ArticleBioinformatics (Oxford, England)2018
GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Molecular epidemiology and clinical characteristics of carbapenem-resistantMicrobiology spectrum · 2025Article
- Tracing the Origin, Spread, and Molecular Evolution of Dengue Type 1 Cases That Occurred in Northern Italy in 2023.Pathogens (Basel, Switzerland) · 2024Article
- First report of carbapenems encoding multidrug-resistant gram-negative bacteria from a pediatric hospital in Gaza Strip, Palestine.BMC microbiology · 2024Article
- Design of a Bacteriophage Cocktail Active againstAntibiotics (Basel, Switzerland) · 2022Article
- SARS-CoV-2 Delta variant isolates from vaccinated individuals.BMC genomics · 2022Article
- Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug ResistantViruses · 2022Article
- Horizontal transfer and evolution of wall teichoic acid gene cassettes inF1000Research · 2021Article
- A pan-genome method to determine core regions of theF1000Research · 2021Article
- High Rates of Genome Rearrangements and Pathogenicity ofFrontiers in microbiology · 2021Article
- Article
- Article
- Article
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.
Funding
Abstract
Motivation: The vast number of available sequenced bacterial genomes occasionally exceeds the facilities of comparative genomic methods or is dominated by a single outbreak strain, and thus a diverse and representative subset is required. Generation of the reduced subset currently requires a priori supervised clustering and sequence-only selection of medoid genomic sequences, independent of any additional genome metrics or strain attributes. Results: The Gaussian Genome Representative Selector with Prioritization (GGRaSP) R-package described below generates a reduced subset of genomes that prioritizes maintaining genomes of interest to the user as well as minimizing the loss of genetic variation. The package also allows for unsupervised clustering by modeling the genomic relationships using a Gaussian mixture model to select an appropriate cluster threshold. We demonstrate the capabilities of GGRaSP by generating a reduced list of 315 genomes from a genomic dataset of 4600 Escherichia coli genomes, prioritizing selection by type strain and by genome completeness. Availability and implementaion: GGRaSP is available at https://github.com/JCVenterInstitute/ggrasp/. Supplementary information: Supplementary data are available at Bioinformatics online.
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.