Stochastic sequence-level model of coupled transcription and translation in prokaryotes (Q33882325)

29 July 2017

title

Stochastic sequence-level model of coupled transcription and translation in prokaryotes (English)

1 reference

29 July 2017

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3

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Jason Lloyd-Price

object named as

Jason Lloyd-Price

series ordinal

2

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Andre S Ribeiro

object named as

Andre S Ribeiro

series ordinal

4

1 reference

ORCID Public Data File 2021

author name string

Jarno Mäkelä

series ordinal

1

1 reference

29 July 2017

publication date

26 April 2011

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29 July 2017

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29 July 2017

volume

12

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29 July 2017

page(s)

121

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Bacterial charity work leads to population-wide resistance

29 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=3113936

All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Cooperation between translating ribosomes and RNA polymerase in transcription elongation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

A NusE:NusG complex links transcription and translation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Effects of transcriptional pausing on gene expression dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Stochastic and delayed stochastic models of gene expression and regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Transcriptional pausing without backtracking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Ribosomal translocation: one step closer to the molecular mechanism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

A stochastic single-molecule event triggers phenotype switching of a bacterial cell

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Single-molecule approach to molecular biology in living bacterial cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Biology of trans-translation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Following translation by single ribosomes one codon at a time.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Monitoring RNA transcription in real time by using surface plasmon resonance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Combinatorial promoter design for engineering noisy gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

SGN Sim, a stochastic genetic networks simulator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

A general modeling strategy for gene regulatory networks with stochastic dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

The regulatory roles and mechanism of transcriptional pausing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Sequence-resolved detection of pausing by single RNA polymerase molecules.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Real-time kinetics of gene activity in individual bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Stochasticity in gene expression: from theories to phenotypes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Thinking quantitatively about transcriptional regulation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Promoter clearance and escape in prokaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

FACS-optimized mutants of the green fluorescent protein (GFP)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Rate-limiting steps in RNA chain initiation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Processivity errors of gene expression in Escherichia coli.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Interdependence of translation, transcription and mRNA degradation in the lacZ gene

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Peptidyl transfer RNA dissociates during protein synthesis from ribosomes of Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Effects of molecular memory and bursting on fluctuations in gene expression.

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Stochastic switching as a survival strategy in fluctuating environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Probing gene expression in live cells, one protein molecule at a time.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Cooperation between RNA polymerase molecules in transcription elongation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-121

Effects of the promoter open complex formation on gene expression dynamics.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Fluctuations, pauses, and backtracking in DNA transcription

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113936

Codon usage determines translation rate in Escherichia coli

29 October 2018

1 reference

12 December 2020

Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription

1 reference

12 December 2020

Delayed stochastic model of transcription at the single nucleotide level

1 reference

12 December 2020

Dynamical effects of transcriptional pause-prone sites

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-12-121

1 reference

journals/bmcbi/MakelaLYR11

29 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

29 July 2017

1 reference