Vineet Bafna

Vineet Bafna is a Professor of Computer Science and Engineering at the University of California, San Diego (UCSD), and holds the Chancellor’s Professor III Endowed Chair at the Halıcıoğlu Data Science Institute. He received a B.Tech. from the Indian Institute of Technology in 1989 and a Ph.D. in Computer Science from Pennsylvania State University in 1994. Following his doctorate, he conducted postdoctoral research for two years at the Center for Discrete Mathematics and Theoretical Computer Science. From 1996 to 1999, he was a senior investigator at SmithKline Beecham, focusing on DNA signaling, target discovery, and EST assembly. Subsequently, from 1999 to 2003, he served as Director of Informatics Research at Celera Genomics, where he contributed to the sequence assembly and annotation of the human genome. He joined the UCSD faculty in July 2003 and directed the Bioinformatics and Systems Biology Ph.D. program from 2013 to 2019.

Bafna's research interests encompass computational molecular biology, bioinformatics, and proteomics. He co-introduced the breakpoint graph technique for analyzing genome rearrangements with Pavel Pevzner. His work includes devising scoring functions for protein identification that account for ion fragmentation probability and instrument error, as well as efficient algorithms to compute these scores. At Celera, he led the development of a toolkit for proteome identification and quantification using mass spectrometry. At UCSD, his efforts have focused on computational analysis of peptide mass spectra, applications to protein function, single nucleotide polymorphism analysis for therapeutics and diagnostics, algorithmic solutions for haplotype phasing, and tools like the Conserved Exon Method (CEM) for gene finding, and SCOPE and DiffXPro for mass spectrometry-based protein identification and quantification. More recently, he investigates proteogenomics and extrachromosomal DNA mechanisms in cancer. Bafna has been recognized as an ISCB Fellow in 2019 and an ACM Fellow in 2023. He serves on the editorial board of the Journal of Bioinformatics and Computational Biology and has participated in program committees for RECOMB conferences. He is the scientific co-founder of Abterra, Inc., specializing in antibody analysis and proteomics, and Boundless Bio, Inc., targeting extrachromosomal DNA in cancer. His publications appear in major journals and conferences.

Professional Email: vbafna@cs.ucsd.edu