Professor Bafna is an expert in bioinformatics. He has published on many aspects of this emerging field, including genome rearrangements, multiple alignments, RNA structure, gene finding, DNA signals, mass spectrometric data analysis, and human population genetics. In genome rearrangement, he introduced (with his then-advisor and now UCSD colleague Pavel Pevzner) the breakpoint graph technique that is now commonly used when doing computational analysis of genome rearrangements. In computational proteomics, Bafna made key contributions to the problem of protein identification by devising a scoring function that incorporates ion fragmentation probability as well as instrument error, and an efficient algorithm to compute that score. He led a team at Celera that built a toolkit for identifying and quantitfying the Proteome using mass spectrometry.