Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. - Jamshed Khan; Rob Patro (Bioinform., 2021)

Homothetic Symmetries of Static Cylindrically Symmetric Spacetimes - A Rif Tree Approach. - Jamshed Khan; Tahir Hussain; Dania Santina; Nabil Mlaiki (Axioms, 2022)

An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. - Fatemeh Almodaresi; Jamshed Khan; Sergey Madaminov; Michael Ferdman; Rob Johnson 001; Prashant Pandey 001; Rob Patro (Bioinform., 2022)

Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing. - Jason Fan; Jamshed Khan; Giulio Ermanno Pibiri; Rob Patro (RECOMB, 2023)

Parallel and External-Memory Algorithms for Large-Scale Genomic Sequence-Graph and -Index Construction. - Jamshed Khan (2024)

Fulgor: a fast and compact k-mer index for large-scale matching and color queries. - Jason Fan; Jamshed Khan; Noor Pratap Singh; Giulio Ermanno Pibiri; Rob Patro (Algorithms Mol. Biol., 2024)

Fast, parallel, and cache-friendly suffix array construction. - Jamshed Khan; Tobias Rubel; Erin K. Molloy; Laxman Dhulipala; Rob Patro (Algorithms Mol. Biol., 2024)

Scaling Parallel Algorithms to Massive Datasets using Multi-SSD Machines. - Haohong Li; Jamshed Khan; Laxman Dhulipala (SPAA, 2025)