Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. - Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey Sheetlin; David Landsman; John L. Spouge (ISMB (Supplement of Bioinformatics), 2005)

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. - Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey Sheetlin; David Landsman; John L. Spouge (BMC Bioinform., 2006)

Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. - Hyrum D. Carroll; Maricel G. Kann; Sergey Sheetlin; John L. Spouge (Bioinform., 2010)

The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional lattice. - John L. Spouge; Leonardo Mariño-Ramírez; Sergey Sheetlin (ICCABS, 2012)

Frameshift alignment: statistics and post-genomic applications. - Sergey L. Sheetlin; Yonil Park; Martin C. Frith; John L. Spouge (Bioinform., 2014)

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. - John L. Spouge; Leonardo Mariño-Ramírez; Sergey L. Sheetlin (Int. J. Bioinform. Res. Appl., 2014)

ALP & FALP: C++ libraries for pairwise local alignment E-values. - Sergey Sheetlin; Yonil Park; Martin C. Frith; John L. Spouge (Bioinform., 2016)