[HTML][HTML] Minimally sufficient experimental design using identifiability analysis

JL Gevertz, I Kareva - npj Systems Biology and Applications, 2024 - nature.com
Mathematical models are increasingly being developed and calibrated in tandem with data
collection, empowering scientists to intervene in real time based on quantitative model …

A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study

MC Eisenberg, HV Jain - Journal of theoretical biology, 2017 - Elsevier
Mathematical modeling has a long history in the field of cancer therapeutics, and there is
increasing recognition that it can help uncover the mechanisms that underlie tumor …

In silico models of cancer

LB Edelman, JA Eddy, ND Price - … Reviews: Systems Biology …, 2010 - Wiley Online Library
Cancer is a complex disease that involves multiple types of biological interactions across
diverse physical, temporal, and biological scales. This complexity presents substantial …

Interpretable machine learning for perturbation biology

B Yuan, C Shen, A Luna, A Korkut, DS Marks… - bioRxiv, 2019 - biorxiv.org
Systematic perturbation of cells followed by comprehensive measurements of molecular and
phenotypic responses provides an informative data resource for constructing computational …

[HTML][HTML] A semantics, energy-based approach to automate biomodel composition

N Shahidi, M Pan, K Tran, EJ Crampin, DP Nickerson - PloS one, 2022 - journals.plos.org
Hierarchical modelling is essential to achieving complex, large-scale models. However, not
all modelling schemes support hierarchical composition, and correctly mapping points of …

[HTML][HTML] Improved patient-specific calibration for agent-based cancer modeling

AZ Hyun, P Macklin - Journal of theoretical biology, 2013 - ncbi.nlm.nih.gov
Macklin et al.,(2012) recently introduced a mechanistic agent-based cell model, with
application to ductal carcinoma in situ (DCIS)—a precursor to invasive breast cancer. The …

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

J Tegnér, H Zenil, NA Kiani, G Ball… - … Transactions of the …, 2016 - royalsocietypublishing.org
Systems in nature capable of collective behaviour are nonlinear, operating across several
scales. Yet our ability to account for their collective dynamics differs in physics, chemistry …

Data-driven modelling of biological multi-scale processes

J Hasenauer, N Jagiella, S Hross… - Journal of Coupled …, 2015 - ingentaconnect.com
Biological processes involve a variety of spatial and temporal scales. A holistic
understanding of many biological processes therefore requires multi-scale models which …

Evolutionary approach to model calibration with uncertainty: an application to breast cancer growth model

C Andreu-Vilarroig, J Ceberio, JC Cortés… - Proceedings of the …, 2022 - dl.acm.org
Dynamical systems in most scientific areas can be modelled using ordinary differential
equations or difference equations. However, when analysing and simulating real-world …

A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models

MJ Simpson, OJ Maclaren - bioRxiv, 2022 - biorxiv.org
Interpreting data using mechanistic mathematical models provides a foundation for
discovery and decision-making in all areas of science and engineering. Key steps in using …