ArticlePLoS computational biology2021
PEtab-Interoperable specification of parameter estimation problems in systems biology.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- Review
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- Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding.PLoS computational biology · 2026Article
- Suggested experimental design and computational modeling to infer single-cell lipid dynamics from a single destructive measurement.iScience · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.Bioinformatics (Oxford, England) · 2026Article
- Spatially structured models of viral dynamics: a scoping review.Microbiology and molecular biology reviews : MMBR · 2025Article
- SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences.Bioinformatics (Oxford, England) · 2025Article
- PEtab.jl: advancing the efficiency and utility of dynamic modelling.Bioinformatics (Oxford, England) · 2025Article
- Current state and open problems in universal differential equations for systems biology.NPJ systems biology and applications · 2025Article
- The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions.ACS synthetic biology · 2025Review
- Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor.PLoS computational biology · 2025Article
- BADDADAN: Mechanistic modelling of time-series gene module expression.Quantitative plant biology · 2025Article
- Mathematical basis and toolchain for hierarchical optimization of biochemical networks.PLoS computational biology · 2024Article
- A sphingolipid rheostat controls apoptosis versus apical cell extrusion as alternative tumour-suppressive mechanisms.Cell death & disease · 2024Article
- Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry.Journal of the American Chemical Society · 2024Article
- Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data.Bioinformatics (Oxford, England) · 2024Article
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29 authors.
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Abstract
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.
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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.