ArticleMethods in cell biology2012
Multi-scale modeling of tissues using CompuCell3D.
Article in Methods in cell biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 259 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
259 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- A Comparison of Mechanisms Driving Lesion Outcomes During Lung Tumor and Tuberculosis Granuloma Formation.Bulletin of mathematical biology · 2026Article
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- Comparison of volumetric dynamic optical coherence tomography with biological methods for evaluation of radiation effects in prostate tumor spheroids.Journal of biomedical optics · 2026Article
- Review
- A Latent Inflammatory Tissue-State Variable Mechanistically Links Radiotherapy-Induced Immune Remodeling to Recurrent Tumor Permissiveness.bioRxiv : the preprint server for biology · 2026Article
- Spatio-temporal multiscale cell modeling of skin wound healing.Biophysical journal · 2026Article
- Clusters, fingers, and singles: A mechanical landscape of tumor invasion.PLoS computational biology · 2026Article
- Virtual cells: progress and challenges from mechanistic modeling to data-driven integration.Briefings in bioinformatics · 2026Review
- Multicellular simulations with shape and volume constraints using optimal transport.Science advances · 2026Article
- Mechanical interactions dynamically influence rosette morphogenesis in the migrating zebrafish posterior lateral line primordium.Development (Cambridge, England) · 2026Article
- Virtual photon-counting micro-CT platform for simulation of head and neck cancer imaging in mice.Physics in medicine and biology · 2026Article
- Heterotypic intercellular adhesion tunes efficiency of cell-on-cell migration.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces.NPJ systems biology and applications · 2026Article
- Multiscale predictive cellular modeling: integrating hypothesis grammars, digital twins, and multi-omics for In silico oncology and precision theranostics.Functional & integrative genomics · 2026Review
- TumorTwin: a Python framework for patient-specific digital twins in oncology.BMC medical informatics and decision making · 2026Article
- Matters of life and death in computational cell biology.NPJ systems biology and applications · 2026Review
- Biophysical Modeling Reveals How Gene Expression Drives Tissue-Scale Fat Deposition in Beef Breeds.Biology · 2026Article
- Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins.Informatics in medicine unlocked · 2026Article
- Start small: A model for tissue-wide planar cell polarity without morphogens.PLoS computational biology · 2026Article
199 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
6 authors.
Funding
Abstract
The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier-Graner-Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D.
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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.