In 1999, Cooper established the
Henry Wellcome Ancient Biomolecules Centre at the
University of Oxford and in 2002 was made Professor of Ancient Biomolecules at Oxford. In 2004, he was awarded an Australian Research Council (ARC) Federation Fellowship. He resigned from Oxford in 2005, following an internal investigation into allegations that he fabricated data in grant applications. He subsequently moved to the
University of Adelaide to establish the Australian Centre for Ancient DNA. At Adelaide, he led the Ancient DNA node of the
Genographic Project examining human origins and dispersal from 2005–2010. He was awarded a series of ARC Fellowships: Federation (2005–2010), Future (2011–2014), and
Laureate (2014–2019) researching human evolution and climate change. In December 2019, the University of Adelaide dismissed Cooper, citing "serious misconduct" for bullying staff and students. In January 2020, he filed a legal petition against the university for unfair dismissal. The case was settled out of court in July 2020. 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.
Research Cooper has published over 30 papers in the journals
Nature and
Science. In 2000, with Henrik Poinar, he suggested that the standards of much ancient DNA research were insufficient to rule out contamination, especially in studies of ancient humans. In 2001, he used these methods to characterise the first complete mitochondrial genome sequences from extinct species, two
New Zealand moa. Cooper has analysed ancient DNA from extinct species preserved in caves, permafrost areas of Alaska and the Yukon, 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). 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. 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. The claims were met with scepticism by other experts. Cooper and colleagues’ ideas were later supported by Mukhopadhyay and colleagues in 2025. ==Awards==