ArticlePloS one2021
Revising transcriptome assemblies with phylogenetic information.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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
10 citing papers in PubMed, 21 citations in OpenAlex.
- Article
- Population genomics of a sailing siphonophore reveals genetic structure in the open ocean.Current biology : CB · 2025Article
- Comparative Genomics Uncovers the Evolutionary Dynamics of Detoxification and Insecticide Target Genes Across 11 Phlebotomine Sand Flies.Genome biology and evolution · 2024Article
- Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea.Proceedings. Biological sciences · 2023Article
- Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record.eLife · 2022Article
- Article
- Phylotranscriptomics Reveals Discordance in the Phylogeny of Hawaiian Drosophila and Scaptomyza (Diptera: Drosophilidae).Molecular biology and evolution · 2022Article
- Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora.Molecular biology and evolution · 2022Article
- A phylogenomic resolution of the sea urchin tree of life.BMC evolutionary biology · 2018Article
- Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution.Molecular phylogenetics and evolution · 2018Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.
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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.