ArticleNature protocols2013
Tracking recent adaptive evolution in microbial species using TimeZone.
Article in Nature protocols, 2013. 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.
- Exploring the evolutionary divergence of cyclic di-nucleotide signaling in diverse mycobacterial species.Archives of microbiology · 2026Article
- Genomic analysis ofFrontiers in microbiology · 2023Article
- Distinct Potentially Adaptive Accumulation of Truncation Mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A.Microbiology spectrum · 2022Article
- Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19?Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
- Pandemic fluoroquinolone resistantProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp.Scientific reports · 2019Article
- Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori.BMC genomics · 2018Article
- Gene inversion potentiates bacterial evolvability and virulence.Nature communications · 2018Article
- Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina.Applied and environmental microbiology · 2016Article
- Ecological Opportunity, Evolution, and the Emergence of Flea-Borne Plague.Infection and immunity · 2016Review
- Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis.PLoS neglected tropical diseases · 2016Article
- PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.Genomics · 2015Article
- Microbial Speciation.Cold Spring Harbor perspectives in biology · 2015Review
- Ordering microbial diversity into ecologically and genetically cohesive units.Trends in microbiology · 2014Review
- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.Genome medicine · 2014Article
- Microbial variome database: point mutations, adaptive or not, in bacterial core genomes.Molecular biology and evolution · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
An important goal of the analysis of sequenced genomes of microbial pathogens is to improve the therapy of infectious diseases. In this context, a major challenge is to detect genomic-level evolutionary changes that increase microbial virulence. TimeZone, a genome analysis software package, is designed to detect footprints of positive selection for functionally adaptive point mutations. The uniqueness of TimeZone lies in its ability to predict recent adaptive mutations that are overlooked by conventional microevolutionary tools. This protocol describes the use of TimeZone to analyze adaptive footprints in either individual genes or in sets of genomes. Three major workflows are described: (i) extraction of orthologous gene sets from multiple genomes; (ii) alignment and phylogenetic analysis of genes; and (iii) identification of candidate genes under positive selection for point mutations, taking into account the effect of recombination events. This software package can be downloaded free from http://sourceforge.net/projects/timezone1/. In the case, for example, of the analysis of 14 Escherichia coli genomes, the protocol described here can be completed in ∼32 h.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.