FStitch: a fast and simple algorithm for detecting nascent RNA transcripts. - Joseph Azofeifa; Mary A. Allen; Manuel E. Lladser; Robin D. Dowell (BCB, 2014)

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq. - Joseph Azofeifa; Mary A. Allen; Manuel E. Lladser; Robin D. Dowell (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease. - Jacob T. Stanley; Alison R. Gilchrist; Alex C. Stabell; Mary A. Allen; Sara L. Sawyer; Robin D. Dowell (PSB, 2020)