Systems-based approaches to study immunometabolism
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 …
sequencing (scRNA-seq), reveal new layers of complexity in cellular systems. An emerging …
[HTML][HTML] Toward modeling metabolic state from single-cell transcriptomics
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 …
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
Motivation Gene regulation is responsible for controlling numerous physiological functions
and dynamically responding to environmental fluctuations. Reconstructing the human …
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 …
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 …
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 …
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 …
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 …
treatment remains mostly limited to symptom management. The gut− brain axis, which …
MDIC3: Matrix decomposition to infer cell-cell communication
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 …
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 …
productivity. However, even in well-controlled culture systems, metabolism is dynamic, with …