DNA Sequencing with Transposons. - Simon Cawley; Terence P. Speed (J. Comput. Biol., 2000)

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

HMM sampling and applications to gene finding and alternative splicing. - Simon Cawley; Lior Pachter (ECCB, 2003)

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

Machine learning in low-level microarray analysis. - Benjamin I. P. Rubinstein; Jon D. McAuliffe; Simon Cawley; Marimuthu Palaniswami; Kotagiri Ramamohanarao; Terence P. Speed (SIGKDD Explor., 2003)

ANOSVA: a statistical method for detecting splice variation from expression data. - Melissa S. Cline; John Blume; Simon Cawley; Tyson Clark; Jing-Shan Hu; Gang Lu; Nathan Salomonis; Hui Wang 007; Alan Williams (ISMB (Supplement of Bioinformatics), 2005)

Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. - Xiaojun Di; Hajime Matsuzaki; Teresa A. Webster; Earl Hubbell; Guoying Liu; Shoulian Dong; Dan Bartell; Jing Huang 024; Richard Chiles; Geoffrey Yang; Mei-mei Shen; David Kulp; et al. (Bioinform., 2005)

LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. - K. Hao; Xiaojun Di; Simon Cawley (Bioinform., 2007)