@inproceedings{b18de9e1cf4d482c88aba551c94948f5,
title = "CSA-RRBS: A comprehensive streamlined analysis of reduced representation bisulfite sequencing (RRBS) data",
abstract = "DNA methylation plays a key role in normal human development and various diseases, including cancer. Coupled with bisulfite treatment, next generation sequencing (RRBS or WGBS) has expanded the scope of DNA methylation studies for the quantitative profiling of DNA methylation of individual CpG loci throughout the genome at a nucleotide resolution. However, analyzing RRBS data is challenging as it needs a significant amount of computational resources and bioinformatics expertise. We developed a comprehensive streamlined pipeline for RRBS data (CSA-RRBS) that integrates read pre-processing, alignment, statistical report of quality, data visualization, and flexible differential methylation analysis between experimental conditions either at single nucleotide resolution (DMC) or with differentially methylated regions (DMRs). Moreover, we also report extensive annotation of the genome region of interest and its overlap with additional genomic features to provide context and perspective to the methylation events. We applied the CSA-RRBS pipeline over two datasets, prostate cell lines (normal and cancer) and a breast cancer patient dataset. The results validate cancer-associated methylation defects and demonstrate that our CSA-RRBS pipeline enables new discoveries about DNA methylation and its role in gene regulation and cancer.",
author = "Ting Gong and Gaddis, {Sara S.} and Yue Lu and Kimie Kondo and Hongbo Zhao and Jianjun Shen and {Marcelo Aldaz}, C. and Estecio, {Marcos R.}",
note = "Publisher Copyright: Copyright ISCA, BICOB 2015.; 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015 ; Conference date: 09-03-2015 Through 11-03-2015",
year = "2015",
language = "English (US)",
series = "Proceedings of the 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015",
publisher = "The International Society for Computers and Their Applications (ISCA)",
pages = "105--110",
editor = "Nurit Haspel and Fahad Saeed",
booktitle = "Proceedings of the 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015",
}