(Q33596981)

English

Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation (English)

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

1 reference

based on heuristic

inferred from title

author name string

Shih Chi Peng

1

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

David Shan Hill Wong

2

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Kai Che Tung

3

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Yan Yu Chen

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Chun Cheih Chao

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Chien Hua Peng

6

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Yung Jen Chuang

7

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Chuan Yi Tang

8

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

publication date

8 June 2010

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

BMC Bioinformatics

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

11

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

308

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

https://scigraph.springernature.com/pub.10.1186/1471-2105-11-308

0 references

Understanding NF-kappaB signaling via mathematical modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Regulatory network of inflammation downstream of proteinase-activated receptors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Transcriptional profiling of the LPS induced NF-kappaB response in macrophages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

NF-kappaB and the immune response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Data-driven modelling of signal-transduction networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Genome-wide gene expression profiling of human mast cells stimulated by IgE or FcepsilonRI-aggregation reveals a complex network of genes involved in inflammatory responses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Lipopolysaccharide induces CXCL2/macrophage inflammatory protein-2 gene expression in enterocytes via NF-kappaB activation: independence from endogenous TNF-alpha and platelet-activating factor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

The NF-kappaB pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Stimulus specificity of gene expression programs determined by temporal control of IKK activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

A network-based analysis of systemic inflammation in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Contraction-induced myokine production and release: is skeletal muscle an endocrine organ?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Modeling and simulation of biological systems with stochasticity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

A computational approach for ordering signal transduction pathway components from genomics and proteomics Data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Mathematical and computational models of immune-receptor signalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Genomic Object Net: I. A platform for modelling and simulating biopathways.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Network component analysis: reconstruction of regulatory signals in biological systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Proinflammatory cytokines and sepsis syndrome: not enough, or too much of a good thing?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Modeling of signaling networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Automated modelling of signal transduction networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

NF-kappaB regulation in the immune system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

The inflammatory network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Stereotyped and specific gene expression programs in human innate immune responses to bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Therapeutic potential of inhibition of the NF-kappaB pathway in the treatment of inflammation and cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

NF-kappaB: a key role in inflammatory diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Principal components analysis to summarize microarray experiments: application to sporulation time series

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

The I kappa B kinase (IKK) and NF-kappa B: key elements of proinflammatory signalling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Signal transduction pathways of apoptosis and inflammation induced by the tumor necrosis factor receptor family

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Genetic approaches in mice to understand Rel/NF-kappaB and IkappaB function: transgenics and knockouts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Emergent properties of networks of biological signaling pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Proinflammatory and anti-inflammatory cytokines as mediators in the pathogenesis of septic shock

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

28 July 2018

Reverse-engineering transcription control networks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Inferring gene regulatory networks from multiple microarray datasets.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

International alliances for quantitative modeling in systems biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Signal transduction in inflammation. Perspective clues from the leukocyte-endothelium interface

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

The kinetics of FGF-2 binding to heparan sulfate proteoglycans and MAP kinase signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Mathematical model of NF-kappaB regulatory module

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Dynamical and integrative cell signaling: challenges for the new biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Analysis and modelling of signal transduction pathways in systems biology.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Biopathways representation and simulation on hybrid functional Petri net.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

An essential role of macrophage inflammatory protein 1alpha/CCL3 on the expression of host's innate immunities against infectious complications.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Regulation of the immune system by NF-kappaB and IkappaB.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Kinetic analysis of multisite phosphorylation using analytic solutions to Michaelis-Menten equations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Linear modes of gene expression determined by independent component analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Reveal, a general reverse engineering algorithm for inference of genetic network architectures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Accessing genetic information with high-density DNA arrays.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2889938

30 October 2018

Modeling and simulation in signal transduction pathways: a systems biology approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Surviving sepsis: bcl-2 overexpression modulates splenocyte transcriptional responses in vivo

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The interleukin-1 receptor/Toll-like receptor superfamily: signal transduction during inflammation and host defense

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Circulating interleukin 6 concentrations and insulin resistance in patients with cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mathematical modeling of the regulation of caspase-3 activation and degradation

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A tumour necrosis factor alpha autocrine loop contributes to proliferation and nuclear factor-kappaB activation of Theileria parva-transformed B cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/20529327

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2105-11-308

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

DBLP publication ID

journals/bmcbi/PengWTCCPCT10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q33596981&oldid=1966412612"