[5][6] In July 2019, he was announced as the new Chair of the Department of Molecular Microbiology at Washington University School of Medicine in St Louis, Missouri.

He served as head of Harvard's PhD Program in Virology,[11] and directed an NIH-funded Center for Excellence in Translational Research.

He began this work as a post-doc in the laboratory of Professor Gail Wertz, developing a system for expressing infectious VSV particles from cDNA clones,[14] which led to a patent on VSV-based gene therapy vectors and vaccines.

[5] With Stephen C. Harrison, he used cryo-EM to determine the structure of the L protein of VSV,[19] revealing several potential drug targets.

[18] As a founding member of the group "Scientists for Science",[20] Whelan has argued that research into infectious pathogens is "essential for a comprehensive understanding of microbial disease pathogenesis, prevention and treatment", and that further regulation of work on dangerous pathogens should only be considered in the context of "input from outside experts with the background and skills to conduct actual risk assessments based on specific experiments and existing laboratories".