Q:
Recently, I have read one of your paper titled “Comparative analysis of regulatory information and circuits across distant species”. In this paper, you wrote that you used simulated annealing to reveal the organization of regulatory factors in three layers of master-regulators, intermediate regulators, and low-level regulators. However, I can’t find the program for this method or the references related to this method. I want to use this method to class the TFs in my own regulatory network. Can you kindly provided this program for me?

A:
An initial version of the code is available from encodenets.gersteinlab.org.

The code used for the analysis can be found
http://encodenets.gersteinlab.org/enets16.hierarchy_levels.m
more recently, our group published an updated method. the code will be released very soon.
http://genomebiology.com/2015/16/1/63/abstract#