ArticleBioinformatics (Oxford, England)2012
Integrating literature-constrained and data-driven inference of signalling networks.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Cluster Gauss-Newton and CellNOpt Parameter Estimation in a Small Protein Signaling Network of Vorinostat and Bortezomib Pharmacodynamics.The AAPS journal · 2021Article
- Insights on TAM Formation from a Boolean Model of Macrophage Polarization Based on In Vitro Studies.Cancers · 2020Article
- Converting networks to predictive logic models from perturbation signalling data with CellNOpt.Bioinformatics (Oxford, England) · 2020Article
- Estimating drivers of cell state transitions using gene regulatory network models.BMC systems biology · 2017Article
- Logic Modeling in Quantitative Systems Pharmacology.CPT: pharmacometrics & systems pharmacology · 2017Article
- caspo: a toolbox for automated reasoning on the response of logical signaling networks families.Bioinformatics (Oxford, England) · 2017Article
- Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search.BioMed research international · 2017Article
- Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data.Scientific reports · 2016Article
- A Six-Stage Workflow for Robust Application of Systems Pharmacology.CPT: pharmacometrics & systems pharmacology · 2016Article
- Inferring causal molecular networks: empirical assessment through a community-based effort.Nature methods · 2016Article
- Constrained inference of protein interaction networks for invadopodium formation in cancer.IET systems biology · 2016Article
- Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.BMC systems biology · 2015Article
- Network biology in medicine and beyond.Circulation. Cardiovascular genetics · 2014Article
- Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data.BMC bioinformatics · 2014Article
- Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines.BMC systems biology · 2014Article
- Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.PloS one · 2014Article
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.BMC systems biology · 2013Article
- CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.BMC systems biology · 2012Article
- Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.PloS one · 2012Article
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5 authors.
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Abstract
motivationRecent developments in experimental methods facilitate increasingly larger signal transduction datasets. Two main approaches can be taken to derive a mathematical model from these data: training a network (obtained, e.g., from literature) to the data, or inferring the network from the data alone. Purely data-driven methods scale up poorly and have limited interpretability, whereas literature-constrained methods cannot deal with incomplete networks.
resultsWe present an efficient approach, implemented in the R package CNORfeeder, to integrate literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. Our method extends a given network with links derived from the data via various inference methods, and uses information on physical interactions of proteins to guide and validate the integration of links. We apply CNORfeeder to a network of growth and inflammatory signalling. We obtain a model with superior data fit in the human liver cancer HepG2 and propose potential missing pathways. AVAILABILITY: CNORfeeder is in the process of being submitted to Bioconductor and in the meantime available at www.cellnopt.org. CONTACT: saezrodriguez@ebi.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.