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
Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7528-0_6
Abstract: PSAMM is an open source software package that supports the iterative curation and analysis of genome-scale models (GEMs). It aims to integrate the annotation and consistency checking of metabolic models with the simulation of metabolic… read more here.
Keywords: curation analysis; analysis genome; metabolic models; model ... 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
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-16279-5
Abstract: The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth.… read more here.
Keywords: genomic selection; metabolic models; molecular markers; growth ... See more keywords
CobraMod: A pathway-centric curation tool for constraint-based metabolic models.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac119
Abstract: SUMMARY COnstraint-Based Reconstruction and Analysis of genome-scale metabolic models has become a widely used tool to understand metabolic network behavior at a large-scale. However, existing reconstruction tools lack functionalities to address modellers' common objective to… read more here.
Keywords: tool; pathway centric; constraint based; metabolic models ... See more keywords
Accelerating flux balance calculations in genome‐scale metabolic models by localizing the application of loopless constraints
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty446
Abstract: Background: Genome‐scale metabolic network models and constraint‐based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cycles (TICs) causing unbounded metabolic flux ranges are often encountered. TICs satisfy the mass balance and… read more here.
Keywords: genome scale; loopless constraints; flux; metabolic models ... See more keywords
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa746
Abstract: Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the… read more here.
Keywords: biochemistry; biochemistry database; metabolic models; database ... See more keywords
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic acids research"
DOI: 10.1093/nar/gkab815
Abstract: Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the… read more here.
Keywords: reconstruction; genome scale; directly metagenomes; metabolic models ... See more keywords
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac459
Abstract: Abstract Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures,… read more here.
Keywords: scale metabolic; merlin; reconstruction; metabolic models ... See more keywords
The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
Sign Up to like & getrecommendations! Published in 2018 at "mBio"
DOI: 10.1128/mbio.01433-18
Abstract: Current understanding of many animal-microbial symbioses involving unculturable bacterial symbionts with much-reduced genomes derives almost entirely from nonquantitative inferences from genome data. To overcome this limitation, we reconstructed multipartner metabolic models that quantify both the… read more here.
Keywords: insects; bacterial symbionts; metabolic models; host ... See more keywords
Current status and applications of genome-scale metabolic models
Sign Up to like & getrecommendations! Published in 2019 at "Genome Biology"
DOI: 10.1186/s13059-019-1730-3
Abstract: Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae… read more here.
Keywords: genome scale; current status; metabolic models; applications genome ... See more keywords