Prior to returning to Berkeley (where he also did his undergraduate degree), he held faculty positions at the University of Rochester and UC San Diego, and postdoctoral appointments at the Smithsonian Institution and at Berkeley. Huelsenbeck is interested in the phylogeny problem - how one can infer the genealogy of a group of organisms using genetic data? - and the genetics of adaptation. In general, Huelsenbeck takes a statistical approach to the analysis of genomic data. His current specific research interests include the analysis of large phylogenetic trees using Bayesian methodology, the treatment of models in phylogenetic analysis as random variables, the detection of the footprint of natural selection in protein coding DNA sequences, accounting for uncertainty in alignment in phylogenetic analysis, and inferring population structure.