Executable cancer models: successes and challenges

MA Clarke, J Fisher - Nature Reviews Cancer, 2020 - nature.com
Making decisions on how best to treat cancer patients requires the integration of different
data sets, including genomic profiles, tumour histopathology, radiological images, proteomic …

Data integration in logic-based models of biological mechanisms

BA Hall, A Niarakis - Current Opinion in Systems Biology, 2021 - Elsevier
Discrete, logic-based models are increasingly used to describe biological mechanisms.
Initially introduced to study gene regulation, these models evolved to cover various …

HOXA9 has the hallmarks of a biological switch with implications in blood cancers

L Talarmain, MA Clarke, D Shorthouse… - Nature …, 2022 - nature.com
Blood malignancies arise from the dysregulation of haematopoiesis. The type of blood cell
and the specific order of oncogenic events initiating abnormal growth ultimately determine …

Verifiable biology

S Konur, M Gheorghe… - Journal of the Royal …, 2023 - royalsocietypublishing.org
The formalization of biological systems using computational modelling approaches as an
alternative to mathematical-based methods has recently received much interest because …

Constructing and analyzing computational models of cell signaling with biomodelanalyzer

BA Hall, J Fisher - Current Protocols in Bioinformatics, 2020 - Wiley Online Library
BioModelAnalyzer (BMA) is an open‐source graphical tool for the development of
executable models of protein and gene networks within cells. Based upon the Qualitative …

Modelling timing in blood cancers

L Talarmain - 2021 - repository.cam.ac.uk
Dysregulation of biological processes in normal cells can lead to the abnormal growth of
tumours. Oncogenesis requires the acquisition of advantageous mutations to expand in a …

A review of modelling and verification approaches for computational biology

S Konur - 2020 - bradscholars.brad.ac.uk
This paper reviews most frequently used computational modelling approaches and formal
verification techniques in computational biology. The paper also compares a number of …

HOXA9 acts as a regulatory switch in acute myeloid leukaemia and myeloproliferative neoplasms

L Talarmain, MA Clarke, D Shorthouse, J Fisher… - bioRxiv, 2021 - biorxiv.org
Blood malignancies arise from the dysregulation of haematopoiesis. The type of blood cell
and the specific order of oncogenic events initiating abnormal growth ultimately determine …