Publications

Översti, S.; Boumasmoud, M.; Günthard, H. F.; Sax, H.; Zinkernagel, A. S.; Kouyos, R. D.; Kühnert, D.: Fast hospital discharge rates blur within-hospital ‘transmission footprint’ in bacterial genomes, as showcased with Staphylococcus aureus. PLOS Computational Biology 22 (3), e1013982 (2026)

Giffin, K.; Weber, A.; Kozakaitė, J.; Friedrich, R.; Jankauskas, R.; Kühnert, D.; Bos, K. I.: Differential sampling for genetic analyses of Treponema pallidum and for radiocarbon dating in archaeological bone. International Journey of Paleopathology 52, 002, pp. 44 - 57 (2026)

Specht, G.; Schmid, C.; Kühnert, D.; Kocher, A.: ggret: an R package for visualising and manipulating tree‑based phylogenetic networks. The Journal of Open Source Software (JOSS) 10 (110), 7773 (2025)

Kutanan, W.; Woravatin, W.; Srikummool, M.; Suwannapoom, C.; Hübner, A.; Kampuansai, J.; Khaokiew, C.; Schaschl, H.; Översti, S.; La, D. D. et al.; Arias, L.; Stoneking, M.: Maternal genetic origin of Chao Lay coastal maritime populations from Thailand. BMC Biology 23 (1), 146 (2025)

Esquivel Gomez, L. R.; Malysheva, N.; Pfeil, J.; Yang, Z.; Bütow, S. M.; Irrgang, C.; Körber, N.; Hattab, G.; Kühnert, D.; Ladewig, K.: Holistic forecasting for future pandemics: a review of pathogens, models, and data. Discover public health 22, 211 (2025)

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.: Leveraging mobility data to analyze persistent SARS-CoV-2 mutations and inform targeted genomic surveillance. eLife 13, RP94045 (2025)

Översti, S.; Gaul, E.; Jensen, B.-E. O.; Kühnert, D.: Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity. Virus Evolution 11 (1), veaf065 (2025)

Översti, S.; Weber, A.; Baran, V.; Kieninger, B.; Dilthey, A.; Houwaart, T.; Walker, A.; Schneider-Brachert, W.; Kühnert, D.: Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies. Bioinformatics and biology insights 19, 11779322251321065 (2025)

Tay, J. H.; Kocher, A.; Duchene, S.: Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal. PLOS Computational Biology 20 (11), e1012371, pp. 1 - 22 (2024)

Goliaei, S.; Foroughmand-Araabi, M.-H.; Roddy, A.; Weber, A.; Översti, S.; Kühnert, D.; McHardy, A. C.: Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature Communications 15 (1), 5267 (2024)

Michel, M.; Skourtanioti, E.; Pierini, F.; Guevara, E. K.; Mötsch, A.; Kocher, A.; Barquera, R.; Bianco, R. A.; Carlhoff, S.; Bove, L. C. et al.; Freilich, S.; Giffin, K.; Hermes, T.; Hiß, A.; Knolle, F.; Nelson, E. A.; Neumann, G. U.; Papac, L.; Penske, S.; Rohrlach, A. B.; Salem, N.; Semerau, L.; Villalba-Mouco, V.; Abadie, I.; Aldenderfer, M.; Beckett, J. F.; Brown, M.; Campus, F. G. R.; Chenghwa, T.; Berrocal, M. C.; Damašek, L.; Carlson, K. S. D.; Durand, R.; Ernée, M.; Fântăneanu, C.; Frenzel, H.; Atiénzar, G. G.; Guillén, S.; Hsieh, E.; Karwowski, M.; Kelvin, D.; Kelvin, N.; Khokhlov, A.; Kinaston, R. L.; Korolev, A.; Krettek, K.-L.; Küßner, M.; Lai, L.; Look, C.; Majander, K.; Mandl, K.; Mazzarello, V.; McCormick, M.; de Ibáñez, P. M.; Murphy, R.; Németh, R. E.; Nordqvist, K.; Novotny, F.; Obenaus, M.; Olmo-Enciso, L.; Onkamo, P.; Orschiedt, J.; Patrushev, V.; Peltola, S.; Romero, A.; Rubino, S.; Sajantila, A.; Salazar-García, D. C.; Serrano, E.; Shaydullaev, S.; Sias, E.; Šlaus, M.; Stančo, L.; Swanston, T.; Teschler-Nicola, M.; Valentin, F.; de Vijver, K. V.; Varney, T. L.; Guirado, A. V.-E.; Waters, C. K.; Weiss-Krejci, E.; Winter, E.; Lamnidis, T. C.; Prüfer, K.; Nägele, K.; Spyrou, M.; Schiffels, S.; Stockhammer, P. W.; Haak, W.; Posth, C.; Warinner, C.; Bos, K. I.; Herbig, A.; Krause, J.: Ancient Plasmodium genomes shed light on the history of human malaria. Nature 631, s41586-024-07546-2, pp. 125 - 133 (2024)

Sun, B.; Valtueña, A. A.; Kocher, A.; Gao, S.; Li, C.; Fu, S.; Zhang, F.; Ma, P.; Yang, X.; Qiu, Y. et al.; Zhang, Q.; Ma, J.; Chen, S.; Xiao, X.; Damchaabadgar, S.; Li, F.; Kovalev, A.; Hu, C.; Chen, X.; Wang, L.; Li, W.; Zhou, Y.; Zhu, H.; Krause, J.; Herbig, A.; Cui, Y.: Origin and dispersal history of Hepatitis B virus in Eastern Eurasia. Nature Communications 15, 2951 (2024)

Esquivel Gomez, L. R.; Weber, A.; Kocher, A.; Kühnert, D.: Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2. Scientific Reports 14 (1), 541 (2024)

Weber, A.; Översti, S.; Kühnert, D.: Reconstructing relative transmission rates in Bayesian phylodynamics: two-fold transmission advantage of Omicron in Berlin, Germany during December 2021. Virus Evolution 9 (2), vead070 (2023)

Heggarty, P.; Anderson, C.; Scarborough, M.; King, B.; Bouckaert, R.; Jocz, L.; Kümmel, M. J.; Jügel, T.; Irslinger, B.; Pooth, R. et al.; Liljegren, H.; Strand, R. F.; Haig, G.; Macák, M.; Kim, R. I.; Anonby, E.; Pronk, T.; Belyaev, O.; Dewey-Findell, T. K.; Boutilier, M.; Freiberg, C.; Tegethoff, R.; Serangeli, M.; Liosis, N.; Stroński, K.; Schulte, K.; Gupta, G. K.; Haak, W.; Krause, J.; Atkinson, Q. D.; Greenhill, S. J.; Kühnert, D.; Gray, R. D.: Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages. Science 381 (6656), eabg0818, pp. 1 - 12 (2023)

Esquivel Gomez, L. R.; Savin, C.; Andrianaivoarimanana, V.; Rahajandraibe, S.; Randriantseheno, L. N.; Zhou, Z.; Kocher, A.; Didelot, X.; Rajerison, M.; Kühnert, D.: Phylogenetic analysis of the origin and spread of plague in Madagascar. PLoS Neglected Tropical Diseases 17 (5), e0010362 (2023)

Begg, T.; Schmidt, A.; Kocher, A.; Larmuseau, M. H.D.; Runfeldt, G.; Maier, P. A.; Wilson, J. D.; Barquera, R.; Maj, C.; Szolek, A. et al.; Sager, M.; Clayton, S.; Peltzer, A.; Hui, R.; Ronge, J.; Reiter, E.; Freund, C.; Burri Promerová, M.; Aron, F.; Tiliakou, A.; Osborn, J.; Behar, D. M.; Boecker, M.; Brandt, G.; Cleynen, I.; Strassburg, C.; Prüfer, K.; Kühnert, D.; Meredith, W. R.; Nöthen, M. M.; Attenborough, R. D.; Kivisild, T.; Krause, J.: Genomic analyses of hair from Ludwig van Beethoven. Current Biology 33 (8), 2023.02.041, pp. 1431 - 1447.e22 (2023)

Kocher, A.; Cornuault, J.; Gantier, J.-C.; Manzi, S.; Chavy, A.; Girod, R.; Dusfour, I.; Forget, P.-M.; Ginouves, M.; Prévot, G. et al.; Guégan, J.-F.; Bañuls, A.-L.; de Thoisy, B.; Murienne, J.: Biodiversity and vector-borne diseases: host dilution and vector amplification occur simultaneously for Amazonian leishmaniases. Molecular Ecology 32 (8), 16341, pp. 1817 - 1831 (2023)

Scire, J.; Barido-Sottani, J.; Kühnert, D.; Vaughan, T. G.; Stadler, T.: Robust phylodynamic analysis of genetic sequencing data from structured populations. Viruses 14 (8), 1648 (2022)

Översti, S.; Palo, J. U.: Variation in the substitution rates among the human mitochondrial Haplogroup U Sublineages. Genome Biology and Evolution 14 (7), evac097, pp. 1 - 14 (2022)