ArticlePloS one2007
Constraint-based modeling and kinetic analysis of the Smad dependent TGF-beta signaling pathway.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed, 88 citations in OpenAlex.
- Construction and Characterization of an Attenuated Vaccine Vector Based on Cucumber Mosaic Virus RNA2.Life (Basel, Switzerland) · 2026Article
- Liebig's law of the minimum in the TGF-β/SMAD pathway.PLoS computational biology · 2024Article
- Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling.PLoS computational biology · 2022Article
- Curcumin Inhibition of TGFβ signaling in bone metastatic breast cancer cells and the possible role of oxidative metabolites.The Journal of nutritional biochemistry · 2022Article
- Modeling the Control of TGF-β/Smad Nuclear Accumulation by the Hippo Pathway Effectors, Taz/Yap.iScience · 2020Article
- PyCoTools: a Python toolbox for COPASI.Bioinformatics (Oxford, England) · 2018Article
- Mathematical model of TGF-βsignalling: feedback coupling is consistent with signal switching.BMC systems biology · 2017Article
- Modelling the molecular mechanisms of aging.Bioscience reports · 2017Review
- Examining Crosstalk among Transforming Growth Factor β, Bone Morphogenetic Protein, and Wnt Pathways.The Journal of biological chemistry · 2017Article
- Enhanced release of primary signals may render intercellular signalling ineffective due to spatial aspects.Scientific reports · 2016Article
- Chemical regulators of epithelial plasticity reveal a nuclear receptor pathway controlling myofibroblast differentiation.Scientific reports · 2016Article
- Robust and efficient parameter estimation in dynamic models of biological systems.BMC systems biology · 2015Article
- Identifying Mechanisms of Homeostatic Signaling in Fibroblast Differentiation.Bulletin of mathematical biology · 2015Article
- Response to Nodal morphogen gradient is determined by the kinetics of target gene induction.eLife · 2015Article
- Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies.Oncotarget · 2015Article
- The self-limiting dynamics of TGF-β signaling in silico and in vitro, with negative feedback through PPM1A upregulation.PLoS computational biology · 2014Article
- Literature-based automated reconstruction, expansion, and refinement of the TGF-β superfamily ligand-receptor network.The Journal of membrane biology · 2014Article
- An integrative modeling framework reveals plasticity of TGF-β signaling.BMC systems biology · 2014Article
- Spatial aspects in the SMAD signaling pathway.Journal of mathematical biology · 2013Article
- Computational modelling of Smad-mediated negative feedback and crosstalk in the TGF-β superfamily network.Journal of the Royal Society, Interface · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInvestigation of dynamics and regulation of the TGF-beta signaling pathway is central to the understanding of complex cellular processes such as growth, apoptosis, and differentiation. In this study, we aim at using systems biology approach to provide dynamic analysis on this pathway. METHODOLOGY/PRINCIPAL
findingsWe proposed a constraint-based modeling method to build a comprehensive mathematical model for the Smad dependent TGF-beta signaling pathway by fitting the experimental data and incorporating the qualitative constraints from the experimental analysis. The performance of the model generated by constraint-based modeling method is significantly improved compared to the model obtained by only fitting the quantitative data. The model agrees well with the experimental analysis of TGF-beta pathway, such as the time course of nuclear phosphorylated Smad, the subcellular location of Smad and signal response of Smad phosphorylation to different doses of TGF-beta. CONCLUSIONS/SIGNIFICANCE: The simulation results indicate that the signal response to TGF-beta is regulated by the balance between clathrin dependent endocytosis and non-clathrin mediated endocytosis. This model is useful to be built upon as new precise experimental data are emerging. The constraint-based modeling method can also be applied to quantitative modeling of other signaling pathways.
Indexed as
Identifiers
What OpenQuestion holds
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.