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“Microbial evolution occurs through complex mechanisms such as horizontal gene transfer (HGT), a process which cannot be represented by a lineal or tree model,” explained Nakhleh. “The main goal of my research is to develop computationally efficient tools for the reconstruction of these complex mechanisms, thereby giving us a greater understanding of microbial genomes.”
The challenges in Nakhleh’s work include accurately detecting and modeling HGT as well as interspecific recombination, a major evolutionary mechanism in viruses, and distinguishing between these processes and other events with similar effects. The final outcome of the research will be a suite of software tools called PhyloNet that will implement the mathematical models and algorithms to analyze microbial genomes, provide an evolutionary history, and even predict microbial genome diversification. Such a tool could be applied to the study of how bacteria acquire antibiotic resistance through HGT and how humans can develop more effective antibiotics.
“Discovering the genomic innovations in microbes bears a great significance on understanding these organisms… The risks that some of them pose, and the contributions that others make,” said Nakhleh.
Nakhleh will work closely with collaborator Hideki Innan, associate professor at the Graduate University for Advanced Studies in Japan, and the DOE’s Joint Genome Institute on these objectives.
The purpose of the DOE Early Career Principal Investigator Program is to support research in applied mathematics, computer science, and high-performance networks performed by exceptionally talented scientists and engineers early in their careers.
The EMT program supports cross-disciplinary research—in this case computer science and biology—and education projects that explore ideas, theory and experiments that venture into a range of uncharted territories in order to advance computing capabilities.
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