Hybrid modeling in bioprocess dynamics: Structural variabilities, implementation strategies, and practical challenges

B Mahanty - Biotechnology and Bioengineering, 2023 - Wiley Online Library
Hybrid modeling, with an appropriate blend of the mechanistic and data‐driven framework,
is increasingly being adopted in bioprocess modeling, model‐based experimental design …

Scientific novelty beyond the experiment

JE Hallsworth, Z Udaondo, C Pedrós‐Alió… - Microbial …, 2023 - Wiley Online Library
Practical experiments drive important scientific discoveries in biology, but theory‐based
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …

[HTML][HTML] Artificial intelligence and bioinformatics: a journey from traditional techniques to smart approaches

H Jamialahmadi, G Khalili-Tanha… - … from Bed to Bench, 2024 - pmc.ncbi.nlm.nih.gov
The incorporation of AI models into bioinformatics has brought about a revolutionary era in
the analysis and interpretation of biological data. This mini-review offers a succinct overview …

Design patterns for the construction of computational biological models

M Herajy, F Liu, M Heiner - Briefings in Bioinformatics, 2024 - academic.oup.com
Computational biological models have proven to be an invaluable tool for understanding
and predicting the behaviour of many biological systems. While it may not be too …

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 …

Splittable systems in biomedical applications

S Yuan, A Bremmer, X Yang, J Li, Q Hu - Biomaterials Science, 2024 - pubs.rsc.org
Splittable systems have emerged as a powerful approach for the precise spatiotemporal
control of biological processes. This concept relies on splitting a functional molecule into …

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 …

Bridging systems biology and tissue engineering: Unleashing the full potential of complex 3D in vitro tissue models of disease

JL Cadavid, NT Li, AP McGuigan - Biophysics Reviews, 2024 - pubs.aip.org
Rapid advances in tissue engineering have resulted in more complex and physiologically
relevant 3D in vitro tissue models with applications in fundamental biology and therapeutic …

Targeted quantification of protein phosphorylation and its contributions towards mathematical modeling of signaling pathways

PP Dakup, S Feng, T Shi, JM Jacobs, HS Wiley… - Molecules, 2023 - mdpi.com
Post-translational modifications (PTMs) are key regulatory mechanisms that can control
protein function. Of these, phosphorylation is the most common and widely studied. Because …

Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of Genome-Scale Metabolic Models in the …

C Alarcon, C Shene - Processes, 2022 - mdpi.com
Schizochytrium sp. is a microorganism cultured for producing docosahexaenoic acid (DHA).
Genome-scale metabolic modeling (GEM) is a promising technique for describing gen …