Hybrid modelling of biological systems: current progress and future prospects

F Liu, M Heiner, D Gilbert - Briefings in Bioinformatics, 2022 - academic.oup.com
Integrated modelling of biological systems is becoming a necessity for constructing models
containing the major biochemical processes of such systems in order to obtain a holistic …

Stochastic models for single‐cell data: Current challenges and the way forward

IS Hsu, AM Moses - The FEBS Journal, 2022 - Wiley Online Library
Although the quantity and quality of single‐cell data have progressed rapidly, making
quantitative predictions with single‐cell stochastic models remains challenging. The …

A modified variational approach to noisy cell signaling

R Cai, Y Lan - The Journal of Chemical Physics, 2024 - pubs.aip.org
Signaling in cells is full of noise and, hence, described with stochastic biochemical models.
Thus, an efficient computation algorithm for these fluctuating reactions is much needed …

A workflow for the hybrid modelling and simulation of multi-timescale biological systems

M Herajy, F Liu, M Heiner - BioSystems, 2025 - Elsevier
With the steady advance of in-silico biological experimentation, model construction and
simulation becomes a ubiquitous tool to understand and predict the behaviour of many …

Addressing data uncertainty of Caulobacter crescentus cell cycles using hybrid Petri nets with fuzzy kinetics

G Assaf, F Liu, M Heiner, M Herajy - Computers in Biology and Medicine, 2025 - Elsevier
Studying and analysing the various phases and key proteins of cell cycles is essential for the
understanding of cell development and differentiation. To this end, mechanistic models play …

Dynamical analysis of the fission yeast cell cycle via Markov chain

S Shafiekhani, P Kraikivski, N Gheibi, M Ahmadian… - Current Genetics, 2021 - Springer
The cell cycle is a complex network involved in the regulation of cell growth and
proliferation. Intrinsic molecular noise in gene expression in the cell cycle network can …

Impact of variability in cell cycle periodicity on cell population dynamics

CM Nowak, T Quarton, L Bleris - PLOS Computational Biology, 2023 - journals.plos.org
The cell cycle consists of a series of orchestrated events controlled by molecular sensing
and feedback networks that ultimately drive the duplication of total DNA and the subsequent …

Tight uncertainty relations for cycle currents

M Polettini, G Falasco, M Esposito - Physical Review E, 2022 - APS
Several recent inequalities bound the precision of a current, ie, a counter of the net number
of transitions in a system, by a thermodynamic measure of dissipation. However, while …

Response to stress via underlying deep gene regulation networks

S Vakulenko, D Grigoriev, A Suchkov… - … Methods in the …, 2024 - Wiley Online Library
Exposure of cells to non‐optimal growth conditions or to any environment that reduces cell
viability can be considered as a stress. In this paper, we are going to highlight the main …

The review of micro-electromechanical systems-based biosensor: A cellular base perspective

A Aditya, E Rufus - … for Next-Generation Electronic Systems and …, 2023 - taylorfrancis.com
This chapter discusses the mass sensors for biological applications in the early detection of
cyto-pathological diseases. We are focusing on design and developing parameters of a …