[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 …
[HTML][HTML] Modelling microbial communities: Harnessing consortia for biotechnological applications
Microbes propagate and thrive in complex communities, and there are many benefits to
studying and engineering microbial communities instead of single strains. Microbial …
studying and engineering microbial communities instead of single strains. Microbial …
[HTML][HTML] Interdisciplinary overview of lipopeptide and protein-containing biosurfactants
RA Júnior, J de Faria Poloni, ÉSM Pinto, M Dorn - Genes, 2023 - ncbi.nlm.nih.gov
Biosurfactants are amphipathic molecules capable of lowering interfacial and superficial
tensions. Produced by living organisms, these compounds act the same as chemical …
tensions. Produced by living organisms, these compounds act the same as chemical …
[HTML][HTML] Interdisciplinary overview of lipopeptide and protein-containing biosurfactants
R Antonioli Júnior, JF Poloni, ÉSM Pinto, M Dorn - Genes, 2022 - mdpi.com
Biosurfactants are amphipathic molecules capable of lowering interfacial and superficial
tensions. Produced by living organisms, these compounds act the same as chemical …
tensions. Produced by living organisms, these compounds act the same as chemical …
Trade-offs in biosensor optimization for dynamic pathway engineering
Recent progress in synthetic biology allows the construction of dynamic control circuits for
metabolic engineering. This technology promises to overcome many challenges …
metabolic engineering. This technology promises to overcome many challenges …
[HTML][HTML] Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality
Genome-scale metabolic models are powerful tools for understanding cellular physiology.
Flux balance analysis (FBA), in particular, is an optimization-based approach widely …
Flux balance analysis (FBA), in particular, is an optimization-based approach widely …
[HTML][HTML] Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects
Network biology finds application in interpreting molecular interaction networks and
providing insightful inferences using graph theoretical analysis of biological systems. The …
providing insightful inferences using graph theoretical analysis of biological systems. The …
[HTML][HTML] Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002
S Vijayakumar, C Angione - STAR protocols, 2021 - Elsevier
Combining a computational framework for flux balance analysis with machine learning
improves the accuracy of predicting metabolic activity across conditions, while enabling …
improves the accuracy of predicting metabolic activity across conditions, while enabling …
Prediction of gene essentiality using machine learning and genome-scale metabolic models
LJ Freischem, M Barahona, DA Oyarzún - IFAC-PapersOnLine, 2022 - Elsevier
The identification of essential genes, ie those that impair cell survival when deleted, requires
large growth assays of knock-out strains. The complexity and cost of such experiments has …
large growth assays of knock-out strains. The complexity and cost of such experiments has …
[HTML][HTML] Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks–What about specialised metabolism?
D Nègre, A Larhlimi, S Bertrand - Plos one, 2023 - journals.plos.org
In recent years, genome sequencing of filamentous fungi has revealed a high proportion of
specialised metabolites with growing pharmaceutical interest. However, detecting such …
specialised metabolites with growing pharmaceutical interest. However, detecting such …