(Q33700661)

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Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

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scholarly article

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Europe PubMed Central

28 July 2017

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression (English)

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Europe PubMed Central

28 July 2017

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4

object named as

Saurabh Sinha

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Europe PubMed Central

28 July 2017

1

object named as

Xin He

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Europe PubMed Central

28 July 2017

author name string

Md Abul Hassan Samee

2

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Europe PubMed Central

28 July 2017

Charles Blatti

3

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Europe PubMed Central

28 July 2017

publication date

16 September 2010

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Europe PubMed Central

28 July 2017

PLOS Computational Biology

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Europe PubMed Central

28 July 2017

6

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Europe PubMed Central

28 July 2017

9

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Europe PubMed Central

28 July 2017

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Creative Commons Attribution 4.0 International

16 September 2010

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April 2022 Public Data File from Crossref

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Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers

1 reference

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21 June 2018

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Combinatorial binding predicts spatio-temporal cis-regulatory activity

1 reference

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21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Modeling the quantitative specificity of DNA-binding proteins from example binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Optimizing static thermodynamic models of transcriptional regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Single-RNA counting reveals alternative modes of gene expression in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Dynamical analysis on gene activity in the presence of repressors and an interfering promoter

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Divergence of transcription factor binding sites across related yeast species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Enhancer responses to similarly distributed antagonistic gradients in development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Genetic reconstruction of a functional transcriptional regulatory network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Transcriptional regulation by competing transcription factor modules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Large-scale turnover of functional transcription factor binding sites in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Extensive low-affinity transcriptional interactions in the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Eukaryotic transcription activation: right on target

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

On schemes of combinatorial transcription logic

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Homotypic regulatory clusters in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

A sigmoidal transcriptional response: cooperativity, synergy and dosage effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Functional evolution of noncoding DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Global analysis of protein activities using proteome chips

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

dCtBP-dependent and -independent repression activities of the Drosophila Knirps protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Relief of gene repression by torso RTK signaling: role of capicua in Drosophila terminal and dorsoventral patterning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Cooperative DNA-binding by Bicoid provides a mechanism for threshold-dependent gene activation in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Specificity, free energy and information content in protein-DNA interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

The enhanceosome and transcriptional synergy.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Transcriptional repression in development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Multiple TAFIIs directing synergistic activation of transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Synergistic activation of transcription by Escherichia coli cAMP receptor protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Competition for overlapping sites in the regulatory region of the Drosophila gene Krüppel.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

21 June 2018

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Control of transcription by Krüppel through interactions with TFIIB and TFIIE beta.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Predicting gene expression from sequence.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

A general mechanism for transcriptional synergy by eukaryotic activators

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Short-range repression permits multiple enhancers to function autonomously within a complex promoter

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

hairy stripe 7 element mediates activation and repression in response to different domains and levels of Krüppel in the Drosophila embryo.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

Identification of a Stat gene that functions in Drosophila development.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000935

21 January 2018

A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm

1 reference

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21 January 2018

Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

30 October 2018

The Drosophila morphogenetic protein Bicoid binds DNA cooperatively.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940721

30 October 2018

Gene regulation. A paradigm for precision

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/20862354

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PCBI.1000935

1 reference

Europe PubMed Central

28 July 2017

DBLP publication ID

journals/ploscb/HeSBS10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

Europe PubMed Central

28 July 2017

1 reference

Europe PubMed Central

28 July 2017

ResearchGate publication ID

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