Physiologically based pharmacokinetic modeling of nanoparticle biodistribution: a review of existing models, simulation software, and data analysis tools

EO Kutumova, IR Akberdin, IN Kiselev… - International Journal of …, 2022 - mdpi.com
Cancer treatment and pharmaceutical development require targeted treatment and less toxic
therapeutic intervention to achieve real progress against this disease. In this scenario …

Construction of multiscale genome-scale metabolic models: Frameworks and challenges

X Bi, Y Liu, J Li, G Du, X Lv, L Liu - Biomolecules, 2022 - mdpi.com
Genome-scale metabolic models (GEMs) are effective tools for metabolic engineering and
have been widely used to guide cell metabolic regulation. However, the single gene–protein …

Delay-differential SEIR modeling for improved modelling of infection dynamics

IN Kiselev, IR Akberdin, FA Kolpakov - Scientific Reports, 2023 - nature.com
Abstract SEIR (Susceptible–Exposed–Infected–Recovered) approach is a classic modeling
method that is frequently used to study infectious diseases. However, in the vast majority of …

Mathematical modeling of antihypertensive therapy

E Kutumova, I Kiselev, R Sharipov, G Lifshits… - Frontiers in …, 2022 - frontiersin.org
Hypertension is a multifactorial disease arising from complex pathophysiological pathways.
Individual characteristics of patients result in different responses to various classes of …

MakeSBML: A tool for converting between Antimony and SBML

BE Jardine, LP Smith, HM Sauro - Journal of Integrative …, 2024 - degruyter.com
We describe a web-based tool, MakeSBML (https://sys-bio. github. io/makesbml/), that
provides an installation-free application for creating, editing, and searching the Biomodels …

[HTML][HTML] Multiomics of Aging and Aging-Related Diseases

OI Kiseleva, VA Arzumanian, YA Ikhalaynen… - International Journal of …, 2024 - mdpi.com
Despite their astonishing biological diversity, surprisingly few shared traits connect all or
nearly all living organisms. Aging, ie, the progressive and irreversible decline in the function …

[HTML][HTML] A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis

M Arbatskiy, D Balandin, I Akberdin… - International Journal of …, 2024 - mdpi.com
Ferroptosis is a regulated cell death process characterized by iron ion catalysis and reactive
oxygen species, leading to lipid peroxidation. This mechanism plays a crucial role in age …

Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli

IR Akberdin, KN Kozlov, FV Kazantsev… - International Journal of …, 2023 - mdpi.com
Earlier studies aimed at investigating the metabolism of endogenous nucleoside
triphosphates in synchronous cultures of E. coli cells revealed an auto-oscillatory mode of …

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

MA Kulyashov, R Hamilton, Y Afshin, SK Kolmykov… - …, 2024 - journals.asm.org
Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient
strategy for integrating and cross-comparing experimental multi-scale data to explore the …

[HTML][HTML] A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach

MA Esembaeva, MA Kulyashov… - International …, 2024 - pmc.ncbi.nlm.nih.gov
Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels,
and other valuable compounds, leveraging the power of microbial systems for enhanced …