Publications

Journal Article (8)

1.

MPG.PuRe

DOI

Journal Article
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)
2.

MPG.PuRe

DOI

pre-print

publisher-version

Journal Article
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), pp. 233 - 243 (2019)
3.

MPG.PuRe

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publisher-version

Journal Article
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) (2019)
4.

MPG.PuRe

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pre-print

Journal Article
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. bioRxiv (2019)
5.

MPG.PuRe

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publisher-version

Journal Article
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 (2019)
6.

MPG.PuRe

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Journal Article
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)
7.

MPG.PuRe

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publisher-version

Journal Article
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 (2018)
8.

MPG.PuRe

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publisher-version

Journal Article
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 (2018)

Other (1)

9.

MPG.PuRe

DOI

pre-print

Other
Scire, J.; Barido-Sottani, J.; Kühnert, D.; Vaughan, T. G.; Stadler, T.: Improved multi-type birth-death phylodynamic inference in BEAST 2, bioRxiv, (2020)