(Q33736281)

29 July 2017

title

CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models (English)

1 reference

29 July 2017

Hiroyuki Kurata

1

1 reference

29 July 2017

Kouichi Masaki

series ordinal

2

1 reference

29 July 2017

Yoshiyuki Sumida

series ordinal

3

1 reference

29 July 2017

Rei Iwasaki

series ordinal

4

1 reference

29 July 2017

publication date

1 April 2005

1 reference

29 July 2017

1 reference

29 July 2017

volume

15

1 reference

29 July 2017

issue

4

1 reference

29 July 2017

page(s)

590-600

1 reference

Isolation of the nitrogen assimilation regulator NR(I), the product of the glnG gene of Escherichia coli

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=1074374

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Inferring genetic networks and identifying compound mode of action via expression profiling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Combining location and expression data for principled discovery of genetic regulatory network models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Inference from clustering with application to gene-expression microarrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Reverse engineering of biological complexity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Systems biology: a brief overview

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Computational studies of gene regulatory networks: in numero molecular biology.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Genetic network inference: from co-expression clustering to reverse engineering

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Engineering stability in gene networks by autoregulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Towards a circuit engineering discipline

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Robust perfect adaptation in bacterial chemotaxis through integral feedback control

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

PII signal transduction proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Construction of a genetic toggle switch in Escherichia coli

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Kinetic analysis of a molecular model of the budding yeast cell cycle

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

E-CELL: software environment for whole-cell simulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Emergent properties of networks of biological signaling pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Robustness in simple biochemical networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Regulation of nitrogen metabolism in Escherichia coli and Klebsiella aerogenes: studies with the continuous-culture technique

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Nac-mediated repression of the serA promoter of Escherichia coli

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Mathematical simulation and analysis of cellular metabolism and regulation.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1074374

Power-Law Distributions in Some Random Boolean Networks

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15805500

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Two-phase partition method for simulating a biological system at an extremely high speed

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15805500

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15805500

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.3463705

1 reference

29 July 2017

1 reference

29 July 2017

1 reference