Ewan Birney's PhD thesis  was in a large part the development of the Wise system for building a system to generate C code for sequence alignment algorithms based on a simple language describing the algorithm. The Dynamite compiler  is used to convert the dynamic programming representation into compilable C code.
- Birney E, Cambridge University, PhD Thesis.
- Birney E and Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 2000 Apr;10(4):547-8.
- Birney E. "Hidden Markov Models in Biological Sequence Analysis" IBM J Res and Dev 2001; 45(3/4): 449-454.
- Birney E, Clamp M, and Durbin R. GeneWise and Genomewise. Genome Res. 2004 May;14(5):988-95. DOI:10.1101/gr.1865504 |