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Biorxiv : the Preprint Server for Biology|February 27, 2026
<i>k</i> ache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming <i>k</i> -mer operationsJamshed Khan, Rob Patro, Prashant Pandey
Bioinformatics (Oxford, England)|July 12, 2021
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collectionsJamshed Khan, Rob Patro
Bioinformatics (Oxford, England)|March 24, 2022
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformationFatemeh Almodaresi, Jamshed Khan, Sergey Madaminov, et al.
Biorxiv : the Preprint Server for Biology|February 20, 2025
Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3Jamshed Khan, Laxman Dhulipala, Rob Patro
Bioinformatics (Oxford, England)|July 15, 2025
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignmentNoor Pratap Singh, Jamshed Khan, Rob Patro
Biorxiv : the Preprint Server for Biology|December 16, 2024
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignmentNoor Pratap Singh, Jamshed Khan, Rob Patro
Genome Biology|September 8, 2022
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2Jamshed Khan, Marek Kokot, Sebastian Deorowicz, et al.
Bioinformatics (Oxford, England)|September 9, 2017
deBGR: an efficient and near-exact representation of the weighted de Bruijn graphPrashant Pandey, Michael A Bender, Rob Johnson, et al.
Algorithms for Molecular Biology : AMB|April 28, 2024
Fast, parallel, and cache-friendly suffix array constructionJamshed Khan, Tobias Rubel, Erin Molloy, et al.
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|March 17, 2020
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph SearchFatemeh Almodaresi, Prashant Pandey, Michael Ferdman, et al.
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