[PDF][PDF] A hybrid flux balance analysis and machine learning pipeline elucidates metabolic adaptation in cyanobacteria
Machine learning has recently emerged as a promising tool for inferring multi-omic
relationships in biological systems. At the same time, genome-scale metabolic models …
relationships in biological systems. At the same time, genome-scale metabolic models …
[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 …
Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions
Cyanobacteria are oxygenic photoautotrophs whose metabolism contains key biochemical
pathways to fix atmospheric CO 2 and synthesize various metabolites. The development of …
pathways to fix atmospheric CO 2 and synthesize various metabolites. The development of …
[HTML][HTML] Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and …
Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a
coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output …
coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output …
Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction
Cyanobacteria are prokaryotes capable of performing oxygenic photosynthesis. This makes
them an attractive candidate for genetic engineering to produce commercially important …
them an attractive candidate for genetic engineering to produce commercially important …
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable
obligate phototroph that is being developed for the bioproduction of high-value chemicals …
obligate phototroph that is being developed for the bioproduction of high-value chemicals …
[HTML][HTML] Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
MA Hernández-Prieto, TA Semeniuk… - Frontiers in genetics, 2014 - frontiersin.org
Cyanobacteria are essential primary producers in marine ecosystems, playing an important
role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and …
role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and …
[HTML][HTML] Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function
Abstract Background Genome-scale models (GSMs) are widely used to predict
cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs …
cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs …
Species-specific transcriptomic network inference of interspecies interactions
The advent of high-throughput 'omics approaches coupled with computational analyses to
reconstruct individual genomes from metagenomes provides a basis for species-resolved …
reconstruct individual genomes from metagenomes provides a basis for species-resolved …
[HTML][HTML] Functional comparison of metabolic networks across species
C Ramon, J Stelling - Nature Communications, 2023 - nature.com
Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history
and environmental adaptation shape these phenotypes is an open problem. Especially for …
and environmental adaptation shape these phenotypes is an open problem. Especially for …