RT Journal
A1 Jühling, Frank
A1 Kretzmer, Helene
A1 Bernhart, Stephan H.
A1 Otto, Christian
A1 Stadler, Peter F.
A1 Hoffmann, Steve
T1 metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
JF Genome Research 
JO Genome Research 
YR 2016 
FD February 01 
VO 26 
IS 2 
SP 256 
OP 262 
DO 10.1101/gr.196394.115 
UL http://genome.cshlp.org/content/26/2/256.abstract 
AB 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.