Pečerska, J.; Kühnert, D.; Meehan, C. J.; Coscollá, M.; de Jong; C., B.; Gagneux, S.; Stadler, T.: Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics 36, 100471, pp. 1 - 9 (2021)

Hoffmann, K.; Bouckaert, R.; Greenhill, S. J.; Kühnert, D.: Bayesian phylogenetic analysis of linguistic data using BEAST. Journal of Language Evolution 6 (2), lzab005, pp. 119 - 135 (2021)

Fischer, M.; Herbst, L.; Galla, M.; Long, Y.; Wicke, K.: Unrooted non-binary tree-based phylogenetic networks. Discrete applied mathematics 294, 2021.01.005, pp. 10 - 30 (2021)

Hufsky, F.; Lamkiewicz, K.; Almeida, A.; Aouacheria, A.; Arighi, C.; Bateman, A.; Baumbach, J.; Beerenwinkel, N.; Brandt, C.; Cacciabue, M. et al.; Chuguransky, S.; Drechsel, O.; Finn, R. D.; Fritz, A.; Fuchs, S.; Hattab, G.; Hauschild, A.-C.; Heider, D.; Hoffmann, M.; Hölzer, M.; Hoops, S.; Kaderali, L.; Kalvari, I.; von Kleist, M.; Kmiecinski, R.; Kühnert, D.; Lasso, G.; Libin, P.; List, M.; Löchel, H. F.; Martin, M. J.; Martin, R.; Matschinske, J.; McHardy, A. C.; Mendes, P.; Mistry, J.; Navratil, V.; Nawrocki, E.; O'Toole, Á. N.; Palacios-Ontiveros, N.; Petrov, A. I.; Rangel-Piñeros, G.; Redaschi, N.; Reimering, S.; Reinert, K.; Reyes, A.; Richardson, L.; Robertson, D. L.; Sadegh, S.; Singer, J. B.; Theys, K.; Upton, C.; Welzel, M.; Williams, L.; Marz, M.: Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and Coronavirus research. Briefings in Bioinformatics 22 (2), bbaa232, pp. 642 - 663 (2021)

Smith, M. R.; Trofimova, M.; Weber, A.; Duport, Y.; Kühnert, D.; von Kleist, M.: Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Nature Communications 12 (1), 6009 (2021)

Sabin, S.; Yeh, H.-Y.; Pluskowski, A.; Clamer, C.; Mitchell, P. D.; Bos, K. I.: Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 375 (1812), 20190576, pp. 1 - 15 (2020)

Scerri, E. M. L.; Kühnert, D.; Blinkhorn, J.; Carleton, W. C.; Roberts, P.; Nicoll, K.; Zerboni, A.; Orijemie, E. A.; Barton, H.; Candy, I. et al.; Goldstein, S. T.; Hawks, J.; Niang, K.; N’Dah, D.; Petraglia, M. D.; Vella, N. C.: Field-based sciences must transform in response to COVID-19. Nature Ecology & Evolution, s41559-020-01317-8 (2020)

Majander, K.; Pfrengle, S.; Kocher, A.; Neukamm, J.; du Plessis, L.; Pla-Díaz, M.; Arora, N.; Akgül, G.; Salo, K.; Schats, R. et al.; Inskip, S.; Oinonen, M.; Valk, H.; Malve, M.; Kriiska, A.; Onkamo, P.; González-Candelas, F.; Kühnert, D.; Krause, J.; Schuenemann, V. J.: Ancient bacterial genomes reveal a high diversity of Treponema pallidum Strains in early Modern Europe. Current Biology 30 (19), 2020.07.058, pp. 3788 - 3803.e10 (2020)

Barquera, R.; Lamnidis, T. C.; Lankapalli, A. K.; Kocher, A.; Hernández-Zaragoza, D. I.; Nelson, E. A.; Zamora-Herrera, A. C.; Perez Ramallo, P.; Bernal-Felipe, N.; Immel, A. et al.; Bos, K.; Acuña-Alonzo, V.; Barbieri, C.; Roberts, P.; Herbig, A.; Kühnert, D.; Márquez-Morfín, L.; Krause, J.: Origin and health status of first-generation Africans from early colonial Mexico. Current Biology 30 (11), 2020.04.002, pp. 2078 - 2091.e11 (2020)

Key, F. M.; Posth, C.; Esquivel Gomez, L. R.; Hübler, R.; Spyrou, M. A.; Neumann, G. U.; Furtwängler, A.; Sabin, S.; Burri Promerová, M.; Wissgott, A. et al.; Lankapalli, A. K.; Vågene, Å. J.; Meyer, M.; Nagel, S.; Tukhbatova, R.; Khokhlov, A.; Chizhevsky, A.; Hansen, S.; Belinsky, A. B.; Kalmykov, A.; Kantorovich, A. R.; Maslov, V. E.; Stockhammer, P. W.; Vai, S.; Zavattaro, M.; Riga, A.; Caramelli, D.; Skeates, R.; Beckett, J.; Gradoli, M. G.; Steuri, N.; Hafner, A.; Ramstein, M.; Siebke, I.; Lösch, S.; Erdal, Y. S.; Alikhan, N.-F.; Zhou, Z.; Achtman, M.; Bos, K.; Reinhold, S.; Haak, W.; Kühnert, D.; Herbig, A.; Krause, J.: Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nature Ecology & Evolution 4 (3), pp. 324 - 333 (2020)

Grant, H. E.; Hodcroft, E. B.; Ssemwanga, D.; Kitayimbwa, J. M.; Yebra, G.; Esquivel Gomez, L. R.; Frampton, D.; Gall, A.; Kellam, P.; de Oliveira, T. et al.; Bbosa, N.; Nsubuga, R. N.; Kibengo, F.; Kwan, T. H.; Lycett, S.; Kao, R.; Robertson, D. L.; Ratmann, O.; Fraser, C.; Pillay, D.; Kaleebu, P.; Leigh Brown, A. J.: Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution 6 (1), veaa004, pp. 1 - 12 (2020)

Burgueño-Sosa, E. E.; Esquivel Gómez, L. R.; Rivadeneyra-Gutiérrez, E.; León-López, A. A.: Generalidades de la familia Filoviridae y el virus del Ébola: una actualización de sus implicaciones en la población humana. Revista Biomédica 31 (1), pp. 58 - 68 (2020)

Sabin, S.; Herbig, A.; Vagene, A. J.; Ahlström, T.; Bozovic, G.; Arcini, C.; Kuehnert, D.; Bos, K. I.: A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biology: Biology for the Post-Genomic Era 21, 201 (2020), pp. 1 - 24 (2020)

Bos, K. I.; Kühnert, D.; Herbig, A.; Esquivel Gomez, L. R.; Andrades Valtueña, A.; Barquera Lozano, R. J.; Giffin, K.; Lankapalli, A. K.; Nelson, E. A.; Sabin, S. et al.; Spyrou, M. A.; Krause, J.: Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annual Review of Microbiology 73 (1), pp. 639 - 666 (2019)

Vasylyeva, T. I.; du Plessis, L.; Pineda-Peña, A. C.; Kühnert, D.; Lemey, P.; Vandamme, A.-M.; Gomes, P.; Camacho, R. J.; Pybus, O. G.; Abecasis, A. B. et al.; Faria, N. R.: Tracing the impact of Public Health Interventions on HIV-1 transmission in Portugal using Molecular Epidemiology. The Journal of Infectious Diseases 220 (2), 085, pp. 233 - 243 (2019)

Bouckaert, R.; Vaughan, T. G.; Barido-Sottani, J.; Duchêne, S.; Fourment, M.; Gavryushkina, A.; Heled, J.; Jones, G.; Kühnert, D.; De Maio, N. et al.; Matschiner, M.; Mendes, F. K.; Müller, N. F.; Ogilvie, H. A.; du Plessis, L.; Popinga, A.; Rambaut, A.; Rasmussen, D.; Siveroni, I.; Suchard, M. A.; Wu, C.-H.; Xie, D.; Zhang, C.; Stadler, T.; Drummond, A. J.: BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 15 (4), e1006650 (2019)

Dengler Haunreiter, V.; Boumasmoud, M.; Häffner, N.; Wipfli, D.; Leimer, N.; Rachmühl, C.; Kühnert, D.; Achermann, Y.; Zbinden, R.; Benussi, S. et al.; Vulin, C.; Zinkernagel, A. S.: In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance. Nature Communications 10, 1149 (2019)

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