title: metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
abstract: The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results.
authors.affiliation: Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;
authors.forename: Frank
authors.initials: F
authors.lastname: Jühling
authors.affiliation: Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;
authors.forename: Helene
authors.initials: H
authors.lastname: Kretzmer
authors.affiliation: Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.affiliation: Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;
authors.forename: Christian
authors.initials: C
authors.lastname: Otto
authors.affiliation: Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology - IZI, 04103 Leipzig, Germany; Santa Fe Institute, Santa Fe, New Mexico 87501, USA; Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Mathematics in Sciences, 04103 Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, 04107 Leipzig, Germany;
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
mesh_terms: D000465:Algorithms; D016022:Case-Control Studies; D002528:Cerebellar Neoplasms / Q000235:genetics; D018899:CpG Islands; D019175:DNA Methylation; D006801:Humans; D008527:Medulloblastoma / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software