RMD specifications


Unique identifier OMICS_28750
Name RMD
Alternative name Regulatory Module Discovery
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline David Gifford

Publication for Regulatory Module Discovery

RMD citations


Co expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum

Sci Rep
PMCID: 5138846
PMID: 27922095
DOI: 10.1038/srep38436

[…] atabases, such as TAIR, BAR, DIP, MINT, IntAct and BioGRID, greatly contributing to PPI network construction. Unlike in Arabidopsis, however, a lack of PPI data has blocked proteomics data mining and regulatory module discovery in cotton. Therefore, co-expression networks have become the preferred method for functional analysis. Currently, a complete genome sequence of G. arboreum has been publish […]


Discovery of protein–DNA interactions by penalized multivariate regression

Nucleic Acids Res
PMCID: 2760818
PMID: 19578060
DOI: 10.1093/nar/gkp554

[…] ted with expression. The set of discovered motifs agreed well with current literature.The MotifExpress framework is easily extensible to support other TF–DNA-binding discovery methods, especially cis-regulatory module discovery methods. Statistically, penalized multivariate regression with CAP is ready to incorporate additional structural information about motifs. Likewise, as high-throughput tran […]

RMD institution(s)
MIT, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
RMD funding source(s)
Supported by National Institutes of Health (grant 1U01HG007037-01.

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