A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. - Zizhen Yao; Jeffrey E. Barrick; Zasha Weinberg; Shane J. Neph; Ronald R. Breaker; Martin Tompa; Walter L. Ruzzo (PLoS Comput. Biol., 2007)

Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. - Aaron Reba; Austin G. Meyer; Jeffrey E. Barrick (ALIFE, 2012)

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. - John R. Houser; Craig Barnhart; Daniel R. Boutz; Sean M. Carroll; Aurko Dasgupta; Joshua K. Michener; Brittany D. Needham; Ophelia Papoulas; Viswanadham Sridhara; Dariya K. Sydykova; Christopher J. Marx; M. Stephen Trent; et al. (PLoS Comput. Biol., 2015)

OSTIR: open source translation initiation rate prediction. - Cameron T. Roots; Alexandra Lukasiewicz; Jeffrey E. Barrick (J. Open Source Softw., 2021)

pLannotate: engineered plasmid annotation. - Matthew J. McGuffie; Jeffrey E. Barrick (Nucleic Acids Res., 2021)

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies. - Ira Zibbu; Claus O. Wilke; Jeffrey E. Barrick (J. Open Source Softw., 2025)