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D. Kühnert · SciRah

Researcher profile · Semantic Scholar

D. Kühnert

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D. Kühnert — researcher profile on SciRah

h-index: 36
Works: 84
Citations: 15K

Most-cited papers

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
R. Bouckaert, J. Heled, D. Kühnert, T. Vaughan +5 more
2014PLoS Comput. Biol.6,265 citations Open access
Semantic Scholar
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
R. Bouckaert, T. Vaughan, J. Barido-Sottani, S. Duchêne +21 more
2018bioRxiv3,979 citations Open access
Semantic Scholar
Swarm Learning for decentralized and confidential clinical machine learning
S. Warnat-Herresthal, Hartmut Schultze, Krishnaprasad Shastry, Sathyanarayanan Manamohan +175 more
2021Nature858 citations Open access
Semantic Scholar
Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
T. Stadler, D. Kühnert, S. Bonhoeffer, A. Drummond
2012Proceedings of the National Academy of Sciences of the United States of America537 citations Open access
Semantic Scholar
The contrasting phylodynamics of human influenza B viruses
D. Vijaykrishna, E. Holmes, Udayan Joseph, M. Fourment +24 more
2015eLife210 citations Open access
Semantic Scholar
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19
B. Krämer, Rainer Knoll, L. Bonaguro, Michael ToVinh +156 more
2021Immunity206 citations Open access
Semantic Scholar
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
D. Kühnert, T. Stadler, T. Vaughan, A. Drummond
2016Molecular biology and evolution179 citations Open access
Semantic Scholar
Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster
N. Arora, V. Schuenemann, Günter Jäger, A. Peltzer +26 more
2016Nature Microbiology165 citations Open access
Semantic Scholar
Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague
M. Spyrou, R. Tukhbatova, Chuan-Chao Wang, A. A. Valtueña +8 more
2018Nature Communications162 citations Open access
Semantic Scholar
Efficient Bayesian inference under the structured coalescent
T. Vaughan, D. Kühnert, A. Popinga, D. Welch +1 more
2014Bioinform.135 citations Open access
Semantic Scholar
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Franziska Hufsky, Kevin Lamkiewicz, A. Almeida, A. Aouacheria +51 more
2020Briefings Bioinform.130 citations Open access
Semantic Scholar
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model
D. Kühnert, T. Stadler, T. Vaughan, A. Drummond
2013Journal of the Royal Society Interface129 citations Open access
Semantic Scholar
The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology
C. Meehan, Pieter Moris, T. Kohl, Jūlija Pečerska +11 more
2018bioRxiv123 citations Open access
Semantic Scholar
Neolithic and medieval virus genomes reveal complex evolution of hepatitis B
B. Krause-Kyora, Julian Susat, F. Key, D. Kühnert +18 more
2018bioRxiv121 citations Open access
Semantic Scholar
Emergence of human-adapted Salmonella enterica is linked to the Neolithization process
F. Key, C. Posth, L. Esquivel-Gómez, Ron Hübler +41 more
2020Nature Ecology & Evolution113 citations Open access
Semantic Scholar
Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data
T. Stadler, D. Kühnert, David A. Rasmussen, L. du Plessis
2014PLOS Currents107 citations Open access
Semantic Scholar
Influenza A Virus Migration and Persistence in North American Wild Birds
J. Bahl, S. Krauss, D. Kühnert, M. Fourment +15 more
2013PLoS Pathogens104 citations Open access
Semantic Scholar
The source of the Black Death in fourteenth-century central Eurasia
M. Spyrou, L. Musralina, G. Gnecchi-Ruscone, Arthur Kocher +9 more
2022Nature103 citations Open access
Semantic Scholar
Ten millennia of hepatitis B virus evolution
Arthur Kocher, L. Papac, Rodrigo Barquera, F. Key +166 more
2021Science99 citations Open access
Semantic Scholar
Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
D. Kühnert, Chieh-Hsi Wu, A. Drummond
2011Infection, Genetics and Evolution93 citations Open access
Semantic Scholar
In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance
Vanina Dengler Haunreiter, Mathilde Boumasmoud, Nicola Häffner, Dennis Wipfli +8 more
2019Nature Communications86 citations Open access
Semantic Scholar
A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
Susanna J Sabin, A. Herbig, Å. J. Vågene, Torbjörn Ahlström +4 more
2019Genome Biology80 citations Open access
Semantic Scholar
Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague
Aida Andrades Valtueña, Gunnar U. Neumann, M. Spyrou, L. Musralina +45 more
2022Proceedings of the National Academy of Sciences of the United States of America75 citations Open access
Semantic Scholar
Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages
Paul Heggarty, Cormac Anderson, Matthew E. Scarborough, Benedict King +29 more
2023Science70 citations Open access
Semantic Scholar
Software for Systematics and Evolution
Joëlle Barido, Sottani, V. Boskova, L. du Plessis +22 more
201770 citations
Semantic Scholar
Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.
K. Majander, S. Pfrengle, Arthur Kocher, Judith Neukamm +16 more
2020Current Biology67 citations Open access
Semantic Scholar
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics
D. Kühnert, R. Kouyos, G. Shirreff, Jūlija Pečerska +8 more
2018PLoS Pathogens66 citations Open access
Semantic Scholar
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
O. Ratmann, Emma B. Hodcroft, M. Pickles, A. Cori +20 more
2016Molecular biology and evolution63 citations Open access
Semantic Scholar
Taming the BEAST—A Community Teaching Material Resource for BEAST 2
J. Barido-Sottani, V. Bošková, L. du Plessis, D. Kühnert +11 more
2017Systematic Biology57 citations Open access
Semantic Scholar
Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam
J. Geoghegan, L. Tan, D. Kühnert, R. Halpin +28 more
2015Journal of Virology57 citations Open access
Semantic Scholar
Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.
K. Bos, D. Kühnert, A. Herbig, L. Esquivel-Gómez +8 more
2019Annual Review of Microbiology53 citations Open access
Semantic Scholar
Origin and Health Status of First-Generation Africans from Early Colonial Mexico.
Rodrigo Barquera, T. C. Lamnidis, A. Lankapalli, Arthur Kocher +14 more
2020Current Biology49 citations Open access
Semantic Scholar
Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus
Vanessa Weber de Melo, Hanan Sheikh Ali, J. Freise, D. Kühnert +6 more
2015Evolutionary Applications48 citations Open access
Semantic Scholar
Genomic analyses of hair from Ludwig van Beethoven.
T. Begg, A. Schmidt, Arthur Kocher, M. Larmuseau +29 more
2023Current Biology44 citations Open access
Semantic Scholar
How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics?
T. Stadler, T. Vaughan, Alex Gavryushkin, S. Guindon +3 more
2015Proceedings of the Royal Society of London. Biological Sciences41 citations Open access
Semantic Scholar
Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage
Mathilde Boumasmoud, Vanina Dengler Haunreiter, Tiziano A. Schweizer, L. Meyer +6 more
2021bioRxiv38 citations Open access
Semantic Scholar
Field-based sciences must transform in response to COVID-19
E. Scerri, D. Kühnert, J. Blinkhorn, Huw S. Groucutt +12 more
2020Nature Ecology & Evolution33 citations Open access
Semantic Scholar
Tuberculosis outbreak investigation using phylodynamic analysis
D. Kühnert, Mireia Coscollá, D. Brites, David Stucki +4 more
2018Epidemics29 citations Open access
Semantic Scholar
Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology
Tetyana I. Vasylyeva, L. du Plessis, A. Pineda-Peña, D. Kühnert +7 more
2019Journal of Infectious Diseases26 citations Open access
Semantic Scholar
Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020
Maureen R. Smith, M. Trofimova, Ariane Weber, Yannick Duport +2 more
2021Nature Communications23 citations Open access
Semantic Scholar
Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana
Vlad Novitsky, D. Kühnert, S. Moyo, E. Widenfelt +2 more
2015Epidemics23 citations Open access
Semantic Scholar
Quantifying transmission fitness costs of multi-drug resistant tuberculosis.
Jūlija Pečerska, D. Kühnert, C. Meehan, Mireia Coscollá +3 more
2021Epidemics22 citations Open access
Semantic Scholar
Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations
J. Sciré, J. Barido-Sottani, D. Kühnert, T. Vaughan +1 more
2022bioRxiv21 citations Open access
Semantic Scholar
The Way Forward to Embrace Artificial Intelligence in Public Health.
Georges Hattab, C. Irrgang, Nils Körber, D. Kühnert +1 more
2024American Journal of Public Health20 citations Open access
Semantic Scholar
Improved multi-type birth-death phylodynamic inference in BEAST 2
J. Sciré, J. Barido-Sottani, D. Kühnert, T. Vaughan +1 more
2020bioRxiv18 citations Open access
Semantic Scholar
Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany
K. Hanke, N. Faria, D. Kühnert, Kaveh Yousef +9 more
2019Journal of Virology17 citations Open access
Semantic Scholar
Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage
L. Reh, Carsten Magnus, Claus Kadelka, D. Kühnert +5 more
2018PLoS Pathogens13 citations Open access
Semantic Scholar
Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2.
Kevin Lamkiewicz, L. R. Esquivel Gomez, D. Kühnert, M. Marz
2023Current Topics in Microbiology and Immunology9 citations
Semantic Scholar
Phylogenetic analysis of the origin and spread of plague in Madagascar
L. R. Esquivel Gomez, C. Savin, V. Andrianaivoarimanana, Soloandry Rahajandraibe +6 more
2022bioRxiv7 citations Open access
Semantic Scholar
Phylogenetic meta-analysis of chronic SARS-CoV-2 infections in immunocompromised patients shows no evidence of elevated evolutionary rates
Sanni Översti, Emily Gaul, B. Jensen, D. Kühnert
2023bioRxiv6 citations Open access
Semantic Scholar

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