Jamshed Khan
Welcome to my profile! I'm Jamshed Khan, a PhD candidate and graduate research assistant at the Department of Computer Science (CS) at The University of Maryland, College Park (UMD). I'm working in Professor Rob Patro's research group here. I've completed my undergraduate studies (B.Sc. in CSE) from the Department of Computer Science and Engineering (CSE) at Bangladesh University of Engineering and Technology (BUET).
My research interests are mainly focused on Theory and Algorithms, Bioinformatics, and Computer Systems. Specifically, I'm interested to work in solving various algorithmic problems with multitudes of algorithmic paradigms, designing novel algorithms and heuristics, employing parallel computing, and using probabilistic graphical models and learning models as frameworks for complex domains.
My current research pertains to designing highly scalable data structures and algorithms to efficiently compress, organize, index, and search high-throughput genomic data.
Recent Highlights
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!
News
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!