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metilene specifications


Unique identifier OMICS_10901
Name metilene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input consists of a single SORTED (for genomic positions) tab-separated file.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.2-4
Stability Stable
Maintained Yes




No version available



  • person_outline Steve Hoffmann

Publication for metilene

metilene citations


An information theoretic approach to the modeling and analysis of whole genome bisulfite sequencing data

BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] e also evaluated the appropriateness of the particular Ising model used by informME by employing Akaike’s information criterion. We finally demonstrated the clear superiority of informME over DSS and metilene, two recently proposed methods for differential analysis of bisulfite sequencing data, and illustrated its effectiveness in producing information about the methylation state of the epigenome […]


Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Nat Commun
PMCID: 5786002
PMID: 29374152
DOI: 10.1038/s41467-017-02762-z

[…] Fully methylated regions (FMRs) represent genomic regions not overlapping with CpG islands, LMRs, UMRs, and PMRs.Replicate-based differential methylation analysis (replicate DMR) was performed using Metilene for FMRs, CpG islands, LMRs, gUMRs, and PMRs. Since genic regions downstream of gUMRs were frequently partially methylated too, PMRs overlapping a single gene to at least 75% were removed fro […]


Similarity Based Segmentation of Multi Dimensional Signals

Sci Rep
PMCID: 5617875
PMID: 28955039
DOI: 10.1038/s41598-017-12401-8

[…] IP-seq experiment. It is of interest therefore, to investigate whether the expensive model training can be replaced by computationally more efficient heuristics. This avenue has been explored e.g. in metilene, which uses a fast heuristic to propose differentially methylated regions that are tested for significance only in a second step.In this contribution we describe a general purpose segmentatio […]


BAT: Bisulfite Analysis Toolkit

PMCID: 5590080
PMID: 28979767
DOI: 10.5256/f1000research.13317.r25076

[…] Finally, the fourth module features the identification and analysis of differentially methylated regions (DMRs) between groups ( BAT_DMRcalling). It employs the DMR calling tool metilene which is based on circular binary segmentation of the group methylation difference signal in conjunction with a two-dimensional non-parametric statistical test. Afterwards, the DMRs reported […]


Integrating Epigenomics into the Understanding of Biomedical Insight

Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] al hierarchical model (MOABS), hidden Markov model (NHMMfdr), three-state HMM (MethPipe), Shannon entropy (QDMR), and a binary segmentation algorithm combined with a two-dimensional statistical test (metilene). Usually, the latest software compares with some previous methods and claims best performance, such as MOABS, which can detect the DMRs with a relative low coverage (~10×) and metilene can i […]


Histological and ultrastructural evaluation of the early healing of the lateral collateral ligament epiligament tissue in a rat knee model

PMCID: 2894748
PMID: 20540800
DOI: 10.1186/1471-2474-11-117

[…] s were processed with disectional microscope and cut with ultramicrotome (LKB, Stockholm-Bromma, Sweden). The scar regions were identified on semi-thin sections (for light microscopy) stained with 1% metilene blue, azure II and basic fuchsin. The EL tissue of the LCL was identified on semi-thin sections from the midsubstance in controls and gap region of the transacted ligament for operated animal […]


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metilene institution(s)
Transcriptome Bioinformatics Group, LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, Faculty of Computer Science, University of Leipzig, Leipzig, Germany; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany; Santa Fe Institute, Santa Fe, New Mexico, USA; Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; Max Planck Institute for Mathematics in Sciences, Leipzig, Germany

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