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Modelling genotypes in their microenvironment to predict single- and multi-cellular behaviour

https://doi.org/10.1101/360446
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Co-evolution of tumor cells and their microenvironment
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Cell migration or cytokinesis and proliferation? – Revisiting the “go or grow” hypothesis in cancer cells in vitro
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Targeting hypoxia in cancer therapy
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Hypoxia — a key regulatory factor in tumour growth
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Single-cell genome sequencing: current state of the science
inferredcites →https://doi.org/10.1038/nrg.2017.8openalex-snapshot
Functional variomics and network perturbation: connecting genotype to phenotype in cancer
inferredcites →https://doi.org/10.1038/nrg3404openalex-snapshot
Genotype to phenotype: lessons from model organisms for human genetics
inferredcites →https://doi.org/10.1038/nrg3868openalex-snapshot
Methods of integrating data to uncover genotype–phenotype interactions
inferredcites →https://doi.org/10.1038/nrg3885openalex-snapshot
Quantitative and logic modelling of molecular and gene networks
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High-throughput functional genomics using CRISPR–Cas9
inferredcites →https://doi.org/10.1038/nrm2503openalex-snapshot
Modelling and analysis of gene regulatory networks
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Hypoxia and metabolic adaptation of cancer cells
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Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion
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Combining experiments with multi-cell agent-based modeling to study biological tissue patterning
inferredcites →https://doi.org/10.1093/bioinformatics/btl485openalex-snapshot
COPASI—a COmplex PAthway SImulator
inferredcites →https://doi.org/10.1093/bioinformatics/btn135openalex-snapshot
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions
inferredcites →https://doi.org/10.1093/bioinformatics/btp416openalex-snapshot
Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model
inferredcites →https://doi.org/10.1093/bioinformatics/btw250openalex-snapshot
BioASF: a framework for automatically generating executable pathway models specified in BioPAX
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A method for estimating the oxygen consumption rate in multicellular tumour spheroids
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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1109/wcre.2000.891463openalex-snapshot
GXL: toward a standard exchange format
inferredcites →https://doi.org/10.1109/wsc.2009.5429318openalex-snapshot
Agent-based modeling and simulation
inferredcites →https://doi.org/10.1126/science.276.5317.1425openalex-snapshot
Geometric Control of Cell Life and Death
inferredcites →https://doi.org/10.1177/1947601911408889openalex-snapshot
Mutations in the p53 Tumor Suppressor Gene: Important Milestones at the Various Steps of Tumorigenesis
inferredcites →https://doi.org/10.1186/s13059-016-0999-8openalex-snapshot
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia
inferredcites →https://doi.org/10.1371/journal.pcbi.1003286openalex-snapshot
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision
inferredcites →https://doi.org/10.1371/journal.pcbi.1003290openalex-snapshot
Perturbation Biology: Inferring Signaling Networks in Cellular Systems
inferredcites →https://doi.org/10.1371/journal.pone.0125232openalex-snapshot
Using the MCF10A/MCF10CA1a Breast Cancer Progression Cell Line Model to Investigate the Effect of Active, Mutant Forms of EGFR in Breast Cancer Development and Treatment Using Gefitinib
inferredcites →https://doi.org/10.1529/biophysj.105.060640openalex-snapshot
A Multiscale Model for Avascular Tumor Growth
inferredcites →https://doi.org/10.18632/oncotarget.5874openalex-snapshot
Collective cancer cell invasion induced by coordinated contractile stresses
inferredcites →https://doi.org/10.3389/fgene.2015.00179openalex-snapshot
The differential view of genotype–phenotype relationships
inferredcites →https://doi.org/10.4161/cbt.23297openalex-snapshot
Alterations of EGFR, p53 and PTEN that mimic changes found in basal-like breast cancer promote transformation of human mammary epithelial cells
inferredcites →https://doi.org/10.4161/cbt.26140openalex-snapshot
The multi-hit hypothesis in basal-like breast cancer

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inferred← citeshttps://doi.org/10.1101/2020.05.29.122200openalex-snapshot
Switching On Static Gene Regulatory Networks to Compute Cellular Decisions
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