Cargando…

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models

SUMMARY: In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform samplin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Haraldsdóttir, Hulda S, Cousins, Ben, Thiele, Ines, Fleming, Ronan M.T, Vempala, Santosh
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447232/ https://www.ncbi.nlm.nih.gov/pubmed/28158334 http://dx.doi.org/10.1093/bioinformatics/btx052

Ejemplares similares

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
por: Haraldsdóttir, Hulda S, et al.
Publicado: (2014)

Cardinality optimization in constraint-based modelling: application to human metabolism
por: Fleming, Ronan M T, et al.
Publicado: (2023)

Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance
por: Jadebeck, Johann F., et al.
Publicado: (2023)

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
por: Haraldsdóttir, Hulda S., et al.
Publicado: (2016)

fastGapFill: efficient gap filling in metabolic networks
por: Thiele, Ines, et al.
Publicado: (2014)

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
por: Heirendt, Laurent, et al.
Publicado: (2017)

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions
por: Thiele, Ines, et al.
Publicado: (2022)

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
por: Heinken, Almut, et al.
Publicado: (2021)

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
por: Preciat Gonzalez, German A., et al.
Publicado: (2017)

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
por: Baldini, Federico, et al.
Publicado: (2019)

Consistent Estimation of Gibbs Energy Using Component Contributions
por: Noor, Elad, et al.
Publicado: (2013)

Crystal Structure of ChrR—A Quinone Reductase with the Capacity to Reduce Chromate
por: Eswaramoorthy, Subramaniam, et al.
Publicado: (2012)

Reduction of Hexavalent Chromium and Detection of Chromate Reductase (ChrR) in Stenotrophomonas maltophilia
por: Baldiris, Rosa, et al.
Publicado: (2018)

PolyRound: polytope rounding for random sampling in metabolic networks
por: Theorell, Axel, et al.
Publicado: (2021)

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication
por: Thiele, Ines, et al.
Publicado: (2022)

ReconMap: an interactive visualization of human metabolism
por: Noronha, Alberto, et al.
Publicado: (2017)

HitWalker: variant prioritization for personalized functional cancer genomics
por: Bottomly, Daniel, et al.
Publicado: (2013)

CD-HIT: accelerated for clustering the next-generation sequencing data
por: Fu, Limin, et al.
Publicado: (2012)

HitWalker2: visual analytics for precision medicine and beyond
por: Bottomly, Daniel, et al.
Publicado: (2016)

CD-HIT Suite: a web server for clustering and comparing biological sequences
por: Huang, Ying, et al.
Publicado: (2010)

cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly
por: Lewis, T E, et al.
Publicado: (2019)

Etats hémodynamiques et respiratoires des opérées de fistules obstétricales sous rachianesthésie au CHRR Manakara, Madagascar
por: Martinetti, Andrianimaro Florelia, et al.
Publicado: (2016)

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
por: Heinken, Almut, et al.
Publicado: (2022)

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
por: Niu, Beifang, et al.
Publicado: (2011)

COBREXA.jl: constraint-based reconstruction and exascale analysis
por: Kratochvíl, Miroslav, et al.
Publicado: (2021)

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae
por: Tardu, Mehmet, et al.
Publicado: (2017)

Robust flux balance analysis of multiscale biochemical reaction networks
por: Sun, Yuekai, et al.
Publicado: (2013)

Quantitative systems pharmacology and the personalized drug–microbiota–diet axis
por: Thiele, Ines, et al.
Publicado: (2017)

Modeling RNA loops using sequence homology and geometric constraints
por: Schudoma, Christian, et al.
Publicado: (2010)

FBA-SimVis: interactive visualization of constraint-based metabolic models
por: Grafahrend-Belau, Eva, et al.
Publicado: (2009)

The random projection method
por: Vempala, Santosh S
Publicado: (2005)

Inferring the impacts of evolutionary history and ecological constraints on spore size and shape in the ferns
por: Barrington, David S., et al.
Publicado: (2020)

CobraMod: a pathway-centric curation tool for constraint-based metabolic models
por: Camborda, Stefano, et al.
Publicado: (2022)

A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
por: Mao, Longfei, et al.
Publicado: (2015)

GenomeWarp: an alignment-based variant coordinate transformation
por: McLean, Cory Y, et al.
Publicado: (2019)

Task constraints and stepping movement of fast-pitch softball hitting
por: Takamido, Ryota, et al.
Publicado: (2019)

Hit-and-run lymphomagenesis by the Bcl6 oncogene
por: Green, Michael R, et al.
Publicado: (2014)

Hit‐and‐run trophallaxis of small hive beetles
por: Neumann, Peter, et al.
Publicado: (2015)

“Hit-and-Run” transcription: de novo transcription initiated by a transient bZIP1 “hit” persists after the “run”
por: Doidy, Joan, et al.
Publicado: (2016)

Uniform Sampling of Steady States in Metabolic Networks: Heterogeneous Scales and Rounding
por: De Martino, Daniele, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_cr8auqofg0qovtsf5gj0aa073f