@article {1230,
	title = {A new parallel pipeline for DNA methylation analysis of long reads datasets.},
	journal = {BMC bioinformatics},
	volume = {18},
	year = {2017},
	month = {2017 Mar 09},
	pages = {161},
	abstract = {BACKGROUND: DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. RESULTS: In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools. CONCLUSIONS: The developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads.},
	keywords = {Methyl-Seq, NGS},
	issn = {1471-2105},
	doi = {10.1186/s12859-017-1574-3},
	url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1574-3},
	author = {Olanda, Ricardo and P{\'e}rez, Mariano and Ordu{\~n}a, Juan M and T{\'a}rraga, Joaqu{\'\i}n and Joaqu{\'\i}n Dopazo}
}
@article {1074,
	title = {A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition.},
	journal = {Cancer research},
	volume = {74},
	number = {19},
	year = {2014},
	month = {2014 Aug 8},
	pages = {5608{\textendash}19},
	abstract = {Epithelial-to-mesenchymal transition (EMT) is a plastic process in which fully differentiated epithelial cells are converted into poorly differentiated, migratory and invasive mesenchymal cells and it has been related to the metastasis potential of tumors. This is a reversible process and cells can also eventually undergo mesenchymal-to-epithelial transition (MET). The existence of a dynamic EMT process suggests the involvement of epigenetic shifts in the phenotype. Herein, we obtained the DNA methylomes at single-base resolution of MDCK cells undergoing epithelial-to-mesenchymal transition (EMT) and translated the identified differentially methylated regions (DMRs) to human breast cancer cells undergoing a gain of migratory and invasive capabilities associated with the EMT phenotype. We noticed dynamic and reversible changes of DNA methylation, both on promoter sequences and gene-bodies in association with transcription regulation of EMT-related genes. Most importantly, the identified DNA methylation markers of EMT were present in primary mammary tumors in association with the epithelial or the mesenchymal phenotype of the studied breast cancer samples.},
	keywords = {Methyl-Seq, Methylomics, Next Generation Sequencing},
	issn = {1538-7445},
	doi = {10.1158/0008-5472.CAN-13-3659},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/25106427},
	author = {Carmona, F Javier and Davalos, Veronica and Vidal, Enrique and Gomez, Antonio and Heyn, Holger and Hashimoto, Yutaka and Vizoso, Miguel and Martinez-Cardus, Anna and Sayols, Sergi and Ferreira, Humberto and Sanchez-Mut, Jose and Moran, Sebastian and Margeli, Mireia and Castella, Eva and Berdasco, Maria and Stefansson, Olafur Andri and Eyfjord, Jorunn E and Gonzalez-Suarez, Eva and Dopazo, Joaquin and Orozco, Modesto and Gut, Ivo and Esteller, Manel}
}
