M3D statistics

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Citations per year

Number of citations per year for the bioinformatics software tool M3D

Tool usage distribution map

This map represents all the scientific publications referring to M3D per scientific context
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M3D specifications


Unique identifier OMICS_06803
Name M3D
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
parallel, BiocGenerics, IRanges, GenomicRanges, testthat, S4Vectors, BiocStyle, SummarizedExperiment, Rcpp, knitr, R(>=3.3.0), BiSeq
Maintained Yes


No version available


Publication for M3D

M3D citations


Integrating Epigenomics into the Understanding of Biomedical Insight

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

[…] Seq), weighted generalized linear model (BSmooth), bump hunting with batch effect removal and peak detection (bumphunting), tunable kernel smoothing (DMR-cate), nonparametric and kernel-based method (M3D), beta-binomial model (methylSig), beta-binomial hierarchical model (MOABS), hidden Markov model (NHMMfdr), three-state HMM (MethPipe), Shannon entropy (QDMR), and a binary segmentation algorithm […]


Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

Front Microbiol
PMCID: 5121216
PMID: 27933038
DOI: 10.3389/fmicb.2016.01819

[…] Gene expression data were collected from the Gene Expression Omnibus (GEO) (Edgar et al., ) and M3D databases (Faith et al., ), as well as from the laboratory of Dr. Paul Dunman in the case of S. aureus. Expression data were downloaded in the form of Affymetrix GeneChip® cell intensity (CEL) fil […]


Cautions about the reliability of pairwise gene correlations based on expression data

Front Microbiol
PMCID: 4481165
PMID: 26167162
DOI: 10.3389/fmicb.2015.00650

[…] able . We then combined other GSEs to create the rest of the other partial compendia.A similar approach was taken for E. coli, S. oneidensis and S. aureus. For example, E. coli data was obtained from M3D. M3D has collected data from GEO, as well as data deposited directly to M3D by other labs. To create partial compendia for E. coli we created a single partial compendium for all GEO data that is i […]


The genome scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

Nucleic Acids Res
PMCID: 4288151
PMID: 25429971
DOI: 10.1093/nar/gku1229

[…] Publicly-available gene expression (transcriptome) data for E. coli were downloaded from the M3D database (http://m3d.mssm.edu; ()). This comprises Robust Multi-array Average (RMA)-normalized gene expression measurements from Affymetrix microarrays across ∼300 conditions. Pearson correlation […]


Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

BMC Bioinformatics
PMCID: 3462729
PMID: 22873695
DOI: 10.1186/1471-2105-13-193

[…] nsity (CEL) files for substantial numbers of microarray experiments. We obtained these CEL files from multiple sources: NCBI’s Gene Expression Omnibus [GEO; [], the Many Microbe Microarrays Database [M3D; [], and, in one case, a private laboratory (Dr. Paul Dunman, personal communication). Expression data from GEO and M3D is available via direct download from those repositories, while expression d […]

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M3D institution(s)
IANC, School of Informatics, University of Edinburgh, Edinburgh and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK

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