Paul Ahlquist

Paul Ahlquist

Director, John W. and Jeanne M. Rowe Center for Research in Virology



(608) 316-4460


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Research website

I am honored to lead the John and Jeanne Rowe Center for Research in Virology at the Morgridge Institute.  To address expanding viral threats exemplified by the COVID-19 pandemic, the Rowe Center’s growing cluster of group leaders and their research teams are advancing understanding of viruses, viral diseases, and related cellular and organismal biology, and using their discoveries to develop more effective and broader spectrum antiviral controls.  My Morgridge Institute activities are complemented and mutually strengthened by my roles at UW–Madison, where I am the Kaesberg Professor of Oncology, Molecular Virology and Plant Pathology, the Steenbock Professor of Microbiological Sciences, and the Associate Director for Basic Sciences at the UW Carbone Cancer Center.

Our own group’s research covers multiple important viruses and spans fundamental laboratory studies to clinical / translational studies with large collections of patient samples.  Our current research focus on crucial targets to control viruses and their diseases, including the structure, assembly and function of RNA virus genome replication complexes; mechanisms of HIV gene expression, latency and transmission; and genome-wide molecular changes associated with human papillomavirus-induced cancers.

Areas of Expertise

  • Molecular mechanisms of viral replication and gene expression
  • Evolution, interrelationships and engineering of viral genomes
  • Mechanisms of viral pathology and oncogenesis
  • Prevention, diagnosis and therapy of virus infections and virus-associated cancers


B.S., Physics, Iowa State University

Ph.D., Biophysics, University of Wisconsin–Madison


  • Elected member, National Academy of Sciences USA
  • Elected fellow, American Association for the Advancement of Science
  • US National Institutes of Health MERIT Award
  • US National Science Foundation Presidential Young Investigator Award
  • Van Arkel Honorary Faculty Chair in Biochemistry, Leiden University, The Netherlands
  • Hilldale Award in Biological Sciences, University of Wisconsin – Madison
  • UW Carbone Cancer Center Ride Scholar
  • Allen Research Award, American Phytopathology Society

Selected Publications

  • Bruce JW, Bracken M, Evans E, Sherer N, Ahlquist P. (2021) ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses. PLoS Pathogens 17:e1009364.
  • Unchwaniwala N, Zhan H, den Boon JA, Ahlquist P. (2021) Cryo-electron microscopy of nodavirus RNA replication organelles illuminates positive-strand RNA virus genome replication. Current Opinion in Virology 51:74-79.
  • Benner BE, Bruce JW, Kentala JR, Murray M, Becker JT, Garcia-Miranda P, Ahlquist P, Butcher SE, Sherer NM. (2021) Perturbing HIV-1 ribosomal frameshifting frequency reveals a cis preference for Gag-Pol incorporation into assembling virions.  Journal of Virology  JVI01349-21 (in press).
  • Nishikiori, M and Ahlquist P.  (2021)  Transmembrane redox regulation of genome replication functions in positive-strand RNA viruses.  Current Opinion in Virology 47:25-31.
  • Unchwaniwala N and Ahlquist P.  (2020) Coronavirus dons a new crown.  Science 369:1306-1307.
  • Unchwaniwala N, Zhan H, Pennington J, Horswill M, den Boon JA and Ahlquist P. (2020) Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication. Proc Natl Acad Sci U S A. 117:18680-18691.
  • Nishikiori M and Ahlquist P. (2018) Organelle Luminal Dependence of (+)strand RNA Virus Replication Reveals a Hidden Druggable Target.  Science Advances  4:eaap8258.
  • Ertel KJ, Benefield D, Castaño-Diez D, Pennington J, Horswill M, den Boon JA, Otegui MS, Ahlquist P.  (2017)  Cryo-Electron Tomography Reveals Novel Features of a Viral RNA Replication Compartment.  eLife 6:e25940.
  • Spurgeon M, den Boon J, Horswill M, Barthakur S, Forouzan O, Rader J, Beebe J, Roopra A, Ahlquist P, and Lambert PF. (2017) Human Papillomavirus Oncogenes Reprogram the Cervical Cancer Micro-environment Independently of and Synergistically with Estrogen. Proc Natl Acad Sci USA 114:E9076-E9085.
  • Pocock GM, Becker JT, Swanson CM, Ahlquist P, Sherer NM. (2016) HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors.  PLoS Pathogens 12:e1005565.
  • den Boon J,  Pyeon D, Wang S, Horswill M, Schiffman M, Sherman M, Zuna R, Wang Z, Hewitt S, Pearson R, Schott M, Chung L, He Q, Lambert P, Walker J, Newton M, Wentzensen N, and Ahlquist P (2015)  Molecular Transitions from Papillomavirus Infection to Cervical Precancer and Cancer: Role of Stromal Estrogen Receptor Signaling.  Proc Natl Acad Sci USA 112:E3255-64.
  • Diaz A, Zhang J, Ollwerther A, Wang X, and Ahlquist P.  (2015)  Host ESCRT Proteins Are Required for Bromovirus RNA Replication Compartment Assembly and Function.  PLoS Pathogens 11:e1004742 (26 pages).
  • Chasman, D., B. Gancarz, L, Hao, M. Ferris, P, Ahlquist and M. Craven.  (2014)  Inferring host gene subnetworks involved in viral replication. PLoS Comput Biol 10:e1003626 (22 pp).
  • Bruce, J., R. Reddington, E. Mathieu, M. Bracken, J.A. Young and P. Ahlquist (2013)  ZASC1 stimulates HIV-1 transcription elongation by recruiting P-TEFb and TAT to the LTR promoter. PLoS Pathogens 10: e1003712.