TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets. - Ales Varabyou; Geo Pertea; Christopher Pockrandt; Mihaela Pertea (Bioinform., 2021)

Investigating open reading frames in known and novel transcripts using ORFanage. - Ales Varabyou; Beril Erdogdu; Steven L. Salzberg; Mihaela Pertea (Nat. Comput. Sci., 2023)