String Matching with Stopper Encoding and Code Splitting. - Jussi Rautio; Jani Tanninen; Jorma Tarhio (CPM, 2002)

String Matching with Stopper Compression. - Jussi Rautio; Jani Tanninen; Jorma Tarhio (DCC, 2002)

Context-dependent stopper encoding. - Jussi Rautio (Stringology, 2005)

GAST, a Genomic Alignment Search Tool. - Kalle Karhu; Juho Mäkinen; Jussi Rautio; Jorma Tarhio; Hugh Salamon (BIOINFORMATICS, 2011)

Speeding up Compressed Matching with SBNDM2. - Kerttu Pollari-Malmi; Jussi Rautio; Jorma Tarhio (Stringology, 2014)