ArticleJournal of molecular evolution2006
Computational prediction of genomic functional cores specific to different microbes.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- Inferring gene function from evolutionary change in signatures of translation efficiency.Genome biology · 2014Article
- scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes.PloS one · 2013Article
- Article
- The essential genome of a bacterium.Molecular systems biology · 2011Article
- Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions.BMC genomics · 2010Article
- Translational selection is ubiquitous in prokaryotes.PLoS genetics · 2010Article
- Chromosomal periodicity and positional networks of genes in Escherichia coli.Molecular systems biology · 2010Article
- Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa.BMC genomics · 2010Article
- Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi.BMC microbiology · 2009Article
- An evaluation of minimal cellular functions to sustain a bacterial cell.BMC systems biology · 2009Article
- Bacteria as computers making computers.FEMS microbiology reviews · 2009Review
- Toward minimal bacterial cells: evolution vs. design.FEMS microbiology reviews · 2009Review
- Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Codon bias is a major factor explaining phage evolution in translationally biased hosts.Journal of molecular evolution · 2008Article
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1 author.
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Abstract
Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiments suggest a much larger set of essential genes (certainly more than several hundreds, even under the most restrictive hypotheses) that is dependent on the biological complexity and environmental specificity of the organism. Highly biased genes, which are generally also the most expressed in translationally biased organisms, tend to be over represented in the class of genes deemed to be essential for any given bacterial species. This association is far from perfect; nevertheless, it allows us to propose a new computational method to detect, to a certain extent, ubiquitous genes, nonorthologous genes, environment-specific genes, genes involved in the stress response, and genes with no identified function but highly likely to be essential for the cell. Most of these groups of genes cannot be identified with previously attempted computational and experimental approaches. The large variety of life-styles and the unusually detectable functional signals characterizing translationally biased organisms suggest using them as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds.
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