Two 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
(in preparation)

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:

• EGASP '05 - The Human Genome Annotation Assessment Project
• Twinscan & it's derivatives
• Genscan