regulatory motifs may lead to distinct expression patterns

1 reference

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31 October 2018

High-throughput mapping of the chromatin structure of human promoters.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

31 October 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771022

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Evolution of alternative transcriptional circuits with identical logic

1 reference

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Evidence for nucleosome depletion at active regulatory regions genome-wide

1 reference

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On the selection and evolution of regulatory DNA motifs

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Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast.

1 reference

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1 reference

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12 December 2020

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inferred from PubMed ID database lookup

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10.1186/1471-2105-10-345

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Europe PubMed Central

PubMed publication ID

27 July 2017

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journals/bmcbi/WangM09

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DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

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PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 July 2017

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