ReviewBMC systems biology2008
Optimization in computational systems biology.
Review in BMC systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 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
90 citing papers in PubMed.
- Mathematical and Computational Models of Biochemical Reactions and Cell Signaling-From Ordinary Differential Equations to Machine Learning.International journal of molecular sciences · 2026Review
- Article
- Article
- Mathematical basis and toolchain for hierarchical optimization of biochemical networks.PLoS computational biology · 2024Article
- Kombucha-Proteinoid Crystal Bioelectric Circuits.ACS omega · 2024Article
- CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability.Biotechnology and bioengineering · 2023Article
- Bayesian Optimization for Design of Multiscale Biological Circuits.ACS synthetic biology · 2023Article
- Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT.International journal of molecular sciences · 2023Article
- Approximating scaffold printability utilizing computational methods.Biofabrication · 2023Article
- ASAS-NANP symposium: Mathematical Modeling in Animal Nutrition: The power of identifiability analysis for dynamic modeling in animal science:a practitioner approach.Journal of animal science · 2023Article
- PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects.GigaByte (Hong Kong, China) · 2023Article
- MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling.BMC bioinformatics · 2022Article
- Mathematical Modelling in Plant Synthetic Biology.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Optimal proteome allocation and the temperature dependence of microbial growth laws.NPJ systems biology and applications · 2021Article
- Using optimal control to understand complex metabolic pathways.BMC bioinformatics · 2020Article
- Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach.Journal of mathematical biology · 2020Article
- Calibration of ionic and cellular cardiac electrophysiology models.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation.Bioinformatics (Oxford, England) · 2020Article
- Systems Genetics for Mechanistic Discovery in Heart Diseases.Circulation research · 2020Review
- The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling.NPJ systems biology and applications · 2020Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on applications of mathematical optimization in computational systems biology. Examples are given where optimization methods are used for topics ranging from model building and optimal experimental design to metabolic engineering and synthetic biology. Finally, several perspectives for future research are outlined.
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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.