Vân Anh Huynh-Thu
GENIE3Three implementations of GENIE3 are available:
You have also the possibility to run GENIE3 on the GP-DREAM platform.
Inferring regulatory networks from expression data using tree-based methods
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., and Geurts, P.
PLoS ONE, 5(9):e12776, 2010.
GENIE3 was best performer in the:
GENIE3 variantsWe derived two extensions of GENIE3, for the inference of networks from time series data and systems genetics data (i.e. expression data + genomic data) respectively.
The GENIE3 extension for time series data is described in chapter 8 of my thesis.
The GENIE3 extension for systems genetics data is described in the following book chapter:
Gene regulatory network inference from systems genetics data using tree-based methods
Huynh-Thu V. A., Wehenkel L., and Geurts P.
In: A. de la Fuente (Ed.), Gene Network Inference - Verification of Methods for Systems Genetics Data, Springer, pp. 63-85, 2013.
Python and MATLAB implementations of both GENIE3 extensions are available. Please contact me if you are interested.
- MATLAB [Zip file]
Combining tree-based and dynamical systems for the inference of gene regulatory networks
Huynh-Thu, V. A. and Sanguinetti, G.
Bioinformatics, 31(10):1614-1622, 2015.