Spectral biclustering

Q:
I recently read
your 2003 paper titled "Spectral biclustering of microarray data: Coclustering
genes and conditions".

I would like to investigate implementing your approach on a GPU.
Is there any code (Matlab? Python?) you would be willing to share as a result of the paper?

A:
Sorry we’re just using simple SVD routines in matlab. No meaningful code available. -marK

OrthoClust – for more than two species

Q:
I just read your recently published paper on OrthoClust approach. It is a well grounded work in both practically and mathematically point of views.

I ran your R scripts for my own data and It worked perfectly fine, however I am wondering how can I use the script for more than two species?

It could be appreciated if you help me to find the solution.

A:
Thanks for your interest in OrthoClust. Orthoclust definitely works on more than 2. The R script is a primitive version for illustrating the concept outlined in the paper. We understand the importance of N-species generalization. We have put a new MATLAB code for N-species. It made use of an efficient code written by Mucha and Porter that implemented the Louvain algorithm for modularity optimization. The 3rd party code as well as our wrapper is now in the gersteinlab github.
Apart from MATLAB, we are planning to provide wrapper for Python or R later.
The N-species code is not exactly the thing we did for the paper. So if you find any bug or question, please let me know. we are trying to make a more user friendly package anyway.

rulefit3 in encodenets

Q:
I read your paper about the co-associations among TF binding events, (Architecture of the human regulatory network derived from ENCODE data), and got interested in your original clustering algorithm. Now, in our laboratory, we are developing a new clustering algorithm for a large number of genomic data, and implemented its prototype algorithm. However, the accuracy of our algorithm is not so completed, and we have to evaluate it. Thus, we want to use your algorithm as the fine basis, so how can we use it? If the program is available for us, can you tell us the way to use it?

A:
In that paper we used the Rulefit3 package from Prof. Jerome Friedman; there is an R package available at the link below. Our use of the algorithm is extensively documented in Section C of the Supplementary Materials.

Rulefit3
http://dx.doi.org/10.1214/07-Aoas148
http://www-stat.stanford.edu/~jhf/r-rulefit/rulefit3/R_RuleFit3.html

Architecture of the human regulatory network derived from ENCODE data http://dx.doi.org/10.1038/Nature11245