Matches in SemOpenAlex for { <https://semopenalex.org/work/W4387014014> ?p ?o ?g. }
Showing items 1 to 43 of
43
with 100 items per page.
- W4387014014 abstract "Metabolic capacity can vary substantially within a bacterial species, leading to ecological niche separation, as well as differences in virulence and antimicrobial susceptibility. Genome-scale metabolic models are useful tools for studying the metabolic potential of individuals, and with the rapid expansion of genomic sequencing there is a wealth of data that can be leveraged for comparative analysis. However, there exist few tools to construct strain-specific metabolic models at scale.Here we describe Bactabolize (github.com/kelwyres/Bactabolize), a reference-based tool which rapidly produces strain-specific metabolic models and growth phenotype predictions. We describe a pan reference model for the priority antimicrobial-resistant pathogen, Klebsiella pneumoniae (github.com/kelwyres/KpSC-pan-metabolic-model), and a quality control framework for using draft genome assemblies as input for Bactabolize.The Bactabolize-derived model for K. pneumoniae reference strain KPPR1 performed comparatively or better than currently available automated approaches CarveMe and gapseq across 507 substrate and 2317 knockout mutant growth predictions. Novel draft genomes passing our systematically-defined quality control criteria resulted in models with a high degree of completeness (≥99% genes and reactions captured compared to models derived from matched complete genomes) and high accuracy (mean 0.97, n=10).We anticipate the tools and framework described herein will facilitate large-scale metabolic modelling analyses that broaden our understanding of diversity within bacterial species and inform novel control strategies for priority pathogens." @default.
- W4387014014 created "2023-09-26" @default.
- W4387014014 creator A5053221025 @default.
- W4387014014 date "2023-09-25" @default.
- W4387014014 modified "2023-09-26" @default.
- W4387014014 title "eLife assessment: Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models" @default.
- W4387014014 doi "https://doi.org/10.7554/elife.87406.2.sa0" @default.
- W4387014014 hasPublicationYear "2023" @default.
- W4387014014 type Work @default.
- W4387014014 citedByCount "0" @default.
- W4387014014 crossrefType "peer-review" @default.
- W4387014014 hasAuthorship W4387014014A5053221025 @default.
- W4387014014 hasBestOaLocation W43870140141 @default.
- W4387014014 hasConcept C104317684 @default.
- W4387014014 hasConcept C141231307 @default.
- W4387014014 hasConcept C41008148 @default.
- W4387014014 hasConcept C54355233 @default.
- W4387014014 hasConcept C60987743 @default.
- W4387014014 hasConcept C70721500 @default.
- W4387014014 hasConcept C86803240 @default.
- W4387014014 hasConceptScore W4387014014C104317684 @default.
- W4387014014 hasConceptScore W4387014014C141231307 @default.
- W4387014014 hasConceptScore W4387014014C41008148 @default.
- W4387014014 hasConceptScore W4387014014C54355233 @default.
- W4387014014 hasConceptScore W4387014014C60987743 @default.
- W4387014014 hasConceptScore W4387014014C70721500 @default.
- W4387014014 hasConceptScore W4387014014C86803240 @default.
- W4387014014 hasLocation W43870140141 @default.
- W4387014014 hasOpenAccess W4387014014 @default.
- W4387014014 hasPrimaryLocation W43870140141 @default.
- W4387014014 hasRelatedWork W1603543036 @default.
- W4387014014 hasRelatedWork W2020416941 @default.
- W4387014014 hasRelatedWork W2056463789 @default.
- W4387014014 hasRelatedWork W2069184423 @default.
- W4387014014 hasRelatedWork W2122868133 @default.
- W4387014014 hasRelatedWork W2146529826 @default.
- W4387014014 hasRelatedWork W2914415623 @default.
- W4387014014 hasRelatedWork W3034237829 @default.
- W4387014014 hasRelatedWork W3185880145 @default.
- W4387014014 hasRelatedWork W2187207551 @default.
- W4387014014 isParatext "false" @default.
- W4387014014 isRetracted "false" @default.
- W4387014014 workType "peer-review" @default.