YEASTNET: A consensus reconstruction of yeast metabolism
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YEASTNET: A consensus reconstruction of yeast metabolism
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YEASTNET
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YeastNet
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
YEASTNET: A consensus reconstruction of yeast metabolism
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YEASTNET
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YeastNet
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: YEASTNET, YeastNet
Names
More detailed information about this field from each metasource.
YEASTNET: A consensus reconstruction of yeast metabolism
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YEASTNET
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
YeastNet
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.
Description
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This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Functional gene networks for Saccharomyces cerevisiae
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://yeast.sourceforge.net/Webpage
More detailed information about this field from each metasource.
http://yeast.sourceforge.net/
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.inetbio.org/yeastnet/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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https://creativecommons.org/licenses/by-sa/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
PMID: 18846089
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism
PMID: 24678285
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt981
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
PMID: 18846089
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism
PMID: 24678285
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gkt981
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
PubMed citations: 234.
234 articles citing: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
From Petri Plates to Petri Nets, a revolution in yeast biology. PMID:35142857
Genome-scale modeling of yeast metabolism: retrospectives and perspectives. PMID:35094064
Exploring the transportome of the biosurfactant producing yeast Starmerella bombicola. PMID:34998388
Intelligent host engineering for metabolic flux optimisation in biotechnology. PMID:34673920
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
New Cross-Talks between Pathways Involved in Grapevine Infection with 'Candidatus Phytoplasma solani' Revealed by Temporal Network Modelling. PMID:33805409
Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism. PMID:33574263
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. PMID:33323978
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Serum Metabolomics for Biomarker Screening of Esophageal Squamous Cell Carcinoma and Esophageal Squamous Dysplasia Using Gas Chromatography-Mass Spectrometry. PMID:33110968
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth. PMID:32675233
A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models. PMID:31934349
Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica. PMID:31890234
Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges. PMID:31602620
Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation? PMID:31398879
ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast. PMID:31299083
Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. PMID:31216234
Current status and applications of genome-scale metabolic models. PMID:31196170
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PMID:31071110
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PMID:31009451
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. PMID:30899000
A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity. PMID:30804813
Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. PMID:30794534
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. PMID:30634957
Quantitative flux coupling analysis. PMID:30535964
Light-driven fine chemical production in yeast biohybrids. PMID:30442806
Synthetic biology tools for engineering Yarrowia lipolytica. PMID:30315870
Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts. PMID:30195436
An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life. PMID:30166494
Metabolic profiling of isolated mitochondria and cytoplasm reveals compartment-specific metabolic responses. PMID:29628813
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae. PMID:29468121
Metabolic adjustment upon repetitive substrate perturbations using dynamic 13C-tracing in yeast. PMID:28946905
Genome-scale modeling of yeast: chronology, applications and critical perspectives. PMID:28899034
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways. PMID:28725465
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. PMID:28725459
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PMID:28520713
Multi-omics approaches to disease. PMID:28476144
Enhancing Drug Efficacy and Therapeutic Index through Cheminformatics-Based Selection of Small Molecule Binary Weapons That Improve Transporter-Mediated Targeting: A Cytotoxicity System Based on Gemcitabine. PMID:28396636
Constraint-based stoichiometric modelling from single organisms to microbial communities. PMID:28334697
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. PMID:28250014
Perspectives and Challenges of Microbial Application for Crop Improvement. PMID:28232839
Spectral consensus strategy for accurate reconstruction of large biological networks. PMID:28105915
Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models. PMID:28085902
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PMID:28072816
A Dormant Microbial Component in the Development of Preeclampsia. PMID:27965958
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
The metabolome 18 years on: a concept comes of age. PMID:27695392
In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. PMID:27637876
Saccharomyces cerevisiae metabolism in ecological context. PMID:27634775
Computational Metabolomics: A Framework for the Million Metabolome. PMID:27629808
MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites. PMID:27597830
The metabolic background is a global player in Saccharomyces gene expression epistasis. PMID:27572163
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
Recon 2.2: from reconstruction to model of human metabolism. PMID:27358602
A Bacterial Component to Alzheimer's-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease. PMID:27340854
Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing. PMID:27239440
Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data. PMID:27200361
Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. PMID:27075000
Microbial network for waste activated sludge cascade utilization in an integrated system of microbial electrolysis and anaerobic fermentation. PMID:27042212
A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information. PMID:27014700
Technology development for natural product biosynthesis in Saccharomyces cerevisiae. PMID:26994377
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Measuring the robustness of link prediction algorithms under noisy environment. PMID:26733156
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Genome-scale modelling of microbial metabolism with temporal and spatial resolution. PMID:26614655
Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. PMID:26609959
Growth and metabolism of Beauveria bassiana spores and mycelia. PMID:26581712
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): aiming to increase biomass. PMID:26564982
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. PMID:26500611
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Modeling cancer metabolism on a genome scale. PMID:26130389
Many InChIs and quite some feat. PMID:26081259
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PMID:26001086
Linking metabolomics data to underlying metabolic regulation. PMID:25988163
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. PMID:25888284
Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. PMID:25852671
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
Genome-scale modeling for metabolic engineering. PMID:25578304
Improving collaboration by standardization efforts in systems biology. PMID:25538939
The virtue of innovation: innovation through the lenses of biological evolution. PMID:25505138
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Computational strategies for a system-level understanding of metabolism. PMID:25427076
How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. PMID:25400580
Identification of novel knockout targets for improving terpenoids biosynthesis in Saccharomyces cerevisiae. PMID:25386654
Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods. PMID:25374614
Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach. PMID:25365344
Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures. PMID:25243355
Multi-capillary column-ion mobility spectrometry of volatile metabolites emitted by Saccharomyces cerevisiae. PMID:25197771
Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism. PMID:25084685
Network thermodynamic curation of human and yeast genome-scale metabolic models. PMID:25028891
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli. PMID:24987114
CASMI-The Small Molecule Identification Process from a Birmingham Perspective. PMID:24957998
Human metabolic network: reconstruction, simulation, and applications in systems biology. PMID:24957377
Event-based text mining for biology and functional genomics. PMID:24907365
Untangling complex dynamical systems via derivative-variable correlations. PMID:24848769
Optimizing genome-scale network reconstructions. PMID:24811519
Importance of understanding the main metabolic regulation in response to the specific pathway mutation for metabolic engineering of Escherichia coli. PMID:24688678
Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. PMID:24678285
Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors. PMID:24672514
A future of the model organism model. PMID:24577733
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. PMID:24532766
Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations. PMID:24529069
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. PMID:24528924
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species. PMID:24516375
Systematic construction of kinetic models from genome-scale metabolic networks. PMID:24324546
Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance. PMID:24305546
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions. PMID:24153255
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. PMID:24059635
Economic and environmental impacts of microbial biodiesel. PMID:24022152
Analyzing LC/MS metabolic profiling data in the context of existing metabolic networks. PMID:24010053
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
Computational approaches for understanding energy metabolism. PMID:23897661
Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. PMID:23892182
An analysis of a 'community-driven' reconstruction of the human metabolic network. PMID:23888127
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. PMID:23831062
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
Simple topological properties predict functional misannotations in a metabolic network. PMID:23812979
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Nucleotide degradation and ribose salvage in yeast. PMID:23670538
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. PMID:23631471
Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. PMID:23608777
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response. PMID:23531303
Sequencing and annotation of the Ophiostoma ulmi genome. PMID:23496816
A community-driven global reconstruction of human metabolism. PMID:23455439
Concise review: new paradigms for Down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. PMID:23413375
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. PMID:23357920
Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory. PMID:23349810
Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica. PMID:23236514
Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing. PMID:23185279
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PMID:23029152
Understanding the immune response to seasonal influenza vaccination in older adults: a systems biology approach. PMID:23002979
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. PMID:22934043
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. PMID:22857267
Literature retrieval and mining in bioinformatics: state of the art and challenges. PMID:22778730
Improving metabolic flux predictions using absolute gene expression data. PMID:22713172
The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PMID:22685547
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PMID:22666308
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. PMID:22663945
Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants. PMID:22645563
Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering. PMID:22640729
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. PMID:22558935
Synthetic biology: mapping the scientific landscape. PMID:22539946
Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how. PMID:22527402
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. PMID:22472172
Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? PMID:22252984
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. PMID:22233419
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. PMID:22184244
Using the reconstructed genome-scale human metabolic network to study physiology and pathology. PMID:22142339
A vision for a biomedical cloud. PMID:22142244
Evolutionary significance of metabolic network properties. PMID:22130553
YMDB: the Yeast Metabolome Database. PMID:22064855
Software for systems biology: from tools to integrated platforms. PMID:22048662
Chemical basis of metabolic network organization. PMID:22022254
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
Whole-genome metabolic network reconstruction and constraint-based modeling. PMID:21943909
Engineering strategy of yeast metabolism for higher alcohol production. PMID:21902829
Integrating systems biology models and biomedical ontologies. PMID:21835028
Synergies between synthetic biology and metabolic engineering. PMID:21822239
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
Mining metabolites: extracting the yeast metabolome from the literature. PMID:21687783
Social engineering for virtual 'big science' in systems biology. PMID:21587248
Extending biochemical databases by metabolomic surveys. PMID:21566124
Unpredictability of metabolism--the key role of metabolomics science in combination with next-generation genome sequencing. PMID:21556754
The strength of chemical linkage as a criterion for pruning metabolic graphs. PMID:21551141
Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PMID:21483480
Mass-balanced randomization of metabolic networks. PMID:21436128
Customizable views on semantically integrated networks for systems biology. PMID:21414991
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. PMID:21283140
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. PMID:21251315
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. PMID:21244678
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. PMID:21190580
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. PMID:21176163
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. PMID:21132020
Environments that induce synthetic microbial ecosystems. PMID:21124952
Software that goes with the flow in systems biology. PMID:21114874
Systematic integration of experimental data and models in systems biology. PMID:21114840
Parameter balancing in kinetic models of cell metabolism. PMID:21038890
Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. PMID:21035178
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. PMID:20967426
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. PMID:20959003
Quantitative analysis of cellular metabolic dissipative, self-organized structures. PMID:20957111
A compartmental model analysis of integrative and self-regulatory ion dynamics in pollen tube growth. PMID:20949135
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. PMID:20846443
In silico models of cancer. PMID:20836040
Towards whole-body systems physiology. PMID:20823847
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. PMID:20712863
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PMID:20567500
PathText: a text mining integrator for biological pathway visualizations. PMID:20529930
IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. PMID:20513391
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. PMID:20500839
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
Nutrient control of eukaryote cell growth: a systems biology study in yeast. PMID:20497545
BioMet Toolbox: genome-wide analysis of metabolism. PMID:20483918
Dynamic transcriptional and metabolic responses in yeast adapting to temperature stress. PMID:20450442
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Reconstruction annotation jamborees: a community approach to systems biology. PMID:20393581
How to understand the cell by breaking it: network analysis of gene perturbation screens. PMID:20195495
Towards genome-scale signalling network reconstructions. PMID:20177425
Systems metabolic engineering: genome-scale models and beyond. PMID:20151446
Towards a genome-scale kinetic model of cellular metabolism. PMID:20109182
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. PMID:19946878
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. PMID:19889834
Applications of genome-scale metabolic reconstructions. PMID:19888215
Evolution of biomolecular networks: lessons from metabolic and protein interactions. PMID:19851337
Metabolite and reaction inference based on enzyme specificities. PMID:19696044
Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. PMID:19694958
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. PMID:19622150
Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. PMID:19607691
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
(13)C-based metabolic flux analysis. PMID:19478804
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. PMID:19321003
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. PMID:19133145 -
Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism
PubMed citations: 71.
71 articles citing: Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. PMID:35759507
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Genome-scale modeling of yeast metabolism: retrospectives and perspectives. PMID:35094064
Metabolic signatures of regulation by phosphorylation and acetylation. PMID:35072016
Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts. PMID:34674718
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics. PMID:34373465
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. PMID:33594000
Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction. PMID:33441687
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. PMID:33323978
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. PMID:33245091
Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits. PMID:33187110
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism. PMID:32978375
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae. PMID:32845888
Integration of a multi-step heterologous pathway in Saccharomyces cerevisiae for the production of abscisic acid. PMID:31767000
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. PMID:31694544
Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications. PMID:31457023
Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast. PMID:31413270
Energy metabolism controls phenotypes by protein efficiency and allocation. PMID:31405984
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling. PMID:31367232
ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast. PMID:31299083
Current status and applications of genome-scale metabolic models. PMID:31196170
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling. PMID:30849073
Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test. PMID:30830324
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. PMID:30634957
Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements. PMID:30578666
Predicting growth rate from gene expression. PMID:30578321
Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations. PMID:30467356
Synthetic biology tools for engineering Yarrowia lipolytica. PMID:30315870
Escher-FBA: a web application for interactive flux balance analysis. PMID:30257674
Doxorubicin induces an extensive transcriptional and metabolic rewiring in yeast cells. PMID:30209405
CO2 to succinic acid - Estimating the potential of biocatalytic routes. PMID:30197864
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. PMID:30066662
Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. PMID:29771304
Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources. PMID:29160039
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells. PMID:28993899
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach. PMID:28990716
Genome-scale modeling of yeast: chronology, applications and critical perspectives. PMID:28899034
Population FBA predicts metabolic phenotypes in yeast. PMID:28886026
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. PMID:28779005
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. PMID:28725468
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PMID:28520713
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation. PMID:28424673
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal. PMID:28419089
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. PMID:28272430
Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates. PMID:28107392
Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PMID:27997585
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Systems-level analysis of mechanisms regulating yeast metabolic flux. PMID:27789812
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
Yeast metabolic chassis designs for diverse biotechnological products. PMID:27430744
Genome wide analysis of protein production load in Trichoderma reesei. PMID:27354857
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Synthetic Ecology of Microbes: Mathematical Models and Applications. PMID:26522937
Biomass composition: the "elephant in the room" of metabolic modelling. PMID:26491422
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. PMID:26426067
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations. PMID:26393660
A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. PMID:26381164
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Applications of genome-scale metabolic network model in metabolic engineering. PMID:25465049
Multi-capillary column-ion mobility spectrometry of volatile metabolites emitted by Saccharomyces cerevisiae. PMID:25197771
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. PMID:24532766 - http://dx.doi.org/10.1093/nar/gkt981
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network model
metasource: Fairsharing.org
version: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
fungal genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: YEASTNET; YEASTNET: A consensus reconstruction of yeast metabolism; DOI: https://doi.org/10.25504/FAIRsharing.cm6j6r; Last edited: Jan. 8, 2019, 1:20 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
fungal genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
network model genomics fungal genome
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