Publications of Denise Kühnert

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)

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)

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)

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 Ed., pp. 305 - 339 (Eds. 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)

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)

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)