Vikram S. Shivakumar

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

Shredtools uses multi-MUMs to enable efficient querying of pangenome coordinates, allowing rapid extraction of gene regions across multiple genomes.

The paper introduces a new open-source tool for efficient genomic sequence digestion using minimizers, modimizers, or syncmers.

Mumemto efficiently computes multi-MUMs across large pangenomes to visualize synteny and detect structural variations.

The paper extends the Mumemto tool to compute multi-MUMs across large pangenomes using new partitioning strategies, enabling scalability to 474 human haplotypes.

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

The paper improves pangenomic classification accuracy by introducing chain statistics that capture coarse-grained co-linearity without requiring chaining algorithms.

Sigmoni classifies nanopore signals using a compressed pangenome index, enabling efficient and accurate classification of reads against large references.

riboviz 2 provides a flexible and robust workflow for analyzing and visualizing Ribo-seq data with improved functionality and usability.

SNP2SIM provides a modular workflow for generating molecular simulations of protein variants to support functional analysis and drug development.