Evolutionary Rhythm Composition with Trajectory-based Fitness Evaluation. - John Huddleston; Jianna Zhang (AAAI, 2007)

Effects of Musically Meaningful operators in Evolutionary Composition. - John Huddleston; Jianna Zhang (ICMC, 2007)

denovo-db: a compendium of human de novo variants. - Tychele Turner; Qian Yi; Niklas Krumm; John Huddleston; Kendra Hoekzema; Holly A. Stessman; Anna-Lisa Doebley; Raphael A. Bernier; Deborah A. Nickerson; Evan E. Eichler (Nucleic Acids Res., 2017)

Nextstrain: real-time tracking of pathogen evolution. - James Hadfield; Colin Megill; Sidney M. Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A. Neher (Bioinform., 2018)

dms-view: Interactive visualization tool for deep mutational scanning data. - Sarah Hilton; John Huddleston; Allison Black; Khrystyna North; Adam S. Dingens; Trevor Bedford; Jesse D. Bloom (J. Open Source Softw., 2020)

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. - John Huddleston; James Hadfield; Thomas R. Sibley; Jover Lee; Kairsten Fay; Misja Ilcisin; Elias Harkins; Trevor Bedford; Richard A. Neher; Emma B. Hodcroft (J. Open Source Softw., 2021)

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. - Jover Lee; James Hadfield; Allison Black; Thomas R. Sibley; Richard A. Neher; Trevor Bedford; John Huddleston (Frontiers Bioinform., 2023)