[2][3][4] He is a professor and the director emeritus of Center for iPS Cell (induced Pluripotent Stem Cell) Research and Application, Kyoto University;[6] as a senior investigator at the UCSF-affiliated Gladstone Institutes in San Francisco, California; and as a professor of anatomy at University of California, San Francisco (UCSF).

After this, he went through a residency in orthopedic surgery at National Osaka Hospital and a postdoctoral fellowship at the Gladstone Institute of Cardiovascular disease, San Francisco.

Yamanaka is currently a professor and the director emeritus of Center for iPS Research and Application (CiRA), Kyoto University.

His first operation was to remove a benign tumor from his friend Shuichi Hirata, a task he could not complete after one hour when a skilled surgeon would have taken ten minutes or so.

Between 1996 and 1999, he was an assistant professor at Osaka City University Medical School, but found himself mostly looking after mice in the laboratory, not doing actual research.

[10] His wife advised him to become a practicing doctor, but instead he applied for a position at the Nara Institute of Science and Technology.

He stated that he could and would clarify the characteristics of embryonic stem cells, and this can-do attitude won him the job.

[11] Between 2010 and 2022, Yamanaka was the director and a professor at the center for iPS Cell Research and Application (CiRA), Kyoto University.

[2] The 2012 Nobel Prize in Physiology or Medicine was awarded jointly to Sir John B. Gurdon and Shinya Yamanaka "for the discovery that mature cells can be reprogrammed to become pluripotent.

[13] In 1962, John B. Gurdon demonstrated that the nucleus from a differentiated frog intestinal epithelial cell can generate a fully functional tadpole via transplantation to an enucleated egg.

Yamanaka focused on factors that are important for maintaining pluripotency in embryonic stem (ES) cells.

When all 24 genes encoding these transcription factors were introduced into skin fibroblasts, few actually generated colonies that were remarkably similar to ES cells.

They found that 4 transcriptional factors (Myc, Oct3/4, Sox2 and Klf4) were sufficient to convert mouse embryonic or adult fibroblasts to pluripotent stem cells (capable of producing teratomas in vivo and contributing to chimeric mice).

Some issues that current methods of induced pluripotency face are the very low production rate of iPS cells and the fact that the 4 transcriptional factors are shown to be oncogenic.

Yamanaka denied manipulating images in his papers on embryonic mouse stem cells, but he could not find lab notes to confirm that the raw data was consistent with the published results.

[21] In June 2010, Yamanaka was awarded the Kyoto Prize for reprogramming adult skin cells to pluripotential precursors.

Yamanaka developed the method as an alternative to embryonic stem cells, thus circumventing an approach in which embryos would be destroyed.