Contact Info
Email Address: vbafna@cs.ucsd.eduPhone Number: 858-822-4978
Fax: 858-534-7029
Location: Computer Science and Engineering
#4218 EBU3b (CSE Bldg.)
9500 Gilman Drive
La Jolla, CA 92093-0404
Key Publications
Template proteogenomics: sequencing whole proteins using an imperfect database.
Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. Mol Cell Proteomics. 2010 Jun;9(6):1260-70. doi: 10.1074/mcp.M900504-MCP200. Epub 2010 Feb 17.
Shotgun protein sequencing by tandem mass spectra assembly.
Bandeira N, Tang H, Bafna V, Pevzner P. Anal Chem. 2004 Dec 15;76(24):7221-33.
Proteogenomics to discover the full coding content of genomes: a computational perspective
Castellana N, Bafna V. J Proteomics. 2010 Oct 10;73(11):2124-35. doi: 10.1016/j.jprot.2010.06.007. Epub 2010 Jul 8.
View All CCMS Publictions
Research Interests
- Proteomics. We use genomic and mass spectrometry data (aka Proteogenomics) to learn what proteins are expressed, and how they change due to genetics or post-translational events.
- Genomics, especially complex genome rearrangements. I am interested in basic questions (how these rearrangements arise), applications (what impact do they have on the fitness of the individual, cell, or community), and technology (what technologies can we use to identify and characterize these rearrangements).
- Genetics, with a focus on combinatorial approaches to studying allelic variations that are indicative of selection and other demographic forces.