ArticleBMC genetics2015
Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms.
Article in BMC genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Review
- Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species.The Plant journal : for cell and molecular biology · 2022Article
- ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw.BMC genomics · 2021Article
- Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.Briefings in bioinformatics · 2021Review
- Homeolog expression quantification methods for allopolyploids.Briefings in bioinformatics · 2020Review
- Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).PLoS genetics · 2019Article
- Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds.Genome biology and evolution · 2016Article
- Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae).Genome biology and evolution · 2016Article
- HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.Scientific reports · 2016Article
- DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.PLoS genetics · 2016Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome read categorization determines the genome of origin for sequence reads from an allopolyploid organism. Different techniques have been used to perform read categorization, mostly based on homoeo-SNPs identified between extant diploid relatives of allopolyploids. We present a novel technique for read categorization implemented by the software PolyDog. We demonstrate its accuracy and improved categorization relative to other methods. We discuss the situations in which one method or another might be most appropriate.
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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.