[HTML][HTML] Concepts in Boolean network modeling: What do they all mean?

JD Schwab, SD Kühlwein, N Ikonomi, M Kühl… - Computational and …, 2020 - Elsevier
Boolean network models are one of the simplest models to study complex dynamic behavior
in biological systems. They can be applied to unravel the mechanisms regulating the …

Logical modeling and dynamical analysis of cellular networks

W Abou-Jaoudé, P Traynard, PT Monteiro… - Frontiers in …, 2016 - frontiersin.org
The logical (or logic) formalism is increasingly used to model regulatory and signaling
networks. Complementing these applications, several groups contributed various methods …

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

MP Menden, D Wang, MJ Mason, B Szalai… - Nature …, 2019 - nature.com
The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop
resistance that might be overcome with drug combinations. However, the number of possible …

Patient-specific Boolean models of signalling networks guide personalised treatments

A Montagud, J Béal, L Tobalina, P Traynard… - Elife, 2022 - elifesciences.org
Prostate cancer is the second most occurring cancer in men worldwide. To better
understand the mechanisms of tumorigenesis and possible treatment responses, we …

CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy

SR Hosseini, X Zhou - Briefings in bioinformatics, 2023 - academic.oup.com
Combination therapy is a promising strategy for confronting the complexity of cancer.
However, experimental exploration of the vast space of potential drug combinations is costly …

[HTML][HTML] Combined mechanistic modeling and machine-learning approaches in systems biology–A systematic literature review

A Procopio, G Cesarelli, L Donisi, A Merola… - Computer methods and …, 2023 - Elsevier
Background and objective Mechanistic-based Model simulations (MM) are an effective
approach commonly employed, for research and learning purposes, to better investigate …

A network embedding framework based on integrating multiplex network for drug combination prediction

L Yu, M Xia, Q An - Briefings in bioinformatics, 2022 - academic.oup.com
Drug combination is a sensible strategy for disease treatment because it improves the
treatment efficacy and reduces concomitant side effects. Due to the large number of possible …

Network propagation predicts drug synergy in cancers

H Li, T Li, D Quang, Y Guan - Cancer research, 2018 - AACR
Combination therapies are commonly used to treat patients with complex diseases that
respond poorly to single-agent therapies. In vitro high-throughput drug screening is a …

[HTML][HTML] Boolean modelling as a logic-based dynamic approach in systems medicine

AA Hemedan, A Niarakis, R Schneider… - Computational and …, 2022 - Elsevier
Molecular mechanisms of health and disease are often represented as systems biology
diagrams, and the coverage of such representation constantly increases. These static …

Drug resistance mechanisms in colorectal cancer dissected with cell type–specific dynamic logic models

F Eduati, V Doldàn-Martelli, B Klinger, T Cokelaer… - Cancer research, 2017 - AACR
Genomic features are used as biomarkers of sensitivity to kinase inhibitors used widely to
treat human cancer, but effective patient stratification based on these principles remains …