Then, he performed his Ph.D. studies at the Division of Cellular Biochemistry, in the Netherlands Cancer Institute (NKI) under the supervision of Prof. Dr. Ploegh in Amsterdam.

First, from 1991 to 1992, he visited the laboratory of Drs Benoit and Mathis at the Institut de Chimie Biologique, Strasbourg (France).

Then, he obtained a 2-year fellowship from the European Molecular Biology Organization (EMBO) to visit the laboratory of Prof. Dr. Hämmerling at the German Cancer Research Center (DKFZ), in Heidelberg (Germany) from 1992 to 1993.

Since 2016, he is head of the Cell and Chemical Biology department at the Leiden University Medical Center (the Netherlands).

[1] Neefjes’ discoveries on antigen presentation by the class I and II major histocompatibility complexes (MHC) constitute today's textbook knowledge.

Through his exploration of the cell biology of the MHC, Jacques Neefjes became an expert on endocytosis and intracellular transport.

By combining chemistry, cell biology and biochemistry with genetic screens, Neefjes identified inhibitors to disturb bacterial survival strategies, representing one of the first antibiotics acting by targeting the host, rather than the pathogen.

[4] Since 2019, Jacques Neefjes is co-financing the production of a promising cancer drug, Aclarubicin, which disappeared from the European market at the beginning of the 21st century.