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

A generative model for the behavior of RNA polymerase. - Joseph Azofeifa; Robin D. Dowell (Bioinform., 2017)

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)