JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis. - Ioannis A. Tamposis; Konstantinos D. Tsirigos; Margarita C. Theodoropoulou; Panagiota I. Kontou; Georgios N. Tsaousis; Dimitra Sarantopoulou; Zoi I. Litou; Pantelis G. Bagos (Bioinform., 2019)

Comparative evaluation of full-length isoform quantification from RNA-Seq. - Dimitra Sarantopoulou; Thomas G. Brooks; Soumyashant Nayak; Antonijo Mrcela; Nicholas F. Lahens; Gregory R. Grant (BMC Bioinform., 2021)

BEERS2: RNA-Seq simulation through high fidelity in silico modeling. - Thomas G. Brooks; Nicholas F. Lahens; Antonijo Mrcela; Dimitra Sarantopoulou; Soumyashant Nayak; Amruta Naik; Shaon Sengupta; Peter S. Choi; Gregory R. Grant (Briefings Bioinform., 2024)