Cargando…

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annotations being limited to a set of already kno...

Descripción completa

Detalles Bibliográficos
Autores principales:	Vayena, Evangelia, Chiappino-Pepe, Anush, MohammadiPeyhani, Homa, Francioli, Yannick, Hadadi, Noushin, Ataman, Meriç, Hafner, Jasmin, Pavlou, Stavros, Hatzimanikatis, Vassily
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	National Academy of Sciences 2022
Materias:	Biological Sciences
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9674266/ https://www.ncbi.nlm.nih.gov/pubmed/36343249 http://dx.doi.org/10.1073/pnas.2211197119

Ejemplares similares

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism
por: MohammadiPeyhani, Homa, et al.
Publicado: (2021)

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives
por: Hafner, Jasmin, et al.
Publicado: (2021)

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites
por: Hadadi, Noushin, et al.
Publicado: (2019)

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power
por: Hafner, Jasmin, et al.
Publicado: (2020)

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx
por: MohammadiPeyhani, Homa, et al.
Publicado: (2022)

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
por: Chiappino-Pepe, Anush, et al.
Publicado: (2017)

PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models
por: Chiappino-Pepe, Anush, et al.
Publicado: (2021)

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
por: Ataman, Meric, et al.
Publicado: (2017)

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
por: Pandey, Vikash, et al.
Publicado: (2019)

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
por: Masid, Maria, et al.
Publicado: (2020)

Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
por: Masid, Maria, et al.
Publicado: (2020)

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
por: Borer, Benedict, et al.
Publicado: (2019)

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate–product pairs
por: Hafner, Jasmin, et al.
Publicado: (2021)

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
por: Ataman, Meric, et al.
Publicado: (2017)

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
por: Salvy, Pierre, et al.
Publicado: (2019)

Author Correction: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
por: Hadadi, Noushin, et al.
Publicado: (2020)

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
por: Hadadi, Noushin, et al.
Publicado: (2020)

Correction for Vayena et al., A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
Publicado: (2023)

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
por: Pandey, Vikash, et al.
Publicado: (2019)

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
por: Salvy, Pierre, et al.
Publicado: (2020)

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
por: Salvy, Pierre, et al.
Publicado: (2021)

Introduction to Metabolic Engineering Communications
por: Gill, Ryan T., et al.
Publicado: (2014)

Predicting energy and stability of known and hypothetical crystals using graph neural network
por: Pandey, Shubham, et al.
Publicado: (2021)

Strategies to identify and edit improvements in synthetic genome segments episomally
por: Rudolph, Alexandra, et al.
Publicado: (2023)

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism
por: Weilandt, Daniel R., et al.
Publicado: (2019)

The influence of the crowding assumptions in biofilm simulations
por: Angeles-Martinez, Liliana, et al.
Publicado: (2021)

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
por: Angeles-Martinez, Liliana, et al.
Publicado: (2021)

Antihypertensive Drugs Metabolism: An Update to Pharmacokinetic Profiles and Computational Approaches
por: Zisaki, Aikaterini, et al.
Publicado: (2015)

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
por: Tokic, Milenko, et al.
Publicado: (2020)

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli
por: Hameri, Tuure, et al.
Publicado: (2021)

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters
por: Merulla, Davide, et al.
Publicado: (2013)

Statistical inference in ensemble modeling of cellular metabolism
por: Hameri, Tuure, et al.
Publicado: (2019)

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations
por: Sahin, Asli, et al.
Publicado: (2023)

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
por: Stanway, Rebecca R., et al.
Publicado: (2019)

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene
por: Finley, Stacey D, et al.
Publicado: (2010)

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models
por: Isakova, Alina, et al.
Publicado: (2016)

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
por: Miskovic, Ljubisa, et al.
Publicado: (2019)

The Origins of Time-Delay in Template Biopolymerization Processes
por: Mier-y-Terán-Romero, Luis, et al.
Publicado: (2010)

The Hypothetical Rabbit
por: Kattan, Michael W.
Publicado: (2016)

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis
por: Tymoshenko, Stepan, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_7e2o1q5vc7g1jbq0hrcsh4afb3