ArticleGenome research2008
Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 57 citations in OpenAlex.
- Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis.The Plant journal : for cell and molecular biology · 2019Article
- Polymorphisms in plastoquinol oxidase (PTOX) from Arabidopsis accessions indicate SNP-induced structural variants associated with altitude and rainfall.Journal of bioenergetics and biomembranes · 2019Article
- Triparental plants provide direct evidence for polyspermy induced polyploidy.Nature communications · 2017Article
- RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions.BMC genomics · 2013Article
- High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
- Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome.BMC genomics · 2012Article
- Natural variation in Arabidopsis: from molecular genetics to ecological genomics.Plant physiology · 2012Review
- High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes.Journal of parallel and distributed computing · 2012Article
- Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana.PLoS computational biology · 2012Article
- Article
- A QTL Study for Regions Contributing to Arabidopsis thaliana Root Skewing on Tilted Surfaces.G3 (Bethesda, Md.) · 2011Article
- Reference-guided assembly of four diverse Arabidopsis thaliana genomes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.Genome biology and evolution · 2011Article
- Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model.PloS one · 2011Article
- Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity.Frontiers in plant science · 2011Article
- Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.The Journal of molecular diagnostics : JMD · 2010Article
- Conserved RNaseII domain protein functions in cytoplasmic mRNA decay and suppresses Arabidopsis decapping mutant phenotypes.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana.Genetics · 2010Article
- Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana.BMC genomics · 2010Article
- Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.Genome biology · 2010Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located near a SNP as multiple mismatches inhibit hybridization to arrayed oligonucleotides. Contiguous tracts of suppressed hybridization therefore typify polymorphic regions (PRs) such as clusters of SNPs or deletions. We developed a machine learning method, designated margin-based prediction of polymorphic regions (mPPR), to predict PRs from resequencing array data. Conceptually similar to hidden Markov models, the method is trained with discriminative learning techniques related to support vector machines, and accurately identifies even very short polymorphic tracts (<10 bp). We applied this method to resequencing array data previously generated for the euchromatic genomes of 20 strains (accessions) of the best-characterized plant, Arabidopsis thaliana. Nonredundantly, 27% of the genome was included within the boundaries of PRs predicted at high specificity ( approximately 97%). The resulting data set provides a fine-scale view of polymorphic sequences in A. thaliana; patterns of polymorphism not apparent in SNP data were readily detected, especially for noncoding regions. Our predictions provide a valuable resource for evolutionary genetic and functional studies in A. thaliana, and our method is applicable to similar data sets in other species. More broadly, our computational approach can be applied to other segmentation tasks related to the analysis of genomic variation.
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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.