Prashant Pandey

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Research Interests

My research interests lie at the intersection of Systems and Algorithms. Specifically, in memory and resource efficient big-data computing, file systems, and security.

My current research focuses on building efficient approximate membership query data structures, specifically, counting filters and their applications. I am also working on finding efficient methods to represent large DNA sequencing and transcriptome datasets for De bruijn graph traversal and assembly process.

I am also interested in filesystem and write-optimized data structure research. I am currently a member of the team developing BetrFS, an in-kernel file system built using write-optimized indexes. I have also worked on developing an encrypted FUSE file system using Intel SGX as a summer project at Intel Labs.

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


In reverse chronological order:

  1. Rainbowfish: A Succinct Colored de Bruijn Graph Representation (WABI 2017) [biorxiv]

  2. Squeakr: An Exact and Approximate k-mer Counting System (Bioinformatics) [Submitted] [biorxiv]

  3. A Fast x86 Implementation of Select (arxiv 2017)

  4. deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph (ISMB 2017)

  5. A General-Purpose Counting Filter: Making Every Bit Count (SIGMOD 2017)

  6. Writes Wrought Right, and Other Adventures in File System Optimization (ACM Transactions on Storage (TOS) - Special Issue USENIX FAST 2016

  7. Optimizing Every Operation in a Write-optimized File System (FAST 2016) [Awarded Best Paper]

  8. BetrFS: Write-Optimization in a Kernel File System (ACM Transactions on Storage (TOS) - Special Issue USENIX FAST 2015)

  9. BetrFS: A Right-Optimized Write-Optimized File System (FAST 2015) [Runner up for best paper]

Please find my resume here: