SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants. - Matthew McCoy; Vikram Shivakumar; Sridhar Nimmagadda; Mohsin Saleet Jafri; Subha Madhavan (BMC Bioinform., 2019)

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow. - Alexander Cope; Felicity Anderson; John Favate; Michael Jackson; Amanda Mok; Anna Kurowska; Junchen Liu; Emma Mackenzie; Vikram Shivakumar; Peter Tilton; Sophie M. Winterbourne; Siyin Xue; et al. (Bioinform., 2022)

Sigmoni: classification of nanopore signal with a compressed pangenome index. - Vikram Shivakumar; Omar Y. Ahmed; Sam Kovaka; Mohsen Zakeri; Ben Langmead (Bioinform., 2024)

Improved Pangenomic Classification Accuracy with Chain Statistics. - Nathaniel K. Brown; Vikram Shivakumar; Ben Langmead (RECOMB, 2025)

Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract). - Vikram Shivakumar; Ben Langmead (WABI, 2025)

Prefix-free parsing for merging big BWTs. - Diego Díaz-Domínguez; Travis Gagie; Veronica Guerrini; Ben Langmead; Zsuzsanna Lipták; Giovanni Manzini; Francesco Masillo; Vikram Shivakumar (CoRR, 2025)