(Q33505840)

27 July 2017

title

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters (English)

1 reference

Vladimir Espinosa Angarica

27 July 2017

author

Vladimir Espinosa Angarica

2

0 references

Julio Collado-Vides

Julio Collado-Vides

3

0 references

Ana Tereza R Vasconcelos

Ana Tereza Ribeiro Vasconcelos

4

1 reference

https://orcid.org/0000-0002-4632-2086

Abel Gonzalez-Perez

1

Abel González Pérez

1 reference

27 July 2017

language of work or name

1 reference

22 September 2009

1 reference

27 July 2017

published in

BMC Molecular Biology

1 reference

27 July 2017

volume

10

1 reference

27 July 2017

page(s)

92

1 reference

Prediction of TF target sites based on atomistic models of protein-DNA complexes

27 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Transcription factor dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Correlation between binding rate constants and individual information of E. coli Fis binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Energetics of protein-DNA interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Bacterial transcriptional regulators for degradation pathways of aromatic compounds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

On schemes of combinatorial transcription logic

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Bacterial RNA polymerases: the wholo story

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Views of transcription initiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

DNA binding sites: representation and discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Identifying DNA and protein patterns with statistically significant alignments of multiple 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=2761915

Repression of transcription initiation in bacteria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

RNA polymerase-promoter interactions: the comings and goings of RNA polymerase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Quantitative specificity of the Mnt repressor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Identification of consensus patterns in unaligned DNA sequences known to be functionally related.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Control site location and transcriptional regulation in Escherichia 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=2761915

Tetramerization of the LexA repressor in solution: implications for gene regulation of the E.coli SOS system at acidic pH.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Evolutionary dynamics of prokaryotic transcriptional regulatory networks

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Genomic position analyses and the transcription machinery.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight Gamma-proteobacterial Genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

Common History at the Origin of the Position-Function Correlation in Transcriptional Regulators in Archaea and Bacteria

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2761915

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

31 October 2018

1 reference

12 December 2020

Information content and free energy in DNA--protein interactions

1 reference

12 December 2020

Sequence-dependent kinetic model for transcription elongation by RNA polymerase

1 reference

12 December 2020

A kinetic model of transcription initiation by RNA polymerase

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2199-10-92

1 reference

Dimensions Publication ID

27 July 2017

0 references

1 reference

27 July 2017

1 reference