Gradually Expanding Dense Neighbourhoods (GENA)

Gradually expanding neighborhoods with adjustment (GENA) is a new algorithm for the computational prediction of protein complexes by making the realistic assumption that proteins participate in multiple pro-tein complexes and cellular functions. GENA gradually expands neighborhoods in a graph starting from highly informative “seed”nodes. GENA considers proteins as multifunctional molecules allowing them to participate in more thanone protein complex. In addition, GENA accepts weighted PPI graphs by using a weighted evaluationfunction for each cluster.

This is the implementation of GENA in Matlab.

GENA algorithm is published at:

Christos Dimitrakopoulosa, Konstantinos Theofilatos, Andreas Pegkas,Spiros Likothanassis, Seferina Mavroudia, Predicting overlapping protein complexes from weighted proteininteraction graphs by gradually expanding dense neighborhoods, Artificial Intelligence in Medicine 71 (2016) 62–69

Code is published under GNU GENERAL PUBLIC LICENSE Version 3