In 2012 he started as director of the Hubrecht Institute and was awarded three times an ERC Advanced Grant, in 2012, 2017, and 2022.

Van Oudenaarden was born 19 March 1970, in Zuidland, a small town in the Dutch province of South Holland.

He received the Andries Miedema Award (best doctoral research in the field of condensed matter physics in the Netherlands) for his thesis on "Quantum vortices and quantum interference effects in circuits of small tunnel junctions".

In 1998, he moved to Stanford University, where he was a postdoctoral researcher in the departments of Biochemistry and of Microbiology & Immunology, working on force generation of polymerising actin filaments in the Theriot lab and a postdoctoral researcher in the department of Chemistry, working on Micropatterning of supported phospholipid bi-layers in the Boxer lab.

In 2017 he received his second ERC Advanced Grant, for his study titled "a single-cell genomics approach integrating gene expression, lineage, and physical interactions".