Vikram S. Shivakumar

Sigmoni: classification of nanopore signal with a compressed pangenome index

B. Langmead, Mohsen Zakeri, S. Kovaka, 2023, bioRxiv.

Analysis of whole chloroplast genomes from the genera of the Clauseneae, the curry tribe (Rutaceae, Citrus family).

E. Zimmer, M. Appelhans, Gabriel Johnson, 2017, Molecular phylogenetics and evolution.

Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

D. Daly, G. Damasco, PaulV. A. Fine, 2019, Genes.

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development

E. Zimmer, Gabriel Johnson, Vikram S. Shivakumar, 2019, Scientific Reports.

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Premal Shah, K. Kavoussanakis, A. Mok, 2021, bioRxiv.

Sigmoni: classification of nanopore signal with a compressed pangenome index

Mohsen Zakeri, S. Kovaka, Omar Y. Ahmed, 2023, bioRxiv.

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

W. Timp, P. Hook, Roham Razaghi, 2024, bioRxiv.

SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants

Subha Madhavan, Matthew McCoy, Vikram Shivakumar, 2018, BMC Bioinformatics.