He is one of the world's pioneers in applying genetic variations (Variable Number Tandem Repeat (VNTR) and Single Nucleotide Polymorphism (SNP) markers) and whole genome sequencing, leading the research field of personalized medicine.

[3] Furthermore, several genetic polymorphic markers developed and mapped by his research groups at the Japanese Foundation for Cancer Research and the University of Tokyo, have contributed to map and clone genes responsible to hereditary diseases, as well as those related to drug response and involved in cancer.

[6] Nakamura focused on applying genetic information to improve the care of cancer patients, working to bring his laboratory's discoveries into the clinical practice.

[8] To pursue advanced study in genetics and oncology, he went to the US and spent five years as a postdoctoral fellow and then as a faculty member at the Howard Hughes Medical Institute at the University of Utah, an international center for gene mapping.

When the Japanese government launched its Millennium Genome Project in 2000, he was named group leader for the genetic diversity program at the renowned RIKEN SNP Research Center.