Dr. Vikram Shivakumar is a postdoctoral research associate jointly affiliated with EMBL-EBI, the Wellcome Sanger Institute, and the University of Cambridge (Department of Genetics) through an EMBL-EBI–Sanger Postdoctoral (ESPOD) Fellowship. He completed his PhD in Computer Science at Johns Hopkins University with a National Science Foundation Graduate Research Fellowship (NSF GRFP), developing novel computational genomics methods for analysing and building pangenomes using techniques from text compression.Vikram previously received a BS in Bioengineering from UC Berkeley and an MS in Biomedical Engineering from Johns Hopkins University. In his free time, he is a professional cricket umpire and enjoys playing squash and pool.
His work aims to scale computational genomics analyses to use pangenomes — large collections of genomes that broadly capture the genomic variation present across a species. The primary goal is to address “genomic reference bias” by replacing single-reference indexes with more inclusive pangenome indexes, through the development of efficient, scalable software for core bioinformatics tasks. In particular, he is interested in characterising structural variation and genomic conservation using whole-genome alignment methods, drawing on computational techniques from text indexing and compression.
