Coupled Petri nets for computer network risk analysis. - Matthew H. Henry; Ryan M. Layer; David R. Zaret (Int. J. Crit. Infrastructure Prot., 2010)

"Inform, Experience, Implement" - Teaching an intensive high school summer course. - Ryan Layer; Mark Sherriff; Luther A. Tychonievich (FIE, 2012)

Binary Interval Search: a scalable algorithm for counting interval intersections. - Ryan M. Layer; Kevin Skadron; Gabriel Robins; Ira M. Hall; Aaron R. Quinlan (Bioinform., 2013)

Nifty Assignments. - Nick Parlante; Julie Zelenski; Peter-Michael Osera; Marty Stepp; Mark Sherriff; Luther A. Tychonievich; Ryan Layer; Suzanne J. Matthews; Allison Obourn; David R. Raymond; Josh Hug; Stuart Reges (SIGCSE, 2015)

A Parallel Algorithm for $N$-Way Interval Set Intersection. - Ryan M. Layer; Aaron R. Quinlan (Proc. IEEE, 2017)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. - Boris Simovski; Chakravarthi Kanduri; Sveinung Gundersen; Dmytro Titov; Diana Domanska; Christoph Bock; Lara Bossini-Castillo; Maria Chikina; Alexander V. Favorov; Ryan M. Layer; Andrey A. Mironov; Aaron R. Quinlan; et al. (Nucleic Acids Res., 2018)

svtools: population-scale analysis of structural variation. - David E. Larson; Haley J. Abel; Colby Chiang; Abhijit Badve; Indraniel Das; James M. Eldred; Ryan M. Layer; Ira M. Hall (Bioinform., 2019)

Experience Report: Standards-Based Grading at Scale in Algorithms. - Lijun Chen 001; Joshua A. Grochow; Ryan Layer; Michael Levet (ITiCSE (1), 2022)

Biologically inspired graphs to explore massive genetic datasets. - Ryan M. Layer (Nat. Comput. Sci., 2025)