The Distributed Annotation System. - Robin D. Dowell; Rodney M. Jokerst; Allen Day; Sean R. Eddy; Lincoln Stein (BMC Bioinform., 2001)

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. - Robin D. Dowell; Sean R. Eddy (BMC Bioinform., 2004)

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. - Robin D. Dowell; Sean R. Eddy (BMC Bioinform., 2006)

Automated Discovery of Functional Generality of Human Gene Expression Programs. - Georg K. Gerber; Robin D. Dowell; Tommi S. Jaakkola; David K. Gifford (PLoS Comput. Biol., 2007)

Discovering Regulatory Overlapping RNA Transcripts. - Timothy Danford; Robin D. Dowell; Sudeep Agarwala; Paula Grisafi; Gerald Fink; David K. Gifford (J. Comput. Biol., 2011)

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

Inferring ancestry in mouse genomes using a hidden Markov model. - Daniel Malmer; Phillip Andrew Richmond; Aaron Odell; Richard Radcliffe; Robin D. Dowell (BCB, 2014)

A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation. - David A. Knox; Robin D. Dowell (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

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

Model based heritability scores for high-throughput sequencing data. - Pratyaydipta Rudra; W. Jenny Shi; Brian Vestal; Pamela H. Russell; Aaron Odell; Robin D. Dowell; Richard Radcliffe; Laura M. Saba; Katerina J. Kechris (BMC 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)

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)

Internal and external normalization of nascent RNA sequencing run-on experiments. - Zachary L. Maas; Robin D. Dowell (BMC Bioinform., 2024)