| 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 | 256 | 2019 |
| Theory of local k-mer selection with applications to long-read alignment J Shaw, YW Yu Bioinformatics 38 (20), 4659-4669, 2022 | 34 | 2022 |
| Fast and robust metagenomic sequence comparison through sparse chaining with skani J Shaw, YW Yu Nature Methods 20 (11), 1661–1665, 2023 | 15 | 2023 |
| Further investigations into the graph theory of -periods and the invariant 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 | 9 | 2021 |
| 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 | 7* | 2023 |
| How to optimally sample a sequence for rapid analysis MC Frith, J Shaw, JL Spouge Bioinformatics 39 (2), btad057, 2023 | 7 | 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 | 5* | 2022 |
| Mora: abundance aware metagenomic read re-assignment for disentangling similar strains A Zheng, J Shaw, YW Yu BMC bioinformatics 25, 2024 | 1 | 2024 |
| Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph J Shaw, YW Yu bioRxiv, 2023.11. 20.567879, 2023 | 1 | 2023 |
| 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 |
| Fairy: fast approximate coverage for multi-sample metagenomic binning J Shaw, YW Yu bioRxiv, 2024.04. 23.590803, 2024 | | 2024 |
| Floria: Fast and accurate strain haplotyping in metagenomes J Shaw, JS Gounot, H Chen, N Nagarajan, YW Yu bioRxiv, 2024.01. 28.577669, 2024 | | 2024 |
| ChromMiniGraph: Space-Efficient Minimizer-based Pangenome Reference Graph and Haplotype Mapping Tool J Shaw, KJ Gao | | |
