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)

Adding sequence context to a Markov background model improves the identification of regulatory elements. - Nak-Kyeong Kim; Kannan Tharakaraman; John L. Spouge (Bioinform., 2006)

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)

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. - Nak-Kyeong Kim; Kannan Tharakaraman; Leonardo Mariño-Ramírez; John L. Spouge (BMC Bioinform., 2008)