Literature DB >> 29342236

MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.

Corinne E Sexton1, Hayden Z Smith1, Peter D Newell2, Angela E Douglas3, John M Chaston4.   

Abstract

Summary: Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data. Availability and implementation: MAGNAMWAR is available on CRAN. Contact: john_chaston@byu.edu.

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Year:  2018        PMID： 29342236      PMCID： PMC5972563          DOI： 10.1093/bioinformatics/bty001

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

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Journal:  Nature       Date:  2012-09-26       Impact factor: 49.962

5.  OrthoMCL: identification of ortholog groups for eukaryotic genomes.

Authors:  Li Li; Christian J Stoeckert; David S Roos
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

6.  Metagenome-wide association of microbial determinants of host phenotype in Drosophila melanogaster.

Authors:  John M Chaston; Peter D Newell; Angela E Douglas
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7.  Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

Authors:  John A Lees; Minna Vehkala; Niko Välimäki; Simon R Harris; Claire Chewapreecha; Nicholas J Croucher; Pekka Marttinen; Mark R Davies; Andrew C Steer; Steven Y C Tong; Antti Honkela; Julian Parkhill; Stephen D Bentley; Jukka Corander
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  9 in total
  6 in total

1.  Bacterial Metabolism and Transport Genes Are Associated with the Preference of Drosophila melanogaster for Dietary Yeast.

Authors:  Tanner B Call; Emma K Davis; Joseph D Bean; Skyler G Lemmon; John M Chaston
Journal:  Appl Environ Microbiol       Date:  2022-08-01       Impact factor: 5.005

2.  Bacterial Methionine Metabolism Genes Influence Drosophila melanogaster Starvation Resistance.

Authors:  Alec M Judd; Melinda K Matthews; Rachel Hughes; Madeline Veloz; Corinne E Sexton; John M Chaston
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Journal:  G3 (Bethesda)       Date:  2018-03-28       Impact factor: 3.154

Review 4.  Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.

Authors:  James Emmanuel San; Shakuntala Baichoo; Aquillah Kanzi; Yumna Moosa; Richard Lessells; Vagner Fonseca; John Mogaka; Robert Power; Tulio de Oliveira
Journal:  Front Microbiol       Date:  2020-01-30       Impact factor: 5.640

5.  Microbiota Influences Fitness and Timing of Reproduction in the Fruit Fly Drosophila melanogaster.

Authors:  Melinda K Matthews; Jaanna Malcolm; John M Chaston
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6.  Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila.

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  6 in total

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