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
An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays.
Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260. Epub 2013 Oct 18.
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Mol Cell Proteomics. 2010 Dec;9(12):2772-82. doi: 10.1074/mcp.M110.002766. Epub 2010 Sep 20.
Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody.Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody.
Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR. Proteomics. 2011 Feb;11(3):395-405. doi: 10.1002/pmic.201000487. Epub 2011 Jan 5.
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.