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Microbiome|August 14, 2024
Fairy: fast approximate coverage for multi-sample metagenomic binningJim Shaw, Yun William YuNature Methods|September 22, 2023
Fast and robust metagenomic sequence comparison through sparse chaining with skaniJim Shaw, Yun William YuJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|January 18, 2022
flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree PartitioningJim Shaw, Yun William YuBioinformatics (Oxford, England)|September 20, 2022
Theory of local k-mer selection with applications to long-read alignmentJim Shaw, Yun William YuNature Biotechnology|October 8, 2024
Rapid species-level metagenome profiling and containment estimation with sylphJim Shaw, Yun William YuGenome Research|March 29, 2023
Proving sequence aligners can guarantee accuracy in almost <i>O</i>(<i>m</i> log <i>n</i>) time through an average-case analysis of the seed-chain-extend heuristicJim Shaw, Yun William YuBMC Bioinformatics|April 22, 2024
Mora: abundance aware metagenomic read re-assignment for disentangling similar strainsAndrew Zheng, Jim Shaw, Yun William YuBioinformatics (Oxford, England)|September 4, 2024
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elementsXiaolei Brian Zhang, Grace Oualline, Jim Shaw, et al.Genome Research|September 23, 2025
Long-read reconstruction of many diverse haplotypes with deviderJim Shaw, Christina Boucher, Yun William Yu, et al.Bioinformatics (Oxford, England)|June 28, 2024
Floria: fast and accurate strain haplotyping in metagenomesJim Shaw, Jean-Sebastien Gounot, Hanrong Chen, et al.Pageof 4