He was awarded a series of ARC Fellowships: Federation (2005–2010), Future (2011–2014), and Laureate (2014–2019) researching human evolution and climate change.
[14] In June 2023, Charles Sturt University announced that it had appointed Cooper as professor to its Gulbali Institute for Agriculture, Water and Environment, based in Albury-Wodonga.
[16] Cooper has analysed ancient DNA from extinct species preserved in caves, permafrost areas of Alaska and the Yukon,[17] Antarctica, and sedimentary and archaeological deposits around the world.
He has published on the evolutionary history of a range of enigmatic extinct species including: New Zealand moa and Madagascan elephant bird (Aepyornis), the Dodo (Raphus cucullatus), American lion (P. leo atrox) and cheetah-like cat (Miracinonyx), North and South American horses (stilt-legged horse, Hippidion), steppe bison, bears (Arctodus, U. arctos), cave hyenas (Crocuta spelaea), mammoth, and the Falkland Islands wolf (Dusicyon australis).
[citation needed] He has also shown that the calcified plaque on the teeth of ancient skeletons can be used to reconstruct the evolution of the human microbiome through time.
[18] In 2021, Cooper and colleagues published a paper in Science, arguing that the extinction of Neanderthals and the appearance of cave paintings could be linked to a geomagnetic excursion approximately 41,000 years ago, dubbed the Laschamp event.