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Jamshed Khan
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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
432022
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
412021
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
382024
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
21*2022
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
172023
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
12024
Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3
J Khan, L Dhulipala, R Patro
bioRxiv, 2025.02. 02.636161, 2025
2025
Parallel and External-Memory Algorithms for Large-Scale Genomic Sequence-Graph and-Index Construction
J Khan
University of Maryland, College Park, 2024
2024
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment
NP Singh, J Khan, R Patro
bioRxiv, 2024.11. 27.625771, 2024
2024
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