HomeResearchIntramural ResearchResearch Branches at NHGRIGenome Technology Branch Mullikin Lab

Jim Mullikin, Ph.D. Associate Investigator Genome Technology Branch Head Comparative Genomics Unit B.S. Purdue University, 1982 M.S. Purdue University, 1984 Ph.D. Delft University of Technology, Holland, 1993 (301) 496-2416 (301) 480-0634 mullikin@mail.nih.gov 5625 Fishers Ln Room 5N-01Q, MSC 9400 Rockville, MD 20892-9400 Selected Publications

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, analyzing data produced by others or that are available in public databases.

His main research focus involves the development of algorithms for performing complex computations. One such program, called Sequence Search and Alignment by Hashing Algorithm (SSAHA), is used to dramatically accelerate the speed at which gigabases of DNA sequence are searched for single-nucleotide poymorphisms (SNPs). Even though this program was first developed several years ago, Dr. Mullikin continually refines SSAHA in response to the changing needs of genomic scientists, and SSAHA remains the key tool that he and others use to detect sequence variants. He also developed a program called Phusion (pronounced "fusion"), which is used to assemble genome sequences from whole-genome shotgun data. Both the mouse and nematode genome sequences were assembled using Phusion.

Dr. Mullikin's group provides computational support for major NHGRI efforts such as the International Haplotype Map (HapMap) Project, which is primarily focused on determining genes and genetic variants that affect health and disease susceptibility. During the initial phase of this project, investigators produced a working haplotype map, consisting of ~600,000 polymorphic sites spaced an average of ~5 kilobase pairs apart. With the second phase of the project completed, investigators can now access a map of human variation in three populations, which contains over three million polymorphic sites across the human genome. Indeed, this landmark project has provided the foundation for the rapid completion of a large number of genome-wide association studies (GWAS; a list of published GWAS studies is available at

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Last Updated: April 1, 2009