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MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

https://doi.org/10.1101/090456
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Outgoing claims: the papers this work cites, builds on, or argues with.

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The Ki-67 protein: From the known and the unknown
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Convergence of Advances in Genomics, Team Science, and Repositories as Drivers of Progress in Psychiatric Genomics
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Antibiotic resistance of bacterial biofilms
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Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression
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Atomic force microscopy study of the antibacterial effects of chitosans on Escherichia coli and Staphylococcus aureus
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Cell adhesion molecule T-cadherin regulates vascular cell adhesion, phenotype and motility
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Model Driven Quantification of Individual and Collective Cell Migration
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Gene Ontology: tool for the unification of biology
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Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
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Standardizing data
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The Cancer Genome Atlas Pan-Cancer analysis project
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Changing medium and passaging cell lines
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A physical sciences network characterization of non-tumorigenic and metastatic cells
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A high-content image-based method for quantitatively studying context-dependent cell population dynamics
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Systems biology markup language: Level 2 and beyond
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Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration
inferredcites →https://doi.org/10.1073/pnas.1105316108openalex-snapshot
Fluid forces control endothelial sprouting
inferredcites →https://doi.org/10.1074/jbc.275.14.10661openalex-snapshot
Vascular Endothelial Growth Factor (VEGF)-driven Actin-based Motility Is Mediated by VEGFR2 and Requires Concerted Activation of Stress-activated Protein Kinase 2 (SAPK2/p38) and Geldanamycin-sensitive Phosphorylation of Focal Adhesion Kinase
inferredcites →https://doi.org/10.1080/10273660008833042openalex-snapshot
Mathematical Modelling of Tumour Invasion and Metastasis
inferredcites →https://doi.org/10.1087/20120404openalex-snapshot
ORCID: a system to uniquely identify researchers
inferredcites →https://doi.org/10.1088/0951-7715/23/1/r01openalex-snapshot
Nonlinear modelling of cancer: bridging the gap between cells and tumours
inferredcites →https://doi.org/10.1093/bioinformatics/btg015openalex-snapshot
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
inferredcites →https://doi.org/10.1093/bioinformatics/btq437openalex-snapshot
A cell-based simulation software for multi-cellular systems
inferredcites →https://doi.org/10.1093/bioinformatics/btt772openalex-snapshot
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
inferredcites →https://doi.org/10.1093/bioinformatics/btu210openalex-snapshot
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
inferredcites →https://doi.org/10.1093/bioinformatics/btv346openalex-snapshot
TiQuant: software for tissue analysis, quantification and surface reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/btv730openalex-snapshot
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations
inferredcites →https://doi.org/10.1093/database/bav043openalex-snapshot
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
inferredcites →https://doi.org/10.1093/nar/gkr1097openalex-snapshot
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
inferredcites →https://doi.org/10.1093/nar/gks1146openalex-snapshot
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
inferredcites →https://doi.org/10.1093/nar/gku1179openalex-snapshot
Gene Ontology Consortium: going forward
inferredcites →https://doi.org/10.1093/neuonc/nou027openalex-snapshot
Invasion and proliferation kinetics in enhancing gliomas predict IDH1 mutation status
inferredcites →https://doi.org/10.1101/035733openalex-snapshot
Agent-based simulation of large tumors in 3-D microenvironments
inferredcites →https://doi.org/10.1126/science.1115535openalex-snapshot
Regulation of Yeast Replicative Life Span by TOR and Sch9 in Response to Nutrients
inferredcites →https://doi.org/10.1126/science.1158357openalex-snapshot
Multi-University Research Teams: Shifting Impact, Geography, and Stratification in Science
inferredcites →https://doi.org/10.1126/science.1213847openalex-snapshot
Reproducible Research in Computational Science
inferredcites →https://doi.org/10.1126/science.351.6271.325openalex-snapshot
Biden seeks clear course for his cancer moonshot
inferredcites →https://doi.org/10.1128/aac.00736-05openalex-snapshot
Mechanism-Based Pharmacodynamic Models of Fluoroquinolone Resistance in Staphylococcus aureus
inferredcites →https://doi.org/10.1128/aem.00251-06openalex-snapshot
Estimation of Staphylococcus aureus Growth Parameters from Turbidity Data: Characterization of Strain Variation and Comparison of Methods
inferredcites →https://doi.org/10.1146/annurev-bioeng-071910-124729openalex-snapshot
Multiscale Cancer Modeling
inferredcites →https://doi.org/10.1158/0008-5472.can-11-1399openalex-snapshot
Quantifying the Role of Angiogenesis in Malignant Progression of Gliomas: In Silico Modeling Integrates Imaging and Histology
inferredcites →https://doi.org/10.1161/01.res.0000115555.05668.93openalex-snapshot
α 4 β 1 Integrin Mediates Selective Endothelial Cell Responses to Thrombospondins 1 and 2 In Vitro and Modulates Angiogenesis In Vivo
inferredcites →https://doi.org/10.1161/01.res.0000250758.63358.91openalex-snapshot
Extracellular Matrix–Bound Angiopoietin-Like 4 Inhibits Endothelial Cell Adhesion, Migration, and Sprouting and Alters Actin Cytoskeleton
inferredcites →https://doi.org/10.1177/0037549703040939openalex-snapshot
An Overview of CellML 1.1, a Biological Model Description Language
inferredcites →https://doi.org/10.1186/gb-2004-6-1-r8openalex-snapshot
Using ontologies to describe mouse phenotypes
inferredcites →https://doi.org/10.1186/s12918-015-0174-yopenalex-snapshot
SEEK: a systems biology data and model management platform
inferredcites →https://doi.org/10.1186/s12918-016-0337-5openalex-snapshot
Quantifying differences in cell line population dynamics using CellPD
inferredcites →https://doi.org/10.1201/9780203494899openalex-snapshot
Cancer Modelling and Simulation
inferredcites →https://doi.org/10.1371/journal.pcbi.1000622openalex-snapshot
The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling
inferredcites →https://doi.org/10.1371/journal.pcbi.1002970openalex-snapshot
Chaste: An Open Source C++ Library for Computational Physiology and Biology
inferredcites →https://doi.org/10.1371/journal.pcbi.1003008openalex-snapshot
An Integrated Computational/Experimental Model of Lymphoma Growth
inferredcites →https://doi.org/10.1371/journal.pcbi.1004412openalex-snapshot
Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data
inferredcites →https://doi.org/10.1371/journal.pcbi.1005991openalex-snapshot
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
inferredcites →https://doi.org/10.1371/journal.pone.0004670openalex-snapshot
The Number and Transmission of [PSI+] Prion Seeds (Propagons) in the Yeast Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1371/journal.pone.0028708openalex-snapshot
Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology
inferredcites →https://doi.org/10.1371/journal.pone.0111901openalex-snapshot
A Biomimetic Collagen Derived Peptide Exhibits Anti-Angiogenic Activity in Triple Negative Breast Cancer
inferredcites →https://doi.org/10.1371/journal.pone.0114885openalex-snapshot
Computational Pathology to Discriminate Benign from Malignant Intraductal Proliferations of the Breast
inferredcites →https://doi.org/10.1371/journal.pone.0129433openalex-snapshot
Predictive Modeling of Drug Response in Non-Hodgkin’s Lymphoma
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Media Formulations for Various Two-Hybrid Systems
inferredcites →https://doi.org/10.2147/ott.s65055openalex-snapshot
Antiangiogenic cancer drug sunitinib exhibits unexpected proangiogenic effects on endothelial cells
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Graphs in Statistical Analysis
inferredcites →https://doi.org/10.3233/acp-2011-0019openalex-snapshot
A novel, patient-specific mathematical pathology approach for assessment of surgical volume: application to ductal carcinoma in situ of the breast.
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Ontology of units of measure and related concepts
inferredcites →https://doi.org/10.3389/fonc.2013.00066openalex-snapshot
Modeling Tumor-Associated Edema in Gliomas during Anti-Angiogenic Therapy and Its Impact on Imageable Tumor
inferredcites →https://doi.org/10.3892/ijo.12.4.749openalex-snapshot
Regulation of distinct steps of angiogenesis by different angiogenic molecules.
inferredcites →https://doi.org/10.4137/cin.s19338openalex-snapshot
The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells
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A High-Performance Cellular Automaton Model of Tumor Growth with Dynamically Growing Domains

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cell.2025.06.048openalex-snapshot
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
inferred← citeshttps://doi.org/10.1016/j.coisb.2021.100385openalex-snapshot
Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems
inferred← citeshttps://doi.org/10.1038/s41523-018-0084-4openalex-snapshot
Correlating nuclear morphometric patterns with estrogen receptor status in breast cancer pathologic specimens
inferred← citeshttps://doi.org/10.1080/10511970.2021.1881849openalex-snapshot
Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab
inferred← citeshttps://doi.org/10.1101/2020.04.02.019075openalex-snapshot
Iterative community-driven development of a SARS-CoV-2 tissue simulator
inferred← citeshttps://doi.org/10.1101/2025.07.16.664358openalex-snapshot
Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative
inferred← citeshttps://doi.org/10.1111/coin.12515openalex-snapshot
Parallel model exploration for tumor treatment simulations
inferred← citeshttps://doi.org/10.1186/s12859-018-2510-xopenalex-snapshot
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
inferred← citeshttps://doi.org/10.1186/s12874-025-02705-zopenalex-snapshot
Characteristics of cohort data management systems (CDMS): a scoping review
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005991openalex-snapshot
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
inferred← citeshttps://doi.org/10.18297/etd/3925openalex-snapshot
Update of MultiCellular data standard to match PhysiCell "compact" output.
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