ArticleBriefings in bioinformatics2022
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 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
19 citing papers in PubMed.
- TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.bioRxiv : the preprint server for biology · 2026Article
- Digital twins to accelerate target identification and drug development for immune-mediated disorders.FEBS open bio · 2026Review
- ECMSim: A high-performance interactive web application for real-time spatiotemporal simulation of cardiac ECM signaling and diffusion.Matrix biology plus · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- KGBN: Augmenting and optimizing logical gene regulatory networks using knowledge graphs.bioRxiv : the preprint server for biology · 2026Article
- Lessons learned from implementing FAIRification workflows in diabetes research in Germany.PLOS digital health · 2026Article
- Generative diffusion model surrogates for mechanistic agent-based biological models.Machine learning: science and technology · 2025Article
- Computational identification and validation of non-coding rna biomarkers in gastrointestinal cancer.Functional & integrative genomics · 2025Review
- Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies.NPJ digital medicine · 2025Review
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Spike sorting AI agent.bioRxiv : the preprint server for biology · 2025Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- Immune digital twins for complex human pathologies: applications, limitations, and challenges.NPJ systems biology and applications · 2024Review
- Making PBPK models more reproducible in practice.Briefings in bioinformatics · 2024Article
- Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.ACS pharmacology & translational science · 2024Review
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.Frontiers in immunology · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
13 authors.
Funding
Abstract
Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.
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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.