ArticleBMC systems biology2009
Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection.
Article in BMC systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Establishment of a human 3D lung cancer model based on a biological tissue matrix combined with a Boolean in silico model.Molecular oncology · 2014Trial
- Article
- How to Steer and Control ERK and the ERK Signaling Cascade Exemplified by Looking at Cardiac Insufficiency.International journal of molecular sciences · 2019Article
- A combined tissue-engineered/in silico signature tool patient stratification in lung cancer.Molecular oncology · 2018Article
- Cell Monitoring and Manipulation Systems (CMMSs) based on Glass Cell-Culture Chips (GC³s).Micromachines · 2016Review
- Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches.PLoS computational biology · 2015Article
- Genome scale modeling in systems biology: algorithms and resources.Current genomics · 2014Article
- True grit: programmed necrosis in antiviral host defense, inflammation, and immunogenicity.Journal of immunology (Baltimore, Md. : 1950) · 2014Review
- Dynamical systems approach to endothelial heterogeneity.Circulation research · 2012Review
- Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin.The Plant cell · 2012Article
- Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles.BMC systems biology · 2011Article
- Logic-based models for the analysis of cell signaling networks.Biochemistry · 2010Review
- Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies.Advances and applications in bioinformatics and chemistry : AABC · 2009Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe decision pro- or contra apoptosis is complex, involves a number of different inputs, and is central for the homeostasis of an individual cell as well as for the maintenance and regeneration of the complete organism.
resultsThis study centers on Fas ligand (FasL)-mediated apoptosis, and a complex and internally strongly linked network is assembled around the central FasL-mediated apoptosis cascade. Different bioinformatical techniques are employed and different crosstalk possibilities including the integrin pathway are considered. This network is translated into a Boolean network (74 nodes, 108 edges). System stability is dynamically sampled and investigated using the software SQUAD. Testing a number of alternative crosstalk possibilities and networks we find that there are four stable system states, two states comprising cell survival and two states describing apoptosis by the intrinsic and the extrinsic pathways, respectively. The model is validated by comparing it to experimental data from kinetics of cytochrome c release and caspase activation in wildtype and Bid knockout cells grown on different substrates. Pathophysiological modifications such as input from cytomegalovirus proteins M36 and M45 again produces output behavior that well agrees with experimental data.
conclusionA network model for apoptosis and crosstalk in hepatocytes shows four different system states and reproduces a number of different conditions around apoptosis including effects of different growth substrates and viral infections. It produces semi-quantitative predictions on the activity of individual nodes, agreeing with experimental data. The model (SBML format) and all data are available for further predictions and development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.