Computer Resources

Gene signatures

For RNA-seq, microarray, mass-speck and other high-throughput technology users.

These are files with human genes grouped by pathways, function, literature keywords etc.
Rath-Korennykh (comprehensive; all pathways, functions etc)
TargetScan6 (microRNAs)
These files are directly compatible with GSEA .
They can also be used with other gene enrichment analysis programs. 
How to cite:
Rath S, Donovan J, Whitney G, Chitrakar A, Wang W, Korennykh A.
Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15916-21. doi: 10.1073/pnas.1513034112. Epub 2015 Dec 14.
PMID: 26668391

- For larger and more inclusive signature dataset, please inquire

Binding constant from a PDB file

Kd server

Server to predict binding affinity for proteins from PDB structures.
This server works for complexes or crystal packing contacts, and goes substantially beyond "smaller interface / larger interface" kind of evaluation.
GEFOS a test server presently for internal use
for evaluation of human/murine genes enriched in microarray, RNA-seq or other datasets. Server will work with as few as 2-3 genes and with as many as 10,000. Current limit is 10 genes for general users to ease the server load.

Intellectual Property

Patent Applications

Princeton University
2012 Provisional Patent Application
Reporters for detection of the human immune messenger 2-5A for research and diagnostics purposes

Contact Princeton University,
Office of Technology Licensing for more information

2008 International Patent Application (PCT)
Methods and Compositions for Modulating IRE1, SRC and ABL Activity
Pub. No.: WO/2010/031056

2009 International Patent Application (PCT)
Methods of Inhibiting IRE1
Pub. No.: WO/2011/047384UCSF

Contact UCSF,
Office of Technology Managementfor more information

Recent Publications

Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L
Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response
The metabolites NADP+ and NADPH are the targets of the circadian protein Nocturnin (Curled)