ArticlemSphere2025
Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.
Article in mSphere, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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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.
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Who cites it
3 citing papers in PubMed.
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.The ISME journal · 2026Article
- Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.bioRxiv : the preprint server for biology · 2025Article
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3 authors.
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Abstract
Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the
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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.