01755nas a2200217   4500008004100000022001400041245008100055210006900136260001600205300000800221490000700229520109100236653001501327653000801342100002001350700002001370700002101390700002301411700002101434856008201455       2017                        eng d  a1471-210500aA new parallel pipeline for DNA methylation analysis of long reads datasets.0 anew parallel pipeline for DNA methylation analysis of long reads  c2017 Mar 09  a1610 v183 aBACKGROUND: 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.10aMethyl-Seq10aNGS1 aOlanda, Ricardo1 aPérez, Mariano1 aOrduña, Juan, M1 aTárraga, Joaquín1 aDopazo, Joaquín  uhttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1574-302423nas a2200433   4500008004100000022001400041245008500055210006900140260001500209300001400224490000700238520117700245653001501422653001601437653003101453100002001484700002201504700001901526700001901545700001701564700002201581700001901603700002601622700001801648700002301666700002201689700002101711700002001732700001801752700002001770700003001790700002301820700002501843700002001868700002001888700001301908700002001921856004801941       2014                        eng d  a1538-744500aA Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition.0 aComprehensive DNA Methylation Profile of EpithelialtoMesenchymal  c2014 Aug 8  a5608–190 v743 aEpithelial-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.10aMethyl-Seq10aMethylomics10aNext Generation Sequencing1 aCarmona, Javier1 aDavalos, Veronica1 aVidal, Enrique1 aGomez, Antonio1 aHeyn, Holger1 aHashimoto, Yutaka1 aVizoso, Miguel1 aMartinez-Cardus, Anna1 aSayols, Sergi1 aFerreira, Humberto1 aSanchez-Mut, Jose1 aMoran, Sebastian1 aMargeli, Mireia1 aCastella, Eva1 aBerdasco, Maria1 aStefansson, Olafur, Andri1 aEyfjord, Jorunn, E1 aGonzalez-Suarez, Eva1 aDopazo, Joaquin1 aOrozco, Modesto1 aGut, Ivo1 aEsteller, Manel  uhttp://www.ncbi.nlm.nih.gov/pubmed/25106427