Assamagan was appointed to Hampton University where he worked on the Continuous Electron Beam Accelerator Facility. He eventually moved to the ATLAS experiment in CERN. His research considers physics beyond the Standard Model. He moved to Brookhaven National Laboratory in 200, where he worked on the physics analysis tools for ATLAS. He was made coordinator for the software of the Muon Spectrometer. He was part of the ATLAS Collaboration when they first observed the Higgs boson in 2012.

Assamagan is co-founder of the African School of Physics, a non-profit school training African researchers in fundamental physics and applications. In 2019, he co-funded with Fairouz Malek, Simon Connel and others, the African Strategy for Fundamental Physics. He was elected to the African Academy of Sciences in 2019 and the American Physical Society in 2021.