Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations

EL Carter, C Constantinidou… - Briefings in …, 2024 - academic.oup.com
Environmental perturbations are encountered by microorganisms regularly and will require
metabolic adaptations to ensure an organism can survive in the newly presenting …

[HTML][HTML] Toward systems-level metabolic analysis in endocrine disorders and cancer

A Lakhani, YE Kang, JO Park - Endocrinology and …, 2023 - synapse.koreamed.org
Metabolism is a dynamic network of biochemical reactions that support systemic
homeostasis amidst changing nutritional, environmental, and physical activity factors. The …

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

E Zaunseder, U Mütze, JG Okun, GF Hoffmann… - Cell Metabolism, 2024 - cell.com
Comprehensive whole-body models (WBMs) accounting for organ-specific dynamics have
been developed to simulate adult metabolism, but such models do not exist for infants. Here …

Nonlinear programming reformulation of dynamic flux balance analysis models

RD de Oliveira, GAC Le Roux, R Mahadevan - Computers & Chemical …, 2023 - Elsevier
Dynamic flux balance analysis (dFBA) models are very popular in systems biology because
of the many possible applications. dFBA consists of dynamic mass balance equations that …

A novel electrochemical insulin aptasensor: From glassy carbon electrodes to disposable, single-use laser-scribed graphene electrodes

J Liu, B Zhu, H Dong, Y Zhang, M Xu, J Travas-Sejdic… - …, 2022 - Elsevier
Insulin, a peptide hormone secreted by pancreatic β cells, affects the development of
diabetes and associated complications. Herein, we propose an electrochemical aptasensor …

[HTML][HTML] Network modeling approaches for metabolic diseases and diabetes

A Badkas, MP Pacheco, T Sauter - Current Opinion in Systems Biology, 2024 - Elsevier
Metabolic diseases (MD) are amenable to network-based modeling frameworks, given the
systemic perturbations induced by disrupted molecular mechanisms. We present here a …

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks

P Lakrisenko, P Stapor, S Grein… - PLOS Computational …, 2023 - journals.plos.org
Dynamical models in the form of systems of ordinary differential equations have become a
standard tool in systems biology. Many parameters of such models are usually unknown and …

Understanding the metabolism of infants using whole-body metabolic models

SY Lee, GB Kim - Cell Metabolism, 2024 - Elsevier
A whole-body model is a computational representation of sex-specific and organ-resolved
whole-body metabolism. In this issue of Cell Metabolism, Zaunseder et al. report whole-body …

[HTML][HTML] Dynamic models for metabolomics data integration

P Lakrisenko, D Weindl - Current Opinion in Systems Biology, 2021 - Elsevier
As metabolomics datasets are becoming larger and more complex, there is an increasing
need for model-based data integration and analysis to optimally leverage these data …

MitoMAMMAL: a genome scale model of mammalian mitochondria predicts cardiac and BAT metabolism

S Chapman, T Brunet, A Mourier… - Bioinformatics …, 2025 - academic.oup.com
Motivation Mitochondria are essential for cellular metabolism and are inherently flexible to
allow correct function in a wide range of tissues. Consequently, dysregulated mitochondrial …