ArticleBioinformatics (Oxford, England)2015
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 23 citations in OpenAlex.
- Logic-based modeling of inflammatory macrophage cross talk with glomerular endothelial cells in diabetic kidney disease.American journal of physiology. Renal physiology · 2025Article
- Review
- Studying stochastic systems biology of the cell with single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics.PLoS computational biology · 2019Article
- Construction of Boolean logic gates based on dual-vector circuits of multiple gene regulatory elements.Molecular genetics and genomics : MGG · 2019Article
- Gene Regulatory Networks Reconstruction Using the Flooding-Pruning Hill-Climbing Algorithm.Genes · 2018Article
- An improved Bayesian network method for reconstructing gene regulatory network based on candidate auto selection.BMC genomics · 2017Article
- Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.Cancer research · 2017Article
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.PLoS computational biology · 2017Article
- Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.BMC bioinformatics · 2017Article
- A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.PloS one · 2017Article
- Integrated Strategies to Gain a Systems-Level View of Dynamic Signaling Networks.Methods in enzymology · 2017Article
- Learning stochastic process-based models of dynamical systems from knowledge and data.BMC systems biology · 2016Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationSystems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters.
resultsIn this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: julio@iim.csic.es or saezrodriguez@ebi.ac.uk.
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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.