ArticleBMC bioinformatics2013
Practical aliquoting of flowering plant genomes.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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.
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.
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Who cites it
2 citing papers in PubMed.
- Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.Bioinformatics (Oxford, England) · 2017Article
- Gene expression and fractionation resistance.BMC genomics · 2014Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We pose the problem of dissecting an ancient polyploid genome into its constituent subgenomes despite fragmentation and noise caused by genome rearrangements and fractionation of multi-copy genes. We formulate this in terms of decomposition into "defective" k-partite graphs, distinguished by location within the genome. We devise and implement a clustering heuristic for solving realistic instances of the problem. An unusual focus of our method is the focus on prioritizing gene density or lack of gaps in the assembly of fragments into larger regions, rather than maximizing the number of genes. We validate the method against the grape genome in which the ancient core eudicot triplication is readily detectible and is already well known. We then analyze the tomato genome, whose proposed status as a descendant of a more recent Solanum hexaploid is controversial, and confirm this proposal. The solution reveals unexpected information about the evolution of the tomato.
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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.