The 2019 mathematical oncology roadmap

RC Rockne, A Hawkins-Daarud, KR Swanson… - Physical …, 2019‏ - iopscience.iop.org
Whether the nom de guerre is Mathematical Oncology, Computational or Systems Biology,
Theoretical Biology, Evolutionary Oncology, Bioinformatics, or simply Basic Science, there is …

Harmonizing semantic annotations for computational models in biology

ML Neal, M König, D Nickerson, G Mısırlı… - Briefings in …, 2019‏ - academic.oup.com
Life science researchers use computational models to articulate and test hypotheses about
the behavior of biological systems. Semantic annotation is a critical component for …

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

J Ozik, N Collier, JM Wozniak, C Macal, C Cockrell… - BMC …, 2018‏ - Springer
Background Cancer is a complex, multiscale dynamical system, with interactions between
tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host …

PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

M Ponce-de-Leon, A Montagud, V Noël… - npj Systems Biology …, 2023‏ - nature.com
In systems biology, mathematical models and simulations play a crucial role in
understanding complex biological systems. Different modelling frameworks are employed …

Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach

Y Wang, E Brodin, K Nishii, HB Frieboes… - Scientific reports, 2021‏ - nature.com
Colorectal cancer and other cancers often metastasize to the liver in later stages of the
disease, contributing significantly to patient death. While the biomechanical properties of the …

Sharing and reusing cell image data

A Zaritsky - Molecular biology of the cell, 2018‏ - molbiolcell.org
The rapid growth in content and complexity of cell image data creates an opportunity for
synergy between experimental and computational scientists. Sharing microscopy data …

[PDF][PDF] Can computers conceive the complexity of cancer to cure it? Using artificial intelligence technology in cancer modelling and drug discovery

RC Adams, B Rashidieh - Mathematical Biosciences and …, 2020‏ - researchgate.net
Drug discovery and the development of safe and effective therapeutics is an intricate
procedure, further complicated in the context of cancer research by the inherent …

Prelude to a Compositional Systems Biology

E Agmon - Ar**v, 2024‏ - pmc.ncbi.nlm.nih.gov
Composition is a powerful principle for systems biology, focused on the interfaces,
interconnections, and orchestration of distributed processes. Whereas most systems biology …

MAGPIE: Simplifying access and execution of computational models in the life sciences

C Baldow, S Salentin, M Schroeder… - PLoS computational …, 2017‏ - journals.plos.org
Over the past decades, quantitative methods linking theory and observation became
increasingly important in many areas of life science. Subsequently, a large number of …

Open source tools and standardized data in cancer systems biology

P Macklin, SH Friedman, MultiCellDS Project - bioRxiv, 2018‏ - biorxiv.org
To reach the full potential of multicellular systems biology, mathematical and computational
modelers must pool their efforts to share and curate biophysical measurements, create and …