Reactive Game Engine Programming for STEM Outreach. - Alan M. Cleary; Lucas Vandenbergh; John Peterson (SIGCSE, 2015)

Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. - Sudhansu Dash; Jacqueline D. Campbell; Ethalinda K. S. Cannon; Alan M. Cleary; Wei Huang; Scott R. Kalberer; Vijay Karingula; Alex G. Rice; Jugpreet Singh; Pooja E. Umale; Nathan T. Weeks; Andrew P. Wilkey; et al. (Nucleic Acids Res., 2016)

Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny. - Alan M. Cleary; Andrew D. Farmer (Bioinform., 2018)

Poster: Pangenome-Wide Association Studies with Frequented Regions. - Buwani Manuweera; Joann Mudge; Indika Kahanda; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary (BCB, 2019)

Pangenome-Wide Association Studies with Frequented Regions. - Buwani Manuweera; Joann Mudge; Indika Kahanda; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary (BCB, 2019)

Exploring Frequented Regions in Pan-Genomic Graphs. - Alan M. Cleary; Thiruvarangan Ramaraj; Indika Kahanda; Joann Mudge; Brendan Mumey (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Ten simple rules for developing visualization tools in genomics. - Éloi Durant; Mathieu Rouard; Eric W. Ganko; Cédric Muller; Alan M. Cleary; Andrew D. Farmer; Matthieu G. Conte; François Sabot (PLoS Comput. Biol., 2022)

Genotype-to-Phenotype Associations with Frequented Region Variants. - Indika Kahanda; Buwani Manuweera; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary; Joann Mudge (BIBM, 2023)

Constructing the CDAWG CFG using LCP-Intervals. - Alan M. Cleary; Jordan Dood (DCC, 2023)

Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes. - Alan M. Cleary; Andrew D. Farmer (Nucleic Acids Res., 2023)

Revisiting the Folklore Algorithm for Random Access to Grammar-Compressed Strings. - Alan M. Cleary; Joseph Winjum; Jordan Dood; Shunsuke Inenaga (SPIRE, 2024)

The CDAWG Index and Pattern Matching on Grammar-Compressed Strings. - Alan M. Cleary; Joseph Winjum; Jordan Dood; Shunsuke Inenaga (CoRR, 2024)

Bit Packed Encodings for Grammar-Compressed Strings Supporting Fast Random Access. - Alan M. Cleary; Joseph Winjum; Jordan Dood; Hiroki Shibata 001; Shunsuke Inenaga (SEA, 2025)