Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. - Lior Pachter; Marina Alexandersson; Simon Cawley (J. Comput. Biol., 2002)

Picking Alignments from (Steiner) Trees. - Fumei Lam; Marina Alexandersson; Lior Pachter (J. Comput. Biol., 2003)

SLAM web server for comparative gene finding and alignment. - Simon Cawley; Lior Pachter; Marina Alexandersson (Nucleic Acids Res., 2003)