Revealing the metabolic characteristics of human embryonic stem cells by genome‐scale metabolic modeling
Sign Up to like & getrecommendations! Published in 2018 at "FEBS Letters"
DOI: 10.1002/1873-3468.13255
Abstract: Embryonic stem cells (ESCs) are characterized by a dual capacity, self‐renewal and pluripotency, which can be regulated by metabolism. A better understanding of ESC metabolism and regulatory mechanisms is pivotal for research into development, ageing,… read more here.
Keywords: genome scale; metabolic characteristics; embryonic stem; stem ... See more keywords
Optimization of a modeling platform to predict oncogenes from genome‐scale metabolic networks of non‐small‐cell lung cancers
Sign Up to like & getrecommendations! Published in 2021 at "FEBS Open Bio"
DOI: 10.1002/2211-5463.13231
Abstract: Cancer cell dysregulations result in the abnormal regulation of cellular metabolic pathways. By simulating this metabolic reprogramming using constraint‐based modeling approaches, oncogenes can be predicted, and this knowledge can be used in prognosis and treatment.… read more here.
Keywords: genome scale; platform; expression; scale metabolic ... See more keywords
Genome‐Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production
Sign Up to like & getrecommendations! Published in 2019 at "Biotechnology Journal"
DOI: 10.1002/biot.201800377
Abstract: Systems biology approaches are increasingly applied to explore the potential of actinomycetes for the discovery and optimal production of antibiotics. In particular, genome‐scale metabolic models (GEMs) of various actinomycetes are reconstructed at a faster rate… read more here.
Keywords: reconstruction actinomycetes; genome scale; production; actinomycetes antibiotics ... See more keywords
Genome‐Scale Metabolic Model's multi‐objective solving algorithm based on the inflexion point of Pareto front including maximum energy utilization and its application in Aspergillus niger DS03043
Sign Up to like & getrecommendations! Published in 2022 at "Biotechnology and Bioengineering"
DOI: 10.1002/bit.28078
Abstract: The solution of Genome‐Scale Metabolic Model (GSMM) directly affects the simulation accuracy of the metabolic process in digital cells. Single‐objective optimization methods, such as flux balance analysis (FBA), which is widely used in solving GSMM,… read more here.
Keywords: scale metabolic; multi objective; pareto front; gsmm ... See more keywords
How reliable are Chinese Hamster Ovary (CHO) cell genome-scale metabolic models?
Sign Up to like & getrecommendations! Published in 2023 at "Biotechnology and bioengineering"
DOI: 10.1002/bit.28366
Abstract: Genome-scale metabolic models (GEMs) possess the power to revolutionise bioprocess and cell line engineering workflows by their ability to predict and understand whole cell metabolism in silico. Despite this potential, it is unclear how accurately… read more here.
Keywords: scale metabolic; cell; cho cell; cho ... See more keywords
Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells
Sign Up to like & getrecommendations! Published in 2022 at "Computers in biology and medicine"
DOI: 10.1016/j.compbiomed.2021.105177
Abstract: Cancer Stem Cells (CSCs) contribute to cancer aggressiveness, metastasis, chemo/radio-therapy resistance, and tumor recurrence. Recent studies emphasized the importance of metabolic reprogramming of CSCs for the maintenance and progression of the cancer phenotype through both… read more here.
Keywords: cancer; genome scale; scale metabolic; stem cells ... See more keywords
Genome-scale metabolic modelling common cofactors metabolism in microorganisms.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of biotechnology"
DOI: 10.1016/j.jbiotec.2017.04.004
Abstract: The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic… read more here.
Keywords: cell growth; common cofactors; genome scale; scale metabolic ... See more keywords
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Sign Up to like & getrecommendations! Published in 2017 at "Nature Biotechnology"
DOI: 10.1038/nbt.3703
Abstract: Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and… read more here.
Keywords: genome scale; human gut; metabolic reconstructions; generation genome ... See more keywords
Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-00170-3
Abstract: Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based… read more here.
Keywords: genome scale; metabolic pathways; analysis; steady state ... See more keywords
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa280
Abstract: Abstract Motivation Elementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are… read more here.
Keywords: flux modes; genome scale; elementary flux; linear programming ... See more keywords
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac596
Abstract: Abstract Motivation Genome-scale metabolic reconstructions have been assembled for thousands of organisms using a wide range of tools. However, metabolite annotations, required to compare and link metabolites between reconstructions, remain incomplete. Here, we aim to… read more here.
Keywords: scale metabolic; metabolic reconstructions; efficient toolbox; metaboannotator efficient ... See more keywords