ArticlePloS one2013
Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 6 citations in OpenAlex.
- Bacterial transcriptome reorganization in thermal adaptive evolution.BMC genomics · 2015Article
- Phenotypic convergence in bacterial adaptive evolution to ethanol stress.BMC evolutionary biology · 2015Article
- Global coordination in adaptation to gene rewiring.Nucleic acids research · 2015Article
- Growth rate-coordinated transcriptome reorganization in bacteria.BMC genomics · 2013Article
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5 authors at 2 institutions in 1 country.
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Abstract
High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of signals on the probe sequences and the existence of false signals arising from non-specific binding between probe and target. In this study, we have developed a novel algorithm to detect the single-base substitutions by using microarray data based on a thermodynamic model of hybridization. We modified the thermodynamic model by introducing a penalty for mismatches that represent the effects of substitutions on hybridization affinity. This penalty results in significantly higher detection accuracy than other methods, indicating that the incorporation of hybridization free energy can improve the analysis of sequence variants by using microarray data.
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