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- College of Agricultural & Life Sciences CALS Honorary Recognition Award – 2024
- Wolfgang & Patricia Joklik Distinguished Service Award – 2024 ASV
- Fellow of the National Academy of Inventors (NAI) – 2020
- Distinguished Scientist Award, National Jewish Health – 2019
- Sir Michael Stoker Award from the University of Glasgow Centre for Virus Research – 2019
- WARF Innovation Award finalist – 2018
- Fellow of American Academy for the Advancement of Science – 2016
- Wisconsin Alumni Research Foundation (WARF) Named Professorship – Roland Rueckert – 2015
- International Data Corp. High Performance Computing Innovation Excellence Award – 2014
- American Society for Virology, namesake Investigator Awards – 2012 – present
- UW-Madison Biological Sciences Hilldale Award – 2010
- Fellow of the American Academy of Microbiology – 2009
- Elected President American Society for Virology – 2007
- University of Nebraska-Lincoln, Distinguished Scientist Award – 2006
- Awarded American Society for Virology Lifetime Membership – 2001
- Chair, Institute for Molecular Virology, UW-Madison – 1997-2013
- WARF Faculty Mid-Career Award, UW-Madison – 1997
- Vilas Associate Award, UW-Madison – 1996
- H. I. Romnes Faculty Research Award, UW-Madison – 1991
- Pound Research Award, UW-Madison – 1990
- Waksman Institute of Rutgers University, Distinguished Scientist Award – 1989
- Commendation from Pan American Foot-and-Mouth Disease Center for cooperative work in the control and eradication programs in South America – 1988
- Alberta Heritage Foundation Visiting Lecturer Award, Calgary, Canada – 1987
- Amersham Corporation Commendation for Continuing Education Program – 1981