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As an epidemiologist, Lipsitch has focused his research on better understanding the evolution of infectious disease and their effect on humans as well as investigating the triggers and mechanisms for disease immunity. While this research emphasizes the study of specific pathogen characteristics, such as mapping genomic diversity of Streptococcus pneumoniae among different human populations, other research aims include more macro-level concerns such as forecasting disease and assessing pandemic response and preparedness.

As Director of the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health, Lipsitch oversees research engaged in improving the mathematical modeling of infectious disease as well as how such information is effectively communicated to policy-makers and their constituents. This work also contributes to that the National Institute of General Medical Sciences, within the National Institutes of Health, as a Models of Infections Disease Agency Study (MIDAS) funded Center of Excellence.

In addition to his work at Harvard, Lipsitch is credited for his work monitoring nation-wide trends of in pathogens with multiple countries around the globe and currently with the Centers for Disease Control and Prevention’s Active Bacterial Core Surveillance program. In 2009, Lipsitch served as a member of the President’s Council of Advisors on Science and Technology within the H1N1 flu pandemic working group.