Kühnert, D.; Coscolla, M.; Brites, D.; Stucki, D.; Metcalfe, J.; Fenner, L.; Gagneux, S.; Stadler, T.: Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics 25, S. 47 - 53 (2018)

Meehan, C. J.; Moris, P.; Kohl, T. A.; Pečerska, J.; Akter, S.; Merker, M.; Utpatel, C.; Beckert, P.; Gehre, F.; Lempens, P. et al.; Stadler, T.; Kaswa, M. K.; Kühnert, D.; Niemann, S.; de Jong; C., B.: The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 37, S. 410 - 416 (2018)

Spyrou, M. A.; Tukhbatova, R. I.; Wang, C.-C.; Andrades Valtueña, A.; Lankapalli, A. K.; Kondrashin, V. V.; Tsybin, V. A.; Khokhlov, A.; Kühnert, D.; Herbig, A. et al.; Bos, K. I.; Krause, J.: Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nature Communications 9, 2234 (2018)

Krause-Kyora, B.; Susat, J.; Key, F. M.; Kühnert, D.; Bosse, E.; Immel, A.; Rinne, C.; Kornell, S.-C.; Yepes, D.; Franzenburg, S. et al.; Heyne, H. O.; Meier, T.; Lösch, S.; Meller, H.; Friederich, S.; Nicklisch, N.; Alt, K. W.; Schreiber, S.; Tholey, A.; Herbig, A.; Nebel, A.; Krause, J.: Neolithic and medieval virus genomes reveal complex evolution of Hepatitis B. eLife 7, e36666 (2018)

Vågene, Å. J.; Herbig, A.; Campana, M. G.; García, R.; M., N.; Warinner, C.; Sabin, S.; Spyrou, M. A.; Andrades Valtueña, A.; Huson, D. et al.; Tuross, N.; Bos, K. I.; Krause, J.: Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution 2 (3), S. 520 - 528 (2018)

Fischer, M.; Herbst, L.; Kersting, S.; Kühn, A. L.; Wicke, K.: Tree balance indices: a comprehensive survey. Springer Cham, Cham (2023), XV, 404 S.

Lamkiewicz, K.; Gomez, L. R. E.; Kühnert, D.; Marz , M.: Genome structure, life cycle, and taxonomy of Coronaviruses and the evolution of SARS-CoV-2. In: Viral fitness and evolution: population dynamics and adaptive mechanisms, 9, 1 Aufl., S. 305 - 339 (Hg. Domingo, E.; Schuster, P.; Elena, S. F.; Perales, C.). Springer, Cham (2023)

Hufsky, F.; Abecasis, A.; Agudelo-Romero, P.; Bletsa, M.; Brown, K.; Claus, C.; Deinhardt-Emmer, S.; Deng, L.; Friedel, C. C.; Gismondi, M. I. et al.; Kostaki, E. G.; Kühnert, D.; Kulkarni-Kale, U.; Metzner, K. J.; Meyer, I. M.; Miozzi, L.; Nishimura, L.; Paraskevopoulou, S.; Pérez-Cataluña, A.; Rahlff, J.; Thomson, E.; Tumescheit, C.; van der Hoek, L.; Van Espen, L.; Vandamme, A.-M.; Zaheri, M.; Zuckerman, N.; Marz, M.: Women in the European Virus Bioinformatics Center, Viruses 14, (2022)

Severinov, D.; Yi, B.; Dalpke, A.; Rost, F.; Winkler, S.; Beil, J.; Reinhardt, S.; Klemroth, S.; Mehnert, G.; Hartkopf, F. et al.; Hölzer, M.; Kühnert, D.; German COVID-19 OMICS Initiative (DeCOI); Poetsch, A.: Potential novel SARS-CoV-2 variant of interest from lineage AP.1 with N501Y and additional spike mutations identified in Saxony, Germany, Virological, (2021)

Bos, K. I.: TB’s Chinese travels, Nature Ecology & Evolution 2, S. 1842 - 1843 (2018)

Borry, M.; Forsythe, A.; Valtueña, A. A.; Hübner, A.; Ibrahim, A.; Quagliariello, A.; White, A. E.; Kocher, A.; Vågene, Å. J.; Bartholdy, B. P. et al.; Spurīte, D.; Ponce-Soto, G. Y.; Neumann, G.; Huang, I.-T.; Light, I.; Velsko, I. M.; Jackson, I.; Frangenberg, J.; Serrano, J. G.; Fumey, J.; Özdoğan, K. T.; Blevins, K. E.; Daly, K. G.; Lopopolo, M.; Moraitou, M.; Michel, M.; van Os, M.; Bravo-Lopez, M. J.; Sarhan, M. S.; Dagtas, N. D.; Oskolkov, N.; Smith, O. S.; Lebrasseur, O.; Rozwalak, P.; Eisenhofer, R.; Wasef, S.; Ramachandran, S. L.; Vanghi, V.; Warinner, C.; Yates, J. A. F.: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. (2023)

Spott, R.; Pletz, M. W.; Fleischmann-Struzek, C.; Kimmig, A.; Hadlich, C.; Hauert, M.; Lohde, M.; Jundzill, M.; Marquet, M.; Dickmann, P. et al.; Schüchner, R.; Hölzer, M.; Kühnert, D.; Brandt, C.: Exploring the spatial distribution of persistent SARS-CoV-2 mutations. eLife, 94045.1 (2024)

Översti, S.; Gaul, E.; Jensen, B.-E. O.; Kühnert, D.: Phylogenetic meta-analysis of chronic SARS-CoV-2 infections in immunocompromised patients shows no evidence of elevated evolutionary rates. bioRxiv, 565087 (2023)

Fischer, M.; Herbst, L.; Kersting, S.; Kühn, L.; Wicke, K.: Tree balance indices: a comprehensive survey. arXiv, 2109.12281 (2021)

Brandt, C.; Spott, R.; Hölzer, M.; Kühnert, D.; Fuchs, S.; Lohde, M.; Marquet, M.; Viehweger, A.; Rimek, D.; Pletz, M. W.: Molecular epidemiology of SARS-CoV-2: a regional to global perspective. medRxiv, 2021.01.25.21250447 (2021)