Prashant Pandey

GitHubprashantpandey

Email prashant.pandey@stonybrook.edu

Research Interests

My research interests lie at the intersection of Systems and Algorithms. My current research focuses on building efficient approximate membership query data structures, specifically, counting filters and their applications. I am also working on finding compact methods to represent large DNA sequencing and transcriptome datasets for de Bruijn graph traversal and assembly process.

In the past, I have worked on BetrFS, an in-kernel file system built on write-optimized indexes. While interning at Intel Labs, I worked on an encrypted FUSE file system using Intel SGX. At Google, I designed and implemented an extension to the ext4 file system for cryptographically ensuring file integrity. Google is currently working to integrate this extension into Android and the mainline Linux kernel. While at Google, I also worked on the core data structures of Spanner, Google’s geo-distributed big database.

I am being co-advised by Prof. Michael Bender and Prof. Rob Johnson at Stony Brook University, where I am currently pursuing my Ph.D. in Computer Science.

Publications

In reverse chronological order:

  1. Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index (RECOMB 2018)
    Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, and Rob Patro

  2. Rainbowfish: A Succinct Colored de Bruijn Graph Representation (WABI 2017) [biorxiv]
    Fatemeh Almodaresi, Prashant Pandey, and Rob Patro

  3. Squeakr: An Exact and Approximate k-mer Counting System (Bioinformatics 2017) [biorxiv]
    Prashant Pandey, Michael A. Bender, Rob Patro, and Rob Johnson

  4. A Fast x86 Implementation of Select (arXiv 2017)
    Prashant Pandey, Michael A. Bender, and Rob Johnson

  5. deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph (ISMB 2017) (Bioinformatics 2017)
    Prashant Pandey, Michael A. Bender, Rob Patro, and Rob Johnson

  6. A General-Purpose Counting Filter: Making Every Bit Count (SIGMOD 2017)
    Prashant Pandey, Michael A. Bender, Rob Patro, and Rob Johnson

  7. Writes Wrought Right, and Other Adventures in File System Optimization (ACM Transactions on Storage (TOS) - Special Issue USENIX FAST 2016
    Jun Yuan, Yang Zhan, William Jannen, Prashant Pandey, Amogh Akshintala, Kanchan Chandnani, Pooja Deo, Zardosht Kasheff, Michael Bender, Martin Farach-Colton, Rob Johnson, Bradley C. Kuszmaul, and Donald E. Porter

  8. Optimizing Every Operation in a Write-optimized File System (FAST 2016) [Awarded Best Paper]
    Jun Yuan, Yang Zhan, William Jannen, Prashant Pandey, Amogh Akshintala, Kanchan Chandnani, Pooja Deo, Zardosht Kasheff, Michael Bender, Martin Farach-Colton, Rob Johnson, Bradley C. Kuszmaul, and Donald E. Porter

  9. BetrFS: Write-Optimization in a Kernel File System (ACM Transactions on Storage (TOS) - Special Issue USENIX FAST 2015)
    William Jannen, Jun Yuan, Yang Zhan, Amogh Akshintala, John Esmet, Yizheng Jiao, Ankur Mittal, Prashant Pandey, Phaneendra Reddy, Leif Walsh, Michael A. Bender, Martin Farach-Colton, Rob Johnson, Bradley C. Kuszmaul, and Donald E. Porter

  10. BetrFS: A Right-Optimized Write-Optimized File System (FAST 2015) [Runner up for best paper]
    William Jannen, Jun Yuan, Yang Zhan, Amogh Akshintala, John Esmet, Yizheng Jiao, Ankur Mittal, Prashant Pandey, Phaneendra Reddy, Leif Walsh, Michael A. Bender, Martin Farach-Colton, Rob Johnson, Bradley C. Kuszmaul, and Donald E. Porter

Talks

  1. deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph [Extended talk]
    Venue: VMware Research, Palo Alto, CA [August 2017] and                         Google Research, NY [September 2017]
    [pdf] [Talk]

  2. deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph
    Venue: ISMB 2017, Prague, Czech Republic [July 2017]
    [pdf] [Talk]

  3. A General-Purpose Counting Filter: Making Every Bit Count
    Venue: SIGMOD 2017, Chicago, IL [May 2017]
    [pdf] [Talk]

  4. Intel Software Guard Extensions (SGX)
    Venue: Sandia National Laboratories, Livermore, CA [August 2015]
    [pdf]

Please find my resume here.