Hidden Markov Models:

Tutorial on Hidden Markov Models by Roger Boyle, University of Leeds

Review article on Profile HMMs, by Sean Eddy, Bioinformatics 14:755-763 (1998)

Sequence Assembly:

Finishing the euchromatic sequence of the human genome

Whole-Genome DNA Sequencing, by Gene Myers, Computational BiologyMay-June 1999, pp. 33-43

Support Vector Machines:

A Tutorial on Support Vector Machines for Pattern Recognition by Christopher Burges, Datat Mining and Knowledge Discovery, 2, 121--167, Kluwer, 1998.

Gene Finding

Michael Zhang, Computational Prediction of Eukaryotic Protein Coding Genes. Nature Reviews Genetics 3 (2002): 698-709
Michael Zhang, Computational Prediction of Eukaryotic Protein Coding Genes. Nature Reviews Genetics 3 (2002): 698-709