SwiSpot: modeling riboswitches by spotting out switching sequences. - Marco Barsacchi; Eva Maria Novoa; Manolis Kellis; Alessio Bechini (Bioinform., 2016)

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. - Leszek P. Pryszcz; Eva Maria Novoa (Bioinform., 2021)