(Q30441717)

15 August 2017

Dynamic analysis of integrated signaling, metabolic, and regulatory networks (English)

1 reference

15 August 2017

Jason A Papin

4

0 references

Jong Min Lee

object named as

Jong Min Lee

series ordinal

1

0 references

Erwin P Gianchandani

series ordinal

2

object named as

Erwin P Gianchandani

1 reference

15 August 2017

James A Eddy

3

1 reference

15 August 2017

23 May 2008

1 reference

PLOS Computational Biology

15 August 2017

1 reference

15 August 2017

4

1 reference

15 August 2017

e1000086

1 reference

15 August 2017

5

1 reference

Creative Commons Attribution 4.0 International

15 August 2017

start time

23 May 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Predicting biological system objectives de novo from internal state measurements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Novel metaheuristic for parameter estimation in nonlinear dynamic 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=2377155

Matrix formalism to describe functional states of transcriptional regulatory 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=2377155

Parameter estimation in biochemical systems models with alternating regression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Flux balance analysis in the era of metabolomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

A Further Note on the Kinetics of Enzyme Action

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

A Note on the Kinetics of Enzyme Action

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Systems analyses characterize integrated functions of biochemical networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Interlinked fast and slow positive feedback loops drive reliable cell decisions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Integrative model of the response of yeast to osmotic shock

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Multifaceted roles of glycolytic enzymes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Reconstruction of cellular signalling networks and analysis of their properties

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

k-Cone analysis: determining all candidate values for kinetic parameters on a network scale

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Genome-scale models of microbial cells: evaluating the consequences of constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Metabolic enzymes and coenzymes in transcription--a direct link between metabolism and 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=2377155

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Noise minimization in eukaryotic 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=2377155

Just-in-time transcription program in metabolic 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=2377155

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in 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=2377155

Advances in flux balance analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Parameter estimation in biochemical pathways: a comparison of global optimization methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Noise in eukaryotic 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=2377155

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Analysis of optimality in natural and perturbed metabolic networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Transcriptional regulatory networks in Saccharomyces cerevisiae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Dynamic flux balance analysis of diauxic growth in 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=2377155

Yeast go the whole HOG for the hyperosmotic response

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Energy balance for analysis of complex metabolic networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Osmotic stress signaling and osmoadaptation in yeasts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Transcriptional regulation in constraints-based metabolic models 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=2377155

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Regulation of gene expression in flux balance models of metabolism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Osmotic stress-induced gene expression in Saccharomyces cerevisiae requires Msn1p and the novel nuclear factor Hot1p

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Complexity in biological signaling 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=2377155

Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

An osmosensing signal transduction pathway in yeast.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2377155

Towards building the silicon cell: a modular approach

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Non-linear reduction for kinetic models of metabolic reaction networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Modelling the dynamics of the yeast pheromone pathway.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Modelling dynamic processes in yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Three-dimensional cell cycle model with distributed transcription and translation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Parameter estimation in models combining signal transduction and metabolic pathways: the dependent input approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

A hybrid approach for efficient and robust parameter estimation in biochemical pathways.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Metabolic engineering under uncertainty--II: analysis of yeast metabolism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

Control of systems integrating logic, dynamics, and constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000086

10.1371/JOURNAL.PCBI.1000086

21 January 2018

Identifiers

DOI

1 reference

journals/ploscb/0002GEP08

15 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 August 2017

1 reference

PMCID

2377155