Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes D Bertrand, J Shaw, M Kalathiyappan, AHQ Ng, MS Kumar, C Li, ...
Nature biotechnology 37 (8), 937-944, 2019
315 2019 Fast and robust metagenomic sequence comparison through sparse chaining with skani J Shaw, YW Yu
Nature Methods 20 (11), 1661–1665, 2023
62 2023 Theory of local k-mer selection with applications to long-read alignment J Shaw, YW Yu
Bioinformatics 38 (20), 4659-4669, 2022
44 2022 Proving sequence aligners can guarantee accuracy in almost O (m log n) time through an average-case analysis of the seed-chain-extend heuristic J Shaw, YW Yu
Genome Research 33 (7), 1175-1187, 2023
14 * 2023 Rapid species-level metagenome profiling and containment estimation with sylph J Shaw, YW Yu
Nature Biotechnology, 1-12, 2024
13 * 2024 Further investigations into the graph theory of S Hu, O Schnetz, J Shaw, K Yeats
Annales de l’Institut Henri Poincaré D 9 (3), 473-524, 2022
12 2022 Implementing persistence-based clustering of point clouds in the topology toolkit R Cotsakis, J Shaw, J Tierny, JA Levine
Topological Methods in Data Analysis and Visualization VI: Theory …, 2021
11 2021 How to optimally sample a sequence for rapid analysis MC Frith, J Shaw, JL Spouge
Bioinformatics 39 (2), btad057, 2023
9 2023 Flopp: extremely fast Long-Read polyploid haplotype phasing by uniform tree partitioning J Shaw, YW Yu
Journal of Computational Biology 29 (2), 195-211, 2022
6 * 2022 Mora: abundance aware metagenomic read re-assignment for disentangling similar strains A Zheng, J Shaw, YW Yu
BMC bioinformatics 25 (1), 161, 2024
2 2024 Fairy: fast approximate coverage for multi-sample metagenomic binning J Shaw, YW Yu
Microbiome 12 (1), 151, 2024
1 2024 Floria: fast and accurate strain haplotyping in metagenomes J Shaw, JS Gounot, H Chen, N Nagarajan, YW Yu
Bioinformatics 40 (Supplement_1), i30-i38, 2024
1 2024 Using image-based haplotype alignments to map global adaptation of SARS-CoV-2 TW Ouellette, J Shaw, P Awadalla
bioRxiv, 2021.01. 13.426571, 2021
1 2021 skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements XB Zhang, G Oualline, J Shaw, YW Yu
Bioinformatics 40 (Supplement_2), ii155-ii164, 2024
2024 Practical and theoretical problems in biological sequence comparison J Shaw
University of Toronto (Canada), 2024
2024 devider: long-read reconstruction of many diverse haplotypes J Shaw, C Boucher, YW Yu, N Noyes, H Li
bioRxiv, 2024.11. 05.621838, 2024
2024 ChromMiniGraph: Space-Efficient Minimizer-based Pangenome Reference Graph and Haplotype Mapping Tool J Shaw, KJ Gao
