Publications

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.; 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 (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)

Andrades Valtueña, A.; Neumann, G.; Spyrou, M. A.; Musralina, L.; Aron, F.; Beisenov, A.; Belinskiy, A. B.; Bos, K. I.; Buzhilova, A.; Conrad, M. et al.; Djansugurova, L. B.; Dobes, M.; Ernee, M.; Fernandez-Eraso, J.; Frohlich, B.; Furmanek, M.; Hałuszko, A.; Hansen, S.; Harney, E.; Hiss, A. N.; Hübner, A.; Key, F. M.; Khussainova, E.; Kitov, E.; Kitova, A. O.; Knipper, C.; Kühnert, D.; Lalueza-Fox, C.; Littleton, J.; Massy, K.; Mittnik, A.; Mujika-Alustiza, J. A.; Olalde, I.; Papac, L.; Penske, S. E.; Peska, J.; Pinhasi, R.; Reich, D.; Reinhold, S.; Stahl, R.; Stäuble, H.; Tukhbatova, R. I.; Vasilyev, S.; Veselovskaya, E.; Warinner, C.; Stockhammer, P. W.; Haak, W.; Krause, J.; Herbig, A.: Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proceedings of the National Academy of Sciences of the United States of America 119 (17), e2116722119, pp. 1 - 11 (2022)

Vågene, Å. J.; Honap, T. P.; Harkins, K. M.; Rosenberg, M. S.; Giffin, K.; Cárdenas-Arroyo, F.; Leguizamón, L. P.; Arnett, J.; Buikstra, J. E.; Herbig, A. et al.; Krause, J.; Stone, A. C.; Bos, K. I.: Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nature Communications 13 (1), 1195 (2022)

Arimide, D. A.; Esquivel Gómez, L. R.; Kebede, Y.; Sasinovich, S.; Balcha, T.; Björkman, P.; Kühnert, D.; Medstrand, P.: Molecular epidemiology and transmission dynamics of the HIV-1 epidemic in Ethiopia: epidemic decline coincided with behavioral interventions before ART scale-up. Frontiers in Microbiology 13, 821006 (2022)