ArticleNucleic acids research2008
Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed, 66 citations in OpenAlex.
- Habit of elongate amphibole particles as a predictor of mesothelial carcinogenicity.Toxicology reports · 2025Article
- Christensenella minuta protects and restores intestinal barrier in a colitis mouse model by regulating inflammation.NPJ biofilms and microbiomes · 2024Article
- Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome.Microbial genomics · 2023Article
- Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan.Applied and environmental microbiology · 2022Article
- Article
- Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.Current biology : CB · 2021Article
- Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates ofMicrobial genomics · 2020Article
- A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes.BMC genomics · 2020Article
- Determination of Plasmid pSN1216-29 Host Range and the Similarity in Oligonucleotide Composition Between Plasmid and Host Chromosomes.Frontiers in microbiology · 2020Article
- A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms.BMC genomics · 2019Article
- Reconsidering plasmid maintenance factors for computational plasmid design.Computational and structural biotechnology journal · 2019Review
- Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.Journal of molecular evolution · 2019Article
- Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements.Molecular biology and evolution · 2018Article
- CLOUD: a non-parametric detection test for microbiome outliers.Microbiome · 2018Article
- PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.Nucleic acids research · 2018Article
- Visual Learning Induces Changes in Resting-State fMRI Multivariate Pattern of Information.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2015Article
- In Vivo Transmission of an IncA/C Plasmid in Escherichia coli Depends on Tetracycline Concentration, and Acquisition of the Plasmid Results in a Variable Cost of Fitness.Applied and environmental microbiology · 2015Article
- Plasmid Detection, Characterization, and Ecology.Microbiology spectrum · 2015Review
- Development of self-compressing BLSOM for comprehensive analysis of big sequence data.BioMed research international · 2015Article
- Metazoan parasite infection in the swordfish, Xiphias gladius, from the Mediterranean Sea and comparison with Atlantic populations: implications for its stock characterization.Parasite (Paris, France) · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed delta-distance, has been commonly used to measure differences in dinucleotide composition, or 'genomic signature', between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance-covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the delta-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host.
Indexed as
Identifiers
What OpenQuestion holds
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.