(Q30481296)

14 October 2017

TABASCO: A single molecule, base-pair resolved gene expression simulator (English)

1 reference

14 October 2017

1

1 reference

14 October 2017

Jason R Kelly

2

1 reference

14 October 2017

19 December 2007

1 reference

14 October 2017

1 reference

14 October 2017

8

1 reference

14 October 2017

480

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-8-480

14 October 2017

0 references

cites work

Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Probing transcription factor dynamics at the single-molecule level in a living cell

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Stochastic simulation of chemical kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Single-molecule analysis of RNA polymerase transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Efficient step size selection for the tau-leaping simulation method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Delay-induced stochastic oscillations in gene regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

The meaning of systems biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Automatic generation of cellular reaction networks with Moleculizer 1.0.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Promoter clearance and escape in prokaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Stochastic mechanisms in gene expression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

RNA polymerase-dependent mechanism for the stepwise T7 phage DNA transport from the virion into E. coli.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Regulation of transcription from tandem and convergent promoters.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Promoter occlusion: Transcription through a promoter may inhibit its activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Optimal design of feedback control by inhibition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Computer simulation of T3/T7 phage infection using lag times.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Facilitated target location in biological systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Optimal design of feedback control by inhibition: dynamic considerations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Deviant effects in molecular reaction pathways.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Stochastic kinetics description of a simple transcription model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced "bumping".

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Gene expression time delays and Turing pattern formation systems.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Cooperation between RNA polymerase molecules in transcription elongation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

An integrated model of the transcription complex in elongation, termination, and editing

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

Predicting temporal fluctuations in an intracellular signalling pathway.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242808

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

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18093293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Organization and expression of bacteriophage T7 DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18093293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dizzy: stochastic simulation of large-scale genetic regulatory networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18093293

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-8-480

1 reference

journals/bmcbi/KosuriKE07

14 October 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

14 October 2017

1 reference

PMCID

2242808