Systems-based approaches to study immunometabolism

V Purohit, A Wagner, N Yosef… - Cellular & molecular …, 2022 - nature.com
Technical advances at the interface of biology and computation, such as single-cell RNA-
sequencing (scRNA-seq), reveal new layers of complexity in cellular systems. An emerging …

[HTML][HTML] Toward modeling metabolic state from single-cell transcriptomics

K Hrovatin, DS Fischer, FJ Theis - Molecular Metabolism, 2022 - Elsevier
Background Single-cell metabolic studies bring new insights into cellular function, which can
often not be captured on other omics layers. Metabolic information has wide applicability …

Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction

G Pio, P Mignone, G Magazzù, G Zampieri… - …, 2022 - academic.oup.com
Motivation Gene regulation is responsible for controlling numerous physiological functions
and dynamically responding to environmental fluctuations. Reconstructing the human …

A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors

ME Marques Da Costa, S Zaidi, JY Scoazec… - Communications …, 2023 - nature.com
Pediatric patients with recurrent and refractory cancers are in most need for new treatments.
This study developed patient-derived-xenograft (PDX) models within the European …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024 - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data

S Gopalakrishnan, CJ Joshi… - Metabolic …, 2023 - Elsevier
Genome-scale metabolic models comprehensively describe an organism's metabolism and
can be tailored using omics data to model condition-specific physiology. The quality of …

State-of the-art constraint-based modeling of microbial metabolism: from basics to context-specific models with a focus on methanotrophs

MA Kulyashov, SK Kolmykov, TM Khlebodarova… - Microorganisms, 2023 - mdpi.com
Methanotrophy is the ability of an organism to capture and utilize the greenhouse gas,
methane, as a source of energy-rich carbon. Over the years, significant progress has been …

Molecular systems biology approaches to investigate mechanisms of gut− brain communication in neurological diseases

V Boris, V Vanessa - European Journal of Neurology, 2023 - Wiley Online Library
Background Whilst the incidence of neurological diseases is increasing worldwide,
treatment remains mostly limited to symptom management. The gut− brain axis, which …

MDIC3: Matrix decomposition to infer cell-cell communication

Y Liu, Y Zhang, X Chang, X Liu - Patterns, 2024 - cell.com
Crosstalk among cells is vital for maintaining the biological function and intactness of
systems. Most existing methods for investigating cell-cell communications are based on …

COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling

S Gopalakrishnan, W Johnson… - Metabolic …, 2024 - Elsevier
Metabolism governs cell performance in biomanufacturing, as it fuels growth and
productivity. However, even in well-controlled culture systems, metabolism is dynamic, with …