ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data. - André Yoshiaki Kashiwabara; Ígor Bonadio; Vitor Onuchic; Felipe Amado; Rafael Mathias; Alan Mitchell Durham (PLoS Comput. Biol., 2013)

TSSFinder - fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. - Mauro de Medeiros Oliveira; Ígor Bonadio; Alicia Lie de Melo; Glaucia Mendes Souza; Alan Mitchell Durham (Briefings Bioinform., 2021)