GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks

FM Weidner, N Ikonomi, SD Werle, JD Schwab… - …, 2024 - academic.oup.com
Motivation Boolean networks can serve as straightforward models for understanding
processes such as gene regulation, and employing logical rules. These rules can either be …

[HTML][HTML] Identification of dynamic driver sets controlling phenotypical landscapes

SD Werle, N Ikonomi, JD Schwab, JM Kraus… - Computational and …, 2022 - Elsevier
Controlling phenotypical landscapes is of vital interest to modern biology. This task becomes
highly demanding because cellular decisions involve complex networks engaging in …

Information-transfer characteristics in network motifs

F Mori, T Okada - Physical Review Research, 2023 - APS
Information processing in biological systems is realized by the appropriate transmission of
information flows over complex networks, such as gene regulatory, signal transduction, and …

On the feasibility of dynamical analysis of network models of biochemical regulation

LM Rocha - Bioinformatics, 2022 - academic.oup.com
A recent article by Weidner et al.(2021) presents a method to extract graph properties that
are predictive of the dynamical behavior of multivariate, discrete models of biochemical …

Logical modelling of molecular crosstalks for the prediction of complex phenotypes

N Ikonomi - 2023 - oparu.uni-ulm.de
Abstract Systems biology investigates the understanding of complex biological processes,
such as ageing or cancer, by integrating a holistic view, which is mostly unconsidered when …

Dissecting cell state transitions by causal inference

L Xu, TT Cong, H Xu, N Yang, C Tian, S Yang, M Zhu… - bioRxiv, 2023 - biorxiv.org
Trajectory inference methods are frequently used for cell fate analysis, however, most of
them are similarity-based and lack an understanding of the causality underlying …

Classical and quantum-mechanical algorithmic approaches for exploring the dynamics of Boolean networks

F Weidner - 2024 - oparu.uni-ulm.de
Boolean networks allow for the construction of dynamical models of biological processes
such as the cell cycle, cellular differentiation, ageing or diseases such as cancer. The …

Networks to Simulate the Development of Interacting Systems in Molecular Biology

JD Schwab, M Lutz, HA Kestler - Recent Trends and Future …, 2024 - books.google.com
Biological systems must adapt to a variety of changing circumstances over the course of
lifetime. They therefore rely on complex and robust mechanisms. This includes the …

Logical Modelling of Triple Negative Breast Cancer and in silico DRug Synergy Predictions

A Diatchenko - 2022 - ntnuopen.ntnu.no
Brystkreft er den hyppigst diagnostiserte kreften på verdensbasis med mer enn 2 millioner
nye tilfeller hvert år, og dette tallet forventes bare å stige. Brystkreft som mangler …

A First Glance on Coevolution of Boolean Networks to Simulate the Development of Interacting Systems in Molecular Biology

JD Schwab, M Lutz, HA Kestler - European Conference on Data Analysis, 2022 - Springer
Biological systems must adapt to a variety of changing circumstances over the course of
lifetime. They therefore rely on complex and robust mechanisms. This includes the …