ReviewPLoS computational biology2016
Computational Modeling, Formal Analysis, and Tools for Systems Biology.
Review in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 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
53 citing papers in PubMed.
- Systems biology during 20 years of PLoS Computational Biology.PLoS computational biology · 2026Article
- Integrating AI, mechanistic modelling and network approaches in systems biology for translational research.NPJ systems biology and applications · 2026Article
- Biological parts in yeast synthetic biology: from regulatory elements to predictive design platforms.FEMS yeast research · 2026Review
- Design of bacterial DNT sensors based on computational models.Nucleic acids research · 2026Article
- Modeling gonorrhea and HIV coinfection with predictive analytics for disability and mortality risks.Scientific reports · 2025Article
- Merging traditional practices and modern technology through computational plant breeding.Plant physiology · 2025Review
- Personalizing computational models to construct medical digital twins.Journal of the Royal Society, Interface · 2025Article
- Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control.BMC bioinformatics · 2025Article
- Crosstalk among plant hormone regulates the root development.Plant signaling & behavior · 2024Review
- drexml: A command line tool and Python package for drug repurposing.Computational and structural biotechnology journal · 2024Article
- Personalizing computational models to construct medical digital twins.bioRxiv : the preprint server for biology · 2024Article
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Tumor microenvironment and cancer metastasis: molecular mechanisms and therapeutic implications.Frontiers in pharmacology · 2024Review
- Genetic regulation of lateral root development.Plant signaling & behavior · 2023Review
- On the History of Ecosystem Dynamical Modeling: The Rise and Promises of Qualitative Models.Entropy (Basel, Switzerland) · 2023Article
- The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction.Communications biology · 2023Article
- Exploring Cell Migration Mechanisms in Cancer: From Wound Healing Assays to Cellular Automata Models.Cancers · 2023Article
- Efficient parameter generation for constrained models using MCMC.Scientific reports · 2023Article
- Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions.PLoS computational biology · 2023Article
- Structural identifiability of biomolecular controller motifs with and without flow measurements as model output.PLoS computational biology · 2023Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
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.