A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism.
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Summary
A new computational method is presented that uncovers the dependence of gene essentiality on the presence or absence of nutrients in the growth medium and may be applied to learn about the host environment in which a microorganism is embedded given data pertaining to gene lethality, providing a means for the identification of a species natural habitat.
- Type
- article
- Published
- 2009-11-12
- Cited by
- 11
- References
- 49
- OpenAlex
- https://openalex.org/W19593469
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1416839
Keywords
Polygon mesh, Computer science, Rendering (computer graphics), Volume mesh, Polyhedron
References
- IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW,Thompson RW,et al//Proc Natl Acad Sci U S A
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- Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
- Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.
- N-Acetyltransferase phenotype and risk in urinary bladder cancer: approaches in molecular epidemiology. Preliminary results in Sweden and Denmark
- Modular epistasis in yeast metabolism
- The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.
- Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.
- Predicting biological system objectives de novo from internal state measurements
- Systematic condition-dependent annotation of metabolic genes.
- Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine
- Global reconstruction of the human metabolic network based on genomic and bibliomic data
- Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways
- Carbon nutrition of Escherichia coli in the mouse intestine.
Cited by
- Cold Adaptation and Mitochondrial Function in S. cerevisiae
- Use of genome‐scale metabolic models for understanding microbial physiology
- Synechocystis sp. PCC6803 metabolic models for the enhanced production of hydrogen
- Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments
- Emerging bioinformatics approaches for analysis of NGS-derived coding and non-coding RNAs in neurodegenerative diseases
- Fifteen years of large scale metabolic modeling of yeast: developments and impacts.
- MUFINS: multi-formalism interaction network simulator
- Current awareness on yeast
- Scalable parallel volume raycasting for nonrectilinear computational grids
- Hardware Architecture for Voxelization-based Volume Rendering of Unstructured Grids
- Lipid metabolism and Type VII secretion systems dominate the genome scale virulence profile of Mycobacterium tuberculosis in human dendritic cells
- Hypergraph-Partitioning-Based Remapping Models for Image-Space-Parallel Direct Volume Rendering of Unstructured Grids
- Image-space decomposition algorithms for sort-first parallel volume rendering of unstructured grids
- THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY On metabolic networks and multi-omics integration
- Computational Methods for Metabolic Network Analysis of Metabolite Levels and Flux
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