ArticleMolecular systems biology2009
Genome-scale gene/reaction essentiality and synthetic lethality analysis.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
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- Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine.Briefings in bioinformatics · 2025Review
- A fast method for extracting essential and synthetic lethality genes in GEM models.Bioinformatics advances · 2025Article
- Understanding flux switching in metabolic networks through an analysis of synthetic lethals.NPJ systems biology and applications · 2024Article
- Adding metabolic tasks to human GEM models to improve the study of gene targets and their associated toxicities.Scientific reports · 2024Article
- GEM-based computational modeling for exploring metabolic interactions in a microbial community.PLoS computational biology · 2024Article
- Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections.NPJ systems biology and applications · 2024Article
- FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization.Microbial cell factories · 2024Article
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
- Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.Metabolites · 2023Review
- Mslar: Microbial synthetic lethal and rescue database.PLoS computational biology · 2023Review
- Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality.Scientific reports · 2022Article
- Towards the routine use of in silico screenings for drug discovery using metabolic modelling.Biochemical Society transactions · 2020Review
- Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach.Microbial cell factories · 2020Article
- New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections.Scientific reports · 2020Article
- FastMM: an efficient toolbox for personalized constraint-based metabolic modeling.BMC bioinformatics · 2020Article
- An integrated computational and experimental study to investigate Staphylococcus aureus metabolism.NPJ systems biology and applications · 2020Article
- Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data.European journal of nuclear medicine and molecular imaging · 2019Review
- Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen.mSystems · 2019Article
- Modeling the Interplay between Photosynthesis, COScientific reports · 2019Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synthetic lethals are to pairs of non-essential genes whose simultaneous deletion prohibits growth. One can extend the concept of synthetic lethality by considering gene groups of increasing size where only the simultaneous elimination of all genes is lethal, whereas individual gene deletions are not. We developed optimization-based procedures for the exhaustive and targeted enumeration of multi-gene (and by extension multi-reaction) lethals for genome-scale metabolic models. Specifically, these approaches are applied to iAF1260, the latest model of Escherichia coli, leading to the complete identification of all double and triple gene and reaction synthetic lethals as well as the targeted identification of quadruples and some higher-order ones. Graph representations of these synthetic lethals reveal a variety of motifs ranging from hub-like to highly connected subgraphs providing a birds-eye view of the avenues available for redirecting metabolism and uncovering complex patterns of gene utilization and interdependence. The procedure also enables the use of falsely predicted synthetic lethals for metabolic model curation. By analyzing the functional classifications of the genes involved in synthetic lethals, we reveal surprising connections within and across clusters of orthologous group functional classifications.
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