He has been involved in many aspects of the Human Genome Project as well as numerous other genome projects. His Sequence Search and Alignment by Hashing Algorithm (SSAHA) greatly sped up the process of SNP discovery, first for The SNP Consortium Project and later in the International HapMap Project. Dr. Mullikin also developed a whole-genome assembly program, called Phusion. Dr. Mullikin develops and utilizes computer programs to analyze large data sets generated by systematic DNA sequencing projects. A highly skilled computational geneticist, he collaborates extensively with biomedical researchers, developing data analysis methods specifically tailored for each class of project.