Dan Gusfield's background is in Combinatorial Optimization, and various applications of Combinatorial Optimization. He has worked extensively on problems of network flow, matroid optimization, statistical data security, stable marriage and matching, string algorithms and sequence analysis, phylogenetic tree inference, haplotype inference, inference of phylogenetic networks with homoplasy and recombination, and the multi-state perfect phylogeny problem, using chordal graph theory and integer programming.