ArticleMetabolites2015
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models.
Article in Metabolites, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.Molecular systems biology · 2024Article
- Mslar: Microbial synthetic lethal and rescue database.PLoS computational biology · 2023Review
- Genome-scale modeling of yeast metabolism: retrospectives and perspectives.FEMS yeast research · 2022Review
- A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics.Nature communications · 2021Article
- Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.FEMS yeast research · 2021Article
- Genome-scale metabolic reconstruction of the non-model yeastMetabolic engineering communications · 2020Article
- Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis ofSTAR protocols · 2020Article
- A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- SNPeffect: identifying functional roles of SNPs using metabolic networks.The Plant journal : for cell and molecular biology · 2020Article
- Article
- OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models.iScience · 2020Article
- A comprehensive genome-scale model forMetabolic engineering communications · 2019Article
- A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.Nature communications · 2019Article
- Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.Cell systems · 2016Article
- Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations.Metabolites · 2015Review
- Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes inmSystemsArticle
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3 authors.
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Abstract
Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models.
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