Max Planck Research Group Leaders

Denise Kühnert

Dr. Denise Kühnert · GSH

Max Planck Institute for the Science of Human History · Jena, Germany

Email
kuehnert [at] shh [dot] mpg [dot] de
denise [dot] kuehnert [at] gmail [dot] com

Biography

I am a “free-floating” Max Planck Research Group Leader at the Max Planck Institute for the Science of Human History (MPI-SHH), where I am leading the Transmission, Infection, Diversification & Evolution Group (tide). Prior to this, I was a Marie-Heim Vögtlin Fellow in the infectious disease unit of the University Hospital Zurich, and an ETH Zurich fellow at the ETH Zürich, Switzerland, developing phylodynamic methods for the analysis of infectious disease dynamics. I obtained my PhD in Computer Science from the University of Auckland.

Education and positions held

  • 2017-2018: University Hospital Zurich, Marie-Heim Vögtlin Fellow.
  • 2013-2017: ETH Zürich, Postdoctoral Fellow.
  • 2013: University of Auckland, PhD in Computer Science.

Research Summary

The tide group’s main scientific goal is a broader understanding of infectious disease dynamics of modern and ancient pathogen outbreaks, as well as the dynamics of culture and language throughout history, and the potential demography-driven interactions between pathogen outbreaks and language evolution that shaped human history. tide is at the interface of mathematical epidemiology, evolution, ecology and infectious diseases. We develop phylogenetic tools to address important questions in the fields of epidemiology, pathogen evolution and language evolution.

Key publications

  • S. Sabin, A. Herbig, A. J. Vågene, T. Ahlstr ̈om, G. Bozovic, C. Arcini, D. Kühnert*, and K. I. Bos*, “A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex,” Genome Biol, vol. 21, p. 201, Aug 2020. https://doi.org/10.1186/s13059-020-02112-1.
  • R. Barquera, T. C. Lamnidis, A. K. Lankapalli, A. Kocher, D. I. Hernández-Zaragoza, E. A. Nelson, A. C. Zamora-Herrera, P. Ramallo, N. Bernal-Felipe, A. Immel, K. Bos, V. Acuña-Alonzo, C. Barbieri, P. Roberts, A. Herbig, D. Kühnert*, L. Márquez-Morfín*, and J. Krause*, “Origin and health status of first-generation africans from early colonial mexico,” Curr Biol, vol. 30, pp. 2078–2091.e11, Jun 2020. https://doi.org/10.1016/j.cub.2020.04.002
  • D.Kühnert,R.Kouyos,G.Shirreff,J.Pečerska,A.U.Scherrer,J.Böni,S.Yerly,T.Klimkait, V. Aubert, H. F. Günthard, T. Stadler, S. Bonhoeffer, and Swiss HIV Cohort Study, “Quan- tifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics,” PLoS Pathog, vol. 14, p. e1006895, 02 2018. https://doi.org/10.1371/journal.ppat.1006895
  • D. Kühnert, T. Stadler, T. G. Vaughan, and A. J. Drummond, “Phylodynamics with Migra- tion: A Computational Framework to Quantify Population Structure from Genomic Data,” Mol Biol Evol, vol. 33, pp. 2102–16, Aug 2016. https://doi.org/10.1093/molbev/msw064
  • T. Stadler*, D. Kühnert*, S. Bonhoeffer, and A. J. Drummond, “Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV),” Proc Natl Acad Sci USA, vol. 110, no. 1, pp. 228–33, 2013. https://doi.org/10.1073/pnas.1207965110