Three papers have been written on Conrad:
Comparative Gene Prediction using Conditional Random Fields
Jade Vinson, David DeCaprio, Matthew Pearson, Stacey Luoma, James Galagan
Advances in Neural Information Processing Systems 19 (NIPS 2006)
[ps.gz] [pdf] [bibtex]
Conrad: Gene prediction using conditional random fields
David DeCaprio, Jade Vinson, Matthew Pearson, Philip Montgomery, Matthew Doherty, and James Galagan
Genome Research, 9 August 2007.
[abstract]
Gene Prediction with Conditional Random Fields
Matthew Doherty
Master's thesis, Massachusetts Institute of Technology, 2007.
[pdf]
For general information on CRFs there is a great web page by Hannah Wallach listing many references: http://www.inference.phy.cam.ac.uk/hmw26/crf/
For general information on gene calling, there are also several great sources: