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
Accurate mass spectrometry based protein quantification via shared peptides.
Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. J Comput Biol. 2012 Apr;19(4):337-48. doi: 10.1089/cmb.2009.0267. Epub 2012 Mar 13.
Proteogenomic database construction driven from large scale RNA-seq data
Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. J Proteome Res. 2014 Jan 3;13(1):21-8. doi: 10.1021/pr400294c. Epub 2013 Jul 17.
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.
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.