| Megadepth: efficient coverage quantification for BigWigs and BAMs C Wilks, O Ahmed, DN Baker, D Zhang, L Collado-Torres, B Langmead Bioinformatics 37 (18), 3014-3016, 2021 | 29 | 2021 |
| Pan-genomic matching statistics for targeted nanopore sequencing O Ahmed, M Rossi, S Kovaka, MC Schatz, T Gagie, C Boucher, ... Iscience 24 (6), 2021 | 27 | 2021 |
| SPUMONI 2: improved classification using a pangenome index of minimizer digests OY Ahmed, M Rossi, T Gagie, C Boucher, B Langmead Genome Biology 24 (1), 122, 2023 | 23 | 2023 |
| Movi: a fast and cache-efficient full-text pangenome index M Zakeri, NK Brown, OY Ahmed, T Gagie, B Langmead iScience 27 (12), 2024 | 12 | 2024 |
| Sigmoni: classification of nanopore signal with a compressed pangenome index VS Shivakumar, OY Ahmed, S Kovaka, M Zakeri, B Langmead bioRxiv, 2023 | 8 | 2023 |
| DandD: efficient measurement of sequence growth and similarity JK Bonnie, OY Ahmed, B Langmead Iscience 27 (3), 2024 | 7 | 2024 |
| Efficient taxa identification using a pangenome index O Ahmed, M Rossi, C Boucher, B Langmead Genome Research 33 (7), 1069-1077, 2023 | 5 | 2023 |
| Spumoni 2: Improved pangenome classification using a compressed index of minimizer digests O Ahmed, M Rossi, T Gagie, C Boucher, B Langmead bioRxiv, 2022.09. 08.506805, 2022 | 5 | 2022 |
| MEM-based pangenome indexing for k-mer queries S Hwang, NK Brown, OY Ahmed, KM Jenike, S Kovaka, MC Schatz, ... bioRxiv, 2024.05. 20.595044, 2024 | 3 | 2024 |
| Fast and flexible minimizer digestion with digest A Zheng, I Lee, VS Shivakumar, OS Ahmed, B Langmead bioRxiv, 2025.01. 02.631161, 2025 | | 2025 |
| Developing compressed linear pangenome indexes for rapid sequence classification O Ahmed Johns Hopkins University, 2024 | | 2024 |
| Cliffy: robust 16S rRNA classification based on a compressed LCA index O Ahmed, C Boucher, B Langmead bioRxiv, 2024.05. 25.595899, 2024 | | 2024 |
| MEM-based pangenome indexing fork-mer queries S Hwang, NK Brown, OY Ahmed, KM Jenike, S Kovaka, MC Schatz, ... | | 2024 |
| Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests D Draesslerová, O Ahmed, T Gagie, J Holub, B Langmead, G Manzini, ... arXiv preprint arXiv:2402.06935, 2024 | | 2024 |
| r-indexing without backward searching O Ahmed, A Baláž, NK Brown, L Depuydt, A Goga, A Petescia, M Zakeri, ... arXiv preprint arXiv:2312.01359, 2023 | | 2023 |
| HBcompare: Classifying Ligand Binding Preferences with Hydrogen Bond Topology JZ Tam, Z Kong, O Ahmed, L He, BY Chen Biomolecules 12 (11), 1589, 2022 | | 2022 |