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Citations per year

Number of citations per year for the bioinformatics software tool metilene
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Tool usage distribution map

This map represents all the scientific publications referring to metilene per scientific context
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metilene specifications

Information


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

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Documentation


Maintainer


  • person_outline Steve Hoffmann

Publication for metilene

metilene citations

 (6)
library_books

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

2018
BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] e rate), and speed of implementation on simulated data. However, our analysis in the next subsection and in the Additional file , Section 8, clearly demonstrates that DSS is statistically superior to metilene, since the latter method cannot produce differential methylation results that can be considered valid from a statistical perspective. For this reason, we chose to compare the differential per […]

library_books

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

2018
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 […]

library_books

Similarity Based Segmentation of Multi Dimensional Signals

2017
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 […]

library_books

BAT: Bisulfite Analysis Toolkit

2017
F1000Res
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 […]

library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
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 […]

library_books

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

2010
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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