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Jamshed Khan
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Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections
J Khan, R Patro
Bioinformatics 37 (Supplement_1), i177-i186, 2021
342021
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
J Khan, M Kokot, S Deorowicz, R Patro
Genome biology 23 (1), 190, 2022
282022
Fulgor: a fast and compact k-mer index for large-scale matching and color queries
J Fan, J Khan, NP Singh, GE Pibiri, R Patro
Algorithms for Molecular Biology 19 (1), 3, 2024
192024
Spectrum preserving tilings enable sparse and modular reference indexing
J Fan, J Khan, GE Pibiri, R Patro
International Conference on Research in Computational Molecular Biology, 21-40, 2023
132023
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation
F Almodaresi, J Khan, S Madaminov, M Ferdman, R Johnson, P Pandey, ...
Bioinformatics 38 (12), 3155-3163, 2022
11*2022
Fast, parallel, and cache-friendly suffix array construction
J Khan, T Rubel, E Molloy, L Dhulipala, R Patro
Algorithms for Molecular Biology 19 (1), 16, 2024
2024
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