This repository includes some MATLAB scripts comprising the core algorithms of the AR1MA1-VBEM method described in the 4th chapter of my PhD dissertation, entitled:
Bayesian methods for inferring GRNs and protein profiles from gene expression microarrays data, 2012, ISBN: 978-84-9028-501-5
to perform Gene Regulatory Networks (GRNs) reverse engineering from gene expression time series data.
An early VBEM approach, based on a first-order autoregressive (AR1) model, was published in:
A Survey of Statistical Models for Reverse Engineering Gene Regulatory Networks, 2009, DOI: 10.1109/MSP.2008.930647
The present version improves the previous approach by introducing a first-order autoregressive first-order moving-average (AR1MA1) model that fits better the noisy nature of the data. We are updating the current version of the method to (i) handle RNA-Seq as well as microarray data and (ii) to improve it with a friendly user-interface. Hopefully, a new publication in a well rated journal will be released soon.