Understanding antimicrobial resistance using genome-scale metabolic modeling

T Alonso-Vásquez, M Fondi, E Perrin - Antibiotics, 2023 - mdpi.com
The urgent necessity to fight antimicrobial resistance is universally recognized. In the search
of new targets and strategies to face this global challenge, a promising approach resides in …

Bayesian metamodeling of complex biological systems across varying representations

B Raveh, L Sun, KL White, T Sanyal… - Proceedings of the …, 2021 - National Acad Sciences
Comprehensive modeling of a whole cell requires an integration of vast amounts of
information on various aspects of the cell and its parts. To divide and conquer this task, we …

Problems in the development of efficient biotechnology for the synthesis of valuable components from microalgae biomass

DS Dvoretsky, MS Temnov, IV Markin… - … of Chemical Engineering, 2022 - Springer
In recent decades, active research has been under way to find alternative sources of
renewable raw materials for the production of valuable components. Microalgae …

Large scale microalgae biofuel technology—development perspectives in light of the barriers and limitations

M Dębowski, I Świca, J Kazimierowicz, M Zieliński - Energies, 2022 - mdpi.com
Microalgal biomass can be used to derive many different types of biofuels. In order to widely
commercialize this technology, its limitations and weaknesses must be eliminated. Many …

Probing single-cell fermentation fluxes and exchange networks via pH-sensing hybrid nanofibers

V Onesto, S Forciniti, F Alemanno, K Narayanankutty… - ACS …, 2022 - ACS Publications
The homeostatic control of their environment is an essential task of living cells. It has been
hypothesized that, when microenvironmental pH inhomogeneities are induced by high …

Computation of single-cell metabolite distributions using mixture models

MK Tonn, P Thomas, M Barahona… - Frontiers in Cell and …, 2020 - frontiersin.org
Metabolic heterogeneity is widely recognized as the next challenge in our understanding of
non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity …

A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis

GR Lee, SM Lee, HU Kim - Metabolic Engineering, 2023 - Elsevier
Metabolic engineering has served as a systematic discipline for industrial biotechnology as
it has offered systematic tools and methods for strain development and bioprocess …

[HTML][HTML] scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data

MP Pacheco, J Ji, T Prohaska, MM García, T Sauter - Metabolites, 2022 - mdpi.com
Metabolites | Free Full-Text | scFASTCORMICS: A Contextualization Algorithm to
Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data Next …

Abstraction-based segmental simulation of reaction networks using adaptive memoization

M Helfrich, R Andriushchenko, M Češka, J Křetínský… - BMC …, 2024 - Springer
Background Stochastic models are commonly employed in the system and synthetic biology
to study the effects of stochastic fluctuations emanating from reactions involving species with …

Compartmentalization of metabolism between cell types in multicellular organisms: a computational perspective

X Li, LS Yilmaz, AJM Walhout - Current opinion in systems biology, 2022 - Elsevier
In multicellular organisms, metabolism is compartmentalized at many levels, including
tissues and organs, different cell types, and subcellular compartments …