ArticlePLoS computational biology2014
Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Shewanella oneidensis: Biotechnological Application of Metal-Reducing Bacteria.Advances in biochemical engineering/biotechnology · 2025Review
- Insights into the biosynthesis of palladium nanoparticles for oxygen reduction reaction by genetically engineered bacteria of Shewanella oneidensis MR-1.Microbial biotechnology · 2024Article
- Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene inACS synthetic biology · 2022Article
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- Genome-Scale Mutational Analysis of Cathode-OxidizingFrontiers in microbiology · 2022Article
- Reconstruction of a Genome-Scale Metabolic Network forFrontiers in bioengineering and biotechnology · 2022Article
- Transposon sequencing analysis of Bradyrhizobium diazoefficiens 110spc4.Scientific reports · 2021Article
- Cold adaptation in the environmental bacteriumCommunications biology · 2019Article
- Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.PLoS genetics · 2018Article
- Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia.Microbial genomics · 2017Article
- Genome Scale Mutational Analysis of Geobacter sulfurreducens Reveals Distinct Molecular Mechanisms for Respiration and Sensing of Poised Electrodes versus Fe(III) Oxides.Journal of bacteriology · 2017Article
- Thermodynamic Constraints Improve Metabolic Networks.Biophysical journal · 2017Article
- SSER: Species specific essential reactions database.BMC systems biology · 2017Article
- Article
- Rapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku.Nature communications · 2016Article
- The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume SymbiontFrontiers in microbiology · 2016Article
- Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks.The Journal of biological chemistry · 2015Article
- Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Analysis of genetic variation and potential applications in genome-scale metabolic modeling.Frontiers in bioengineering and biotechnology · 2015Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposon mutagenesis, in combination with parallel sequencing, is becoming a powerful tool for en-masse mutant analysis. A probability generating function was used to explain observed miniHimar transposon insertion patterns, and gene essentiality calls were made by transposon insertion frequency analysis (TIFA). TIFA incorporated the observed genome and sequence motif bias of the miniHimar transposon. The gene essentiality calls were compared to: 1) previous genome-wide direct gene-essentiality assignments; and, 2) flux balance analysis (FBA) predictions from an existing genome-scale metabolic model of Shewanella oneidensis MR-1. A three-way comparison between FBA, TIFA, and the direct essentiality calls was made to validate the TIFA approach. The refinement in the interpretation of observed transposon insertions demonstrated that genes without insertions are not necessarily essential, and that genes that contain insertions are not always nonessential. The TIFA calls were in reasonable agreement with direct essentiality calls for S. oneidensis, but agreed more closely with E. coli essentiality calls for orthologs. The TIFA gene essentiality calls were in good agreement with the MR-1 FBA essentiality predictions, and the agreement between TIFA and FBA predictions was substantially better than between the FBA and the direct gene essentiality predictions.
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