Lemone

LeMoNe is a software package for Learning Module Networks from gene expression data. The algorithm has been described and validated in the following papers:


  1. * Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8, S5. *contributed equally
  2. Joshi, A., Van de Peer, Y., Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24, 176-83.
  3. Joshi, A., De Smet, R., Marchal, K., Van de Peer, Y., Michoel, T. (2009) Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 25, 490-6.
  4. Michoel, T., De Smet, R., Joshi, A., Van de Peer, Y., Marchal, K. (2009) Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. 3, 49.
  5. Vermeirssen, V., Joshi, A., Michoel, T., Bonnet, E., Casneuf, T., Van de Peer, Y. (2009) Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. Molecular BioSystems 5, 1817-30.
  6. Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Berx, G., Van de Peer, Y. (2010) Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLOS One 5, e10162.
  7. Bonnet, E., Michoel, T., Van de Peer, Y. (2010) Prediction of a regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 26, 638-644.

LeMoNe is freely available for academic use. We ask that you register here before downloading the software.
An extensive tutorial for LeMoNe can be downloaded here.









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VIB / UGent
Bioinformatics & Evolutionary Genomics
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