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tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes
SUMMARY: The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of canc...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267821/ https://www.ncbi.nlm.nih.gov/pubmed/32170925 http://dx.doi.org/10.1093/bioinformatics/btaa182 |
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author | Nagornov, Iurii S Kato, Mamoru |
author_facet | Nagornov, Iurii S Kato, Mamoru |
author_sort | Nagornov, Iurii S |
collection | PubMed |
description | SUMMARY: The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. AVAILABILITY AND IMPLEMENTATION: The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. CONTACT: mamkato@ncc.go.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-7267821 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-72678212020-06-09 tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes Nagornov, Iurii S Kato, Mamoru Bioinformatics Applications Notes SUMMARY: The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. AVAILABILITY AND IMPLEMENTATION: The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. CONTACT: mamkato@ncc.go.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-06 2020-03-14 /pmc/articles/PMC7267821/ /pubmed/32170925 http://dx.doi.org/10.1093/bioinformatics/btaa182 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Nagornov, Iurii S Kato, Mamoru tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title | tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title_full | tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title_fullStr | tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title_full_unstemmed | tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title_short | tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
title_sort | tughall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267821/ https://www.ncbi.nlm.nih.gov/pubmed/32170925 http://dx.doi.org/10.1093/bioinformatics/btaa182 |
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