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 …

Stimulating intrinsic motivation in millennial students: A new generation, a new approach

JD Chaudhuri - Anatomical sciences education, 2020 - Wiley Online Library
There has been a fundamental change in health care pedagogy to address the demands
and challenges posed by the present generation of millennial students. There is also a …

Sharing biological data: why, when, and how

SL Wilson, GP Way, W Bittremieux, JP Armache… - FEBS …, 2021 - pmc.ncbi.nlm.nih.gov
Sharing data has a crucial role in the advancement of biological science. The use of different
types of data within and between scientific fields complicates establishing a single standard …

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

A Niarakis, D Waltemath, J Glazier… - Briefings in …, 2022 - academic.oup.com
Computational models are often employed in systems biology to study the dynamic
behaviours of complex systems. With the rise in the number of computational models, finding …

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 …

Creating a structured adverse outcome pathway knowledgebase via ontology-based annotations

C Ives, I Campia, RL Wang, C Wittwehr… - Applied in vitro …, 2017 - liebertpub.com
Abstract The Adverse Outcome Pathway (AOP) framework is increasingly used to integrate
data based on traditional and emerging toxicity testing paradigms. As the number of AOP …

Agent-based modeling of cancer stem cell driven solid tumor growth

J Poleszczuk, P Macklin, H Enderling - Stem cell heterogeneity: Methods …, 2016 - Springer
Computational modeling of tumor growth has become an invaluable tool to simulate
complex cell–cell interactions and emerging population-level dynamics. Agent-based …

Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model

M Marin-Riera, M Brun-Usan, R Zimm… - …, 2016 - academic.oup.com
Motivation: The transformation of the embryo during development requires complex gene
networks, cell signaling and gene-regulated cell behaviors (division, adhesion, polarization …

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

JAI Johnson, GL Stein-O'Brien, M Booth, R Heiland… - …, 2023 - pmc.ncbi.nlm.nih.gov
Cells are fundamental units of life, constantly interacting and evolving as dynamical systems.
While recent spatial multi-omics can quantitate individual cells' characteristics and …

[PDF][PDF] Key challenges facing data-driven multicellular systems biology

P Macklin - Gigascience, 2019 - academic.oup.com
Increasingly sophisticated experiments, coupled with large-scale computational models,
have the potential to systematically test biological hypotheses to drive our understanding of …