Jamshed Khan

Welcome to my profile! I'm Jamshed Khan. I'm a Distinguished Research Fellow in Computer Science at The Northeastern University. I received my PhD in Computer Science in December 2024 from The University of Maryland, College Park (UMD).

My research interests are mainly focused on Parallel Algorithms, Memory-Hierarchy Aware Algorithms, Large-Scale Data Systems, Algorithm Engineering, and Computational Genomics. Specifically, my research focus is in solving various algorithmic problems at large-scale with multitudes of algorithmic paradigms, employing parallel and memory-hierarchy aware schemes for resource-efficiency and high scalability.

My current research pertains to designing parallel and memory-hierarchy aware scalable algorithms and data structures for large‑scale data systems.

Recent Highlights

May 2025: Our paper on scaling parallel algorithms to massive datasets using multi-SSD machines is accepted for publication in SPAA 2025!
Mar. 2025: The Alevin-fry-atac paper is accepted for publication in ISMB 2025!
Feb. 2025: Pre-print for Cuttlefish 3, state-of-the-art colored compacted de Bruijn graph constructor, is posted!
Dec. 2024: Defended PhD thesis!
Apr. 2024: The CaPS-SA paper is accepted for publication in AMB!
Jan. 2024: The Fulgor paper is accepted for publication in AMB!
Sep. 2023: Attended and presented in WABI 2023 (Houston, Texas)—take a peek here: https://go.umd.edu/48khyOM!
Jun. 2023: The CaPS-SA paper is accepted for publication in WABI 2023!
Jun. 2023: The Fulgor paper is accepted for publication in WABI 2023!
May 2023: Pre-print for Fulgor, a fast and compact colored de Bruijn graph index, is out!

News

May 2025: Out paper on scaling parallel algorithms massively using multi-SSD machines is accepted for publication in SPAA 2025!
Mar. 2025: The Alevin-fry-atac paper is accepted for publication in ISMB 2025!
Feb. 2025: Pre-print for Cuttlefish 3, state-of-the-art colored compacted de Bruijn graph constructor, is posted!
Dec. 2024: Defended PhD thesis!
Apr. 2024: The CaPS-SA paper is accepted for publication in AMB!
Jan. 2024: The Fulgor paper is accepted for publication in AMB!
Sep. 2023: Attended and presented in WABI 2023 (Houston, Texas)—take a peek here: https://go.umd.edu/48khyOM!
Jun. 2023: The CaPS-SA paper is accepted for publication in WABI 2023!
Jun. 2023: The Fulgor paper is accepted for publication in WABI 2023!
May 2023: Pre-print for Fulgor, a fast and compact colored de Bruijn graph index, is out!
Nov. 2022: The SPT paper ("Spectrum preserving tilings enable sparse and modular reference indexing") is accepted for RECOMB 2023!
Oct. 2022: Pre-print for pufferfish2, introducing SPTs (Spectrum Preserving Tilings) is out!
Sep. 2022: The Cuttlefish 2 paper ("Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2") is published in Genome Biology!
Jun. 2022: Pre-print for the Cuttlefish 2 algorithm is updated with new experiments and more theoretical details!
Mar. 2022: The Dynamic Mantis paper ("An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using the Bentley-Saxe Transformation") is published in Bioinformatics!
Jan. 2022: Received Outstanding Research Assistant Award from the UMD Graduate School for the AY 2021-22!
Dec. 2021: Pre-print for Cuttlefish 2 (farther advancing the state-of-the-art on compacted de Bruijn graph construction) is posted!
Jul. 2021: Received the Ian Lawson Van Toch Memorial Award for Outstanding Student Paper in ISMB/ECCB 2021—take a peek here: go.umd.edu/TWY!
Jul. 2021: Attended and presented in ISMB/ECCB 2021 (Lyon, virtual)!
Apr. 2021: The Cuttlefish paper ("Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections") is accepted for ISMB/ECCB 2021!
Feb. 2021: Presented a talk on a new state-of-the-art compacted de Bruijn graph construction algorithm for genome references in DSB 2021 (Università di Milano, virtual)!
Feb. 2021: Pre-print for Dynamic Mantis (a large-scale sequence search index with dynamic extension enabled using LSM trees) is posted!
Jan. 2021: Pre-print for the Cuttlefish algorithm is updated with new results and benchmarking tools!
Nov. 2020: Presented a talk on the Cuttlefish algorithm at CBCB Research in Progress seminar!
Oct. 2020: Pre-print for Cuttlefish (a state-of-the-art algorithm for construction of the compacted de Bruijn graph from genome references) is posted!
Sep. 2019: Got awarded "Excellence as a TA award" for the AY 2018—2019!

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