Prashant Pandey

LOCALE improves DNA sequence search by learning variation-robust embeddings, outperforming existing methods on benchmark datasets and real biological variance tasks.

kache-hash improves k-mer hash table performance for genomic analysis by leveraging minimizers and cache efficiency, achieving faster builds and queries across multiple datasets.

Cuttlefish 3 is a parallel external-memory algorithm for constructing colored compacted de Bruijn graphs, achieving significant speedup over existing tools.

VariantStore efficiently indexes and queries genomic variants across thousands of samples, demonstrating scalability with large datasets.

The paper introduces an updatable and scalable exact sequence-search index based on Mantis, demonstrating its efficiency and scalability over large datasets.

The paper introduces an efficient encoding method for color information in de Bruijn graphs, improving compression and scalability for large-scale genomic applications.

The paper introduces an LSH method for edit distance that considers both k-mer content and order, improving alignment detection efficiency.

Mantis provides a fast, small, and exact sequence search index for large RNA-seq datasets, outperforming existing methods in speed and accuracy.

Squeakr is a k-mer counting and multiset representation system that improves speed and memory efficiency compared to existing methods.

Grouping k-mer color sets into equivalence classes and entropy-compressing them shrinks colored de Bruijn graph color storage up to 20-fold versus VARI, keeping BOSS for topology.