Metaheuristics in large-scale global continues optimization: A survey

S Mahdavi, ME Shiri, S Rahnamayan - Information Sciences, 2015 - Elsevier
Metaheuristic algorithms are extensively recognized as effective approaches for solving high-
dimensional optimization problems. These algorithms provide effective tools with important …

Building Digital Twins for Cardiovascular Health: from principles to clinical impact

K Sel, D Osman, F Zare… - Journal of the …, 2024 - ahajournals.org
The past several decades have seen rapid advances in diagnosis and treatment of
cardiovascular diseases and stroke, enabled by technological breakthroughs in imaging …

Benchmarking optimization methods for parameter estimation in large kinetic models

AF Villaverde, F Fröhlich, D Weindl, J Hasenauer… - …, 2019 - academic.oup.com
Motivation Kinetic models contain unknown parameters that are estimated by optimizing the
fit to experimental data. This task can be computationally challenging due to the presence of …

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

AF Villaverde, JR Banga - Journal of the Royal Society …, 2014 - royalsocietypublishing.org
The interplay of mathematical modelling with experiments is one of the central elements in
systems biology. The aim of reverse engineering is to infer, analyse and understand …

[HTML][HTML] Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

DB Kell, R Goodacre - Drug Discovery Today, 2014 - Elsevier
Highlights•We now have metabolic network models; the metabolome is represented by their
nodes.•Metabolite levels are sensitive to changes in enzyme activities.•Drugs hitchhike on …

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

JA Egea, D Henriques, T Cokelaer, AF Villaverde… - BMC …, 2014 - Springer
Background Optimization is the key to solving many problems in computational biology.
Global optimization methods, which provide a robust methodology, and metaheuristics in …

Mathematical and computational modeling in complex biological systems

Z Ji, K Yan, W Li, H Hu, X Zhu - BioMed research international, 2017 - Wiley Online Library
The biological process and molecular functions involved in the cancer progression remain
difficult to understand for biologists and clinical doctors. Recent developments in high …

Hybrid metaheuristics and multi-agent systems for solving optimization problems: A review of frameworks and a comparative analysis

MAL Silva, SR de Souza, MJF Souza… - Applied Soft …, 2018 - Elsevier
This article presents a review and a comparative analysis between frameworks for solving
optimization problems using metaheuristics. The aim is to identify both the desirable …

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

A Sahin, DR Weilandt, V Hatzimanikatis - Nature Communications, 2023 - nature.com
Deciphering the metabolic functions of organisms requires understanding the dynamic
responses of living cells upon genetic and environmental perturbations, which in turn can be …

Comprehensive review of models and methods for inferences in bio-chemical reaction networks

P Loskot, K Atitey, L Mihaylova - Frontiers in genetics, 2019 - frontiersin.org
The key processes in biological and chemical systems are described by networks of
chemical reactions. From molecular biology to biotechnology applications, computational …