The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks (Q28472336)

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English	The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks	scientific article

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title

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks (English)

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main subject

Petri net

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based on heuristic

inferred from title

author

Prahlad T. Ram

object named as

Prahlad T Ram

series ordinal

5

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Luay Nakhleh

series ordinal

4

object named as

Luay Nakhleh

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author name string

Derek Ruths

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1

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Melissa Muller

series ordinal

2

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Jen-Te Tseng

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3

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language of work or name

English

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publication date

29 February 2008

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published in

PLOS Computational Biology

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volume

4

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issue

2

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page(s)

e1000005

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copyright license

Creative Commons Attribution 4.0 International

start time

29 February 2008

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April 2022 Public Data File from Crossref

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copyrighted

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cites work

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

TSC2 integrates Wnt and energy signals via a coordinated phosphorylation by AMPK and GSK3 to regulate cell growth

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Minimum information requested in the annotation of biochemical models (MIRIAM)

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Formation of regulatory patterns during signal propagation in a Mammalian cellular network

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Feedback inhibition of Akt signaling limits the growth of tumors lacking Tsc2

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Phosphorylation and functional inactivation of TSC2 by Erk implications for tuberous sclerosis and cancer pathogenesis

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Modeling cell signaling networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Regulation of B-Raf kinase activity by tuberin and Rheb is mammalian target of rapamycin (mTOR)-independent

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

A natural class of robust networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

The Hallmarks of Cancer

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

KEGG: kyoto encyclopedia of genes and genomes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

Ultrasensitivity in the mitogen-activated protein kinase cascade

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

19 March 2017

mTOR inhibition induces upstream receptor tyrosine kinase signaling and activates Akt

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

PANTHER: a library of protein families and subfamilies indexed by function

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

Growing roles for the mTOR pathway

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

Signaling--2000 and beyond

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

The energy sensing LKB1-AMPK pathway regulates p27(kip1) phosphorylation mediating the decision to enter autophagy or apoptosis

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

7 April 2017

Network topology determines dynamics of the mammalian MAPK1,2 signaling network: bifan motif regulation of C-Raf and B-Raf isoforms by FGFR and MC1R.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Petri net modelling of biological networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Qualitative networks: a symbolic approach to analyze biological signaling networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Parameter estimate of signal transduction pathways

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Application of Petri net based analysis techniques to signal transduction pathways

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Insulin and amino-acid regulation of mTOR signaling and kinase activity through the Rheb GTPase

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

A computational framework for the topological analysis and targeted disruption of signal transduction networks.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Systems analyses characterize integrated functions of biochemical networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Topology of biological networks and reliability of information processing

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Mechanisms of disease: beta-adrenergic receptors--alterations in signal transduction and pharmacogenomics in heart failure

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Tuberous sclerosis: a GAP at the crossroads of multiple signaling pathways

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Reconstruction of cellular signalling networks and analysis of their properties

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Dysregulation of the TSC-mTOR pathway in human disease

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Modeling and simulation of molecular biology systems using petri nets: modeling goals of various approaches

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Alternative phospholipase D/mTOR survival signal in human breast cancer cells

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Genetic networks with canalyzing Boolean rules are always stable

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Computational approaches for modeling regulatory cellular networks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Metabolic pathways in the post-genome era.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

The Rb-family protein p107 inhibits translation by a PDK1-dependent mechanism

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Signaling networks: the origins of cellular multitasking

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Protein molecules as computational elements in living cells

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

29 September 2017

Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

2 June 2018

Identification of Sonic hedgehog as a candidate gene responsible for holoprosencephaly

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

2 June 2018

Hypothesis generation in signaling networks.

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

Structural modeling and analysis of signaling pathways based on Petri nets

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

Qualitative simulation of the initiation of sporulation in Bacillus subtilis

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

Robustness and fragility of Boolean models for genetic regulatory networks.

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000005

retrieved

21 January 2018

Constructing biological pathway models with hybrid functional Petri nets.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

27 November 2018

Biopathways representation and simulation on hybrid functional Petri net.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265486

retrieved

27 November 2018

Complex biology with no parameters

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/18463702

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The logical analysis of continuous, non-linear biochemical control networks

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/18463702

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000005

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1083457

DBLP publication ID

journals/ploscb/RuthsMTNR08

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

OpenCitations bibliographic resource ID

1083457

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1083457

PMC publication ID

2265486

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1083457

PubMed publication ID

18463702

1 reference

stated in

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1083457

ResearchGate publication ID

5387333

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