Cargando…

Principles of proteome allocation are revealed using proteomic data and genome-scale models

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabol...

Descripción completa

Detalles Bibliográficos
Autores principales:	Yang, Laurence, Yurkovich, James T., Lloyd, Colton J., Ebrahim, Ali, Saunders, Michael A., Palsson, Bernhard O.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2016
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114563/ https://www.ncbi.nlm.nih.gov/pubmed/27857205 http://dx.doi.org/10.1038/srep36734

Ejemplares similares

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth
por: Lloyd, Colton J., et al.
Publicado: (2021)

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
por: Liu, Joanne K., et al.
Publicado: (2019)

Principles of cellular resource allocation revealed by condition-dependent proteome profiling
por: Metzl-Raz, Eyal, et al.
Publicado: (2017)

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

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)

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

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

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome
por: Patel, Arjun, et al.
Publicado: (2023)

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
por: Chen, Ke, et al.
Publicado: (2021)

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
por: Yurkovich, James T., et al.
Publicado: (2017)

Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity
por: Hidalgo, David, et al.
Publicado: (2022)

Is the kinetome conserved?
por: Palsson, Bernhard O, et al.
Publicado: (2022)

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
por: Seif, Yara, et al.
Publicado: (2018)

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
por: Norsigian, Charles J, et al.
Publicado: (2020)

Establishing comprehensive quaternary structural proteomes from genome sequence
por: Catoiu, Edward Alexander, et al.
Publicado: (2023)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
por: Lachance, Jean-Christophe, et al.
Publicado: (2019)

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria
por: Hui, Sheng, et al.
Publicado: (2015)

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
por: Choudhary, Kumari S., et al.
Publicado: (2018)

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
por: Ma, Ding, et al.
Publicado: (2017)

Genome‐scale metabolic modeling reveals key features of a minimal gene set
por: Lachance, Jean‐Christophe, et al.
Publicado: (2021)

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
por: Phaneuf, Patrick V., et al.
Publicado: (2020)

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
por: Mih, Nathan, et al.
Publicado: (2020)

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
por: Kavvas, Erol S., et al.
Publicado: (2018)

Systems biology as an emerging paradigm in transfusion medicine
por: Yurkovich, James T., et al.
Publicado: (2018)

The quantitative metabolome is shaped by abiotic constraints
por: Akbari, Amir, et al.
Publicado: (2021)

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets
por: Mohite, Omkar S., et al.
Publicado: (2022)

Overflow metabolism in E. coli results from efficient proteome allocation
por: Basan, Markus, et al.
Publicado: (2015)

Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation
por: Trötschel, Christian, et al.
Publicado: (2019)

Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis
por: Karayel, Özge, et al.
Publicado: (2020)

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials
por: Yurkovich, James T., et al.
Publicado: (2018)

Systems biology of the structural proteome
por: Brunk, Elizabeth, et al.
Publicado: (2016)

Data Mining in Genomics and Proteomics
por: Bensmail, Halima, et al.
Publicado: (2005)

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
por: O’Brien, Edward J., et al.
Publicado: (2016)

Optimal proteome allocation and the temperature dependence of microbial growth laws
por: Mairet, Francis, et al.
Publicado: (2021)

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

Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data
por: Schweiger, Regev, et al.
Publicado: (2010)

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
por: Wang, Minghui, et al.
Publicado: (2018)

Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia
por: Reyes-González, D., et al.
Publicado: (2022)

Constrained proteome allocation affects coexistence in models of competitive microbial communities
por: Pacciani-Mori, Leonardo, et al.
Publicado: (2021)

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome
por: Benz, Caroline, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_p917cpm0q3ubh5an6oufvua87b