@inproceedings{4ba80462177741c88719d91fe47192e3,
title = "LuxHS: DNA Methylation Analysis with Spatially Varying Correlation Structure",
abstract = "Bisulfite sequencing (BS-seq) is a popular method for measuring DNA methylation in basepair-resolution. Many BS-seq data analysis tools utilize the assumption of spatial correlation among the neighboring cytosines{\textquoteright} methylation states. While being a fair assumption, most existing methods leave out the possibility of deviation from the spatial correlation pattern. Our approach builds on a method which combines a generalized linear mixed model (GLMM) with a likelihood that is specific for BS-seq data and that incorporates a spatial correlation for methylation levels. We propose a novel technique using a sparsity promoting prior to enable cytosines deviating from the spatial correlation pattern. The method is tested with both simulated and real BS-seq data and compared to other differential methylation analysis tools.",
author = "Viivi Halla-aho and Harri L{\"a}hdesm{\"a}ki",
year = "2020",
month = apr,
day = "30",
doi = "10.1007/978-3-030-45385-5_45",
language = "English",
isbn = "978-3-030-45384-8",
series = "Lecture Notes in Computer Science ",
publisher = "Springer",
pages = "505--516",
editor = "Ignacio Rojas and Olga Valenzuela and Fernando Rojas and Herrera, {Luis Javier} and Francisco Ortu{\~n}o",
booktitle = "Bioinformatics and Biomedical Engineering - 8th International Work-Conference, IWBBIO 2020, Proceedings",
note = "International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO ; Conference date: 06-05-2020 Through 08-05-2020",
}