Canonical, stable, general mapping using context schemes. - Adam M. Novak; Yohei Rosen; David Haussler; Benedict Paten (Bioinform., 2015)

Describing the Local Structure of Sequence Graphs. - Yohei Rosen; Jordan Eizenga; Benedict Paten (AlCoB, 2017)

Modelling haplotypes with respect to reference cohort variation graphs. - Yohei Rosen; Jordan Eizenga; Benedict Paten (Bioinform., 2017)

An Average-Case Sublinear Exact Li and Stephens Forward Algorithm. - Yohei M. Rosen; Benedict J. Paten (WABI, 2018)

Superbubbles, Ultrabubbles, and Cacti. - Benedict Paten; Jordan M. Eizenga; Yohei M. Rosen; Adam M. Novak; Erik Garrison; Glenn Hickey (J. Comput. Biol., 2018)

An average-case sublinear forward algorithm for the haploid Li and Stephens model. - Yohei M. Rosen; Benedict J. Paten (Algorithms Mol. Biol., 2019)

The Immersive Graph Genome Explorer: Navigating Genomics in Immersive Virtual Reality. - Maxim Kuznetsov; Aviv Elor; Sri Kurniawan; Colleen M. Bosworth; Yohei Rosen; Nicholas Heyer; Mircea Teodorescu; Benedict Paten; David Haussler (SEGAH, 2021)

Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation Graphs. - Deepro Pasha; Yohei Rosen; Maxim Kuznetsov; Benedict Paten (BCB, 2023)