Emerging tools and best practices for studying gut microbial community metabolism

C Noecker, PJ Turnbaugh - Nature Metabolism, 2024 - nature.com
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our
own cells, with far-reaching consequences for host health and disease. However, our …

[HTML][HTML] Biobased short chain fatty acid production-Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling …

M Atasoy, WT Scott Jr, A Regueira… - Biotechnology …, 2024 - Elsevier
In recent years, there has been growing interest in harnessing anaerobic digestion
technology for resource recovery from waste streams. This approach has evolved beyond its …

Deep learning for metabolic pathway design

G Ryu, GB Kim, T Yu, SY Lee - Metabolic Engineering, 2023 - Elsevier
The establishment of a bio-based circular economy is imperative in tackling the climate crisis
and advancing sustainable development. In this realm, the creation of microbial cell factories …

Enabling pathway design by multiplex experimentation and machine learning

AG Boob, J Chen, H Zhao - Metabolic Engineering, 2024 - Elsevier
The remarkable metabolic diversity observed in nature has provided a foundation for
sustainable production of a wide array of valuable molecules. However, transferring the …

[HTML][HTML] Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality

R Hasibi, T Michoel, DA Oyarzún - npj Systems Biology and …, 2024 - nature.com
Genome-scale metabolic models are powerful tools for understanding cellular physiology.
Flux balance analysis (FBA), in particular, is an optimization-based approach widely …

[HTML][HTML] From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

R Agharafeie, JRC Ramos, JM Mendes, R Oliveira - Fermentation, 2023 - mdpi.com
Deep learning is emerging in many industrial sectors in hand with big data analytics to
streamline production. In the biomanufacturing sector, big data infrastructure is lagging …

Molecular causality in the advent of foundation models

S Lobentanzer, P Rodriguez-Mier, S Bauer… - Molecular Systems …, 2024 - embopress.org
Correlation is not causation: this simple and uncontroversial statement has far-reaching
implications. Defining and applying causality in biomedical research has posed significant …

Cell factory design with advanced metabolic modelling empowered by artificial intelligence

H Lu, L Xiao, W Liao, X Yan, J Nielsen - Metabolic Engineering, 2024 - Elsevier
Advances in synthetic biology and artificial intelligence (AI) have provided new opportunities
for modern biotechnology. High-performance cell factories, the backbone of industrial …

Strategies in engineering sustainable biochemical synthesis through microbial systems

Y Song, KLJ Prather - Current Opinion in Chemical Biology, 2024 - Elsevier
Growing environmental concerns and the urgency to address climate change have
increased demand for the development of sustainable alternatives to fossil-derived fuels and …

[HTML][HTML] Machine Learning Applications in Precision Medicine: Overcoming Challenges and Unlocking potential

H Nilius, S Tsouka, M Nagler, M Masoodi - TrAC Trends in Analytical …, 2024 - Elsevier
Precision medicine, utilizing genomic and phenotypic data, aims to tailor treatments for
individual patients. However, successful implementation into clinical practice is challenging …