flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning. - Jim Shaw; Yun William Yu (J. Comput. Biol., 2022)

Theory of local k-mer selection with applications to long-read alignment. - Jim Shaw; Yun William Yu (Bioinform., 2022)

How to optimally sample a sequence for rapid analysis. - Martin C. Frith; Jim Shaw; John L. Spouge (Bioinform., 2023)

Floria: fast and accurate strain haplotyping in metagenomes. - Jim Shaw; Jean-Sébastien Gounot; Hanrong Chen; Niranjan Nagarajan; Yun William Yu (Bioinform., 2024)

skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements. - Xiaolei Brian Zhang; Grace Oualline; Jim Shaw; Yun William Yu (Bioinform., 2024)

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains. - Andrew Zheng; Jim Shaw; Yun William Yu (BMC Bioinform., 2024)

Devider: Long-Read Reconstruction of Many Diverse Haplotypes. - Jim Shaw; Christina Boucher 001; Yun William Yu; Noelle R. Noyes; Heng Li (RECOMB, 2025)