Dr. Cooper is an evolutionary biologist, microbiologist, and geneticist. As an undergraduate at Amherst College (1990-1994), Dr. Cooper conducted research under evolutionary biologist Dr. Paul Ewald, using experimental evolution to study the evolution of virulence in a baculovirus. Dr. Cooper then moved to Michigan State University in the laboratory of Dr. Richard Lenski. Dr. Cooper’s research with Lenski on the population genetics of bacterial adaptation and specialization led to publications in Science and Nature among others. Dr. Cooper then moved to the University of Michigan as a Postdoctoral Fellow of the Michigan Society of Fellows. He studied the ecology of virulence factors of Vibrio cholerae with Dr. Victor DiRita and the population genetics of opportunistic Burkholderia cepacia strains with Dr. John LiPuma. This research provided the foundation for his subsequent independent work on the evolution of these pathogens.
The major goal of the Cooper laboratory is to quantify the dynamics and effects of evolution in structured environments, with the application of forecasting mutations that enable bacterial populations or cancers to evolve to cause disease. Dr. Cooper has been developing methods for studying evolution in the laboratory for 20 years and has pioneered the study of long-term evolution in bacterial biofilms (Poltak and Cooper, ISMEJ 2011, Traverse et al., PNAS 2013). He has also been at the forefront for measuring evolutionary forces acting on mutations (e.g. Flynn et al, PLoS Genetics, 2013) and cost-effective, high-throughput sequencing methods (Dillon et al, Genetics 2015). In 2010 he was honored by an NSF CAREER award. More recently the lab has been studying similar dynamics in longitudinal clinical samples from various infections, including those affecting persons with cystic fibrosis (CF). With the lab’s recent move to the University of Pittsburgh School of Medicine, new, larger, studies are ongoing in clinically relevant systems, such as the evolution and systems biology of antibiotic resistance, the evolution of microbial communities during pulmonary infections of persons with cystic fibrosis, and even during acute infections, and the evolution of cancers as they become resistant to chemotherapy.
Dr. Cooper is supported by research grants from NIH-NIGMS, NIH-NIAID, the NASA Astrobiology program, and from the National Science Foundation.