Cargando…

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ma, Ding, Yang, Laurence, Fleming, Ronan M. T., Thiele, Ines, Palsson, Bernhard O., Saunders, Michael A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2017
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241643/ https://www.ncbi.nlm.nih.gov/pubmed/28098205 http://dx.doi.org/10.1038/srep40863

Ejemplares similares

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage
por: Thiele, Ines, et al.
Publicado: (2012)

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

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
por: Thiele, Ines, et al.
Publicado: (2009)

solveME: fast and reliable solution of nonlinear ME models
por: Yang, Laurence, et al.
Publicado: (2016)

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
por: Aurich, Maike K., et al.
Publicado: (2016)

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
por: Nogales, Juan, et al.
Publicado: (2008)

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

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

Instrumentation on Multi-Scaled Scattering of Bio-Macromolecular Solutions
por: Chu, Benjamin, et al.
Publicado: (2015)

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
por: Rolfsson, Ottar, et al.
Publicado: (2011)

Prediction of intracellular metabolic states from extracellular metabolomic data
por: Aurich, Maike K., et al.
Publicado: (2014)

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
por: Du, Bin, et al.
Publicado: (2019)

Applications of genome-scale metabolic reconstructions
por: Oberhardt, Matthew A, et al.
Publicado: (2009)

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

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
por: Sigurdsson, Martin I, et al.
Publicado: (2010)

Metabolite coupling in genome-scale metabolic networks
por: Becker, Scott A, et al.
Publicado: (2006)

Macromolecular complexes in crystals and solutions
por: Krissinel, Evgeny
Publicado: (2011)

Principles of proteome allocation are revealed using proteomic data and genome-scale models
por: Yang, Laurence, et al.
Publicado: (2016)

COBRAme: A computational framework for genome-scale models of metabolism and gene expression
por: Lloyd, Colton J., et al.
Publicado: (2018)

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)

Light scattering in liquids and macromolecular solutions
por: Degiorgio, V, et al.
Publicado: (1980)

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

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
por: Aurich, Maike K., et al.
Publicado: (2017)

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
por: Heinken, Almut, et al.
Publicado: (2013)

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
por: Heinken, Almut, et al.
Publicado: (2023)

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
por: McCloskey, Douglas, et al.
Publicado: (2013)

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions
por: Donovan, Preston, et al.
Publicado: (2016)

Reconstruction annotation jamborees: a community approach to systems biology
por: Thiele, Ines, et al.
Publicado: (2010)

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
por: Herrgård, Markus J, et al.
Publicado: (2006)

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
por: Yang, Laurence, et al.
Publicado: (2019)

Estimation of the number of extreme pathways for metabolic networks
por: Yeung, Matthew, et al.
Publicado: (2007)

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale
por: Federowicz, Stephen, et al.
Publicado: (2014)

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
por: Becker, Scott A, et al.
Publicado: (2005)

Formulating genome-scale kinetic models in the post-genome era
por: Jamshidi, Neema, et al.
Publicado: (2008)

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
por: O’Brien, Edward J, et al.
Publicado: (2013)

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining
por: Dauter, Zbigniew, et al.
Publicado: (2014)

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
por: Schellenberger, Jan, et al.
Publicado: (2010)

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
por: Feist, Adam M, et al.
Publicado: (2006)

Macromolecular and Solution Properties of the Recombinant Fusion Protein HUG
por: Sist, Paola, et al.
Publicado: (2022)

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
por: Heinken, Almut, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_dbnpuqa55c298620e7tusddfso