Coordination of microbial metabolism
Beyond fuelling cellular activities with building blocks and energy, metabolism also
integrates environmental conditions into intracellular signals. The underlying regulatory …
integrates environmental conditions into intracellular signals. The underlying regulatory …
The return of metabolism: biochemistry and physiology of the pentose phosphate pathway
The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism.
The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide …
The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide …
Systems-level analysis of mechanisms regulating yeast metabolic flux
INTRODUCTION Metabolism is among the most strongly conserved processes across all
domains of life and is crucial for both bioengineering and disease research, yet we still have …
domains of life and is crucial for both bioengineering and disease research, yet we still have …
[HTML][HTML] Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
D Machado, M Herrgård - PLoS computational biology, 2014 - journals.plos.org
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …
distributions in genome-scale biochemical networks. The number of published methods for …
[HTML][HTML] A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
A Khodayari, CD Maranas - Nature communications, 2016 - nature.com
Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of
multiple genetic interventions would be transformative in our ability to reliably design novel …
multiple genetic interventions would be transformative in our ability to reliably design novel …
Transcriptional regulation is insufficient to explain substrate‐induced flux changes in Bacillus subtilis
One of the key ways in which microbes are thought to regulate their metabolism is by
modulating the availability of enzymes through transcriptional regulation. However, the …
modulating the availability of enzymes through transcriptional regulation. However, the …
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories
Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …
century industry. The production of a great range of chemicals via biotechnological means is …
Dynamic metabolic control: towards precision engineering of metabolism
Advances in metabolic engineering have led to the synthesis of a wide variety of valuable
chemicals in microorganisms. The key to commercializing these processes is the …
chemicals in microorganisms. The key to commercializing these processes is the …
Metabolomics and Microbial Metabolism: Toward a Systematic Understanding
D Holbrook-Smith, J Trouillon… - Annual Review of …, 2023 - annualreviews.org
Over the past decades, our understanding of microbial metabolism has increased
dramatically. Metabolomics, a family of techniques that are used to measure the quantities of …
dramatically. Metabolomics, a family of techniques that are used to measure the quantities of …
Leveraging knowledge engineering and machine learning for microbial bio-manufacturing
Genome scale modeling (GSM) predicts the performance of microbial workhorses and helps
identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and …
identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and …