Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

por Kühnert, Denise, Wu, Chieh-Hsi, Drummond, Alexei J.
Publicado 2011

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model

por Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.
Publicado 2014

Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data

por Stadler, Tanja, Kühnert, Denise, Rasmussen, David A., du Plessis, Louis
Publicado 2014

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

por Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.
Publicado 2016

Efficient Bayesian inference under the structured coalescent

por Vaughan, Timothy G., Kühnert, Denise, Popinga, Alex, Welch, David, Drummond, Alexei J.
Publicado 2014

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

por Scire, Jérémie, Barido-Sottani, Joëlle, Kühnert, Denise, Vaughan, Timothy G., Stadler, Tanja
Publicado 2022

Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

por Smith, Maureen Rebecca, Trofimova, Maria, Weber, Ariane, Duport, Yannick, Kühnert, Denise, von Kleist, Max
Publicado 2021

Tuberculosis outbreak investigation using phylodynamic analysis

por Kühnert, Denise, Coscolla, Mireia, Brites, Daniela, Stucki, David, Metcalfe, John, Fenner, Lukas, Gagneux, Sebastien, Stadler, Tanja
Publicado 2018

How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics?

por Stadler, Tanja, Vaughan, Timothy G., Gavryushkin, Alex, Guindon, Stephane, Kühnert, Denise, Leventhal, Gabriel E., Drummond, Alexei J.
Publicado 2015

A58 Epidemic dynamics of ancient disease outbreaks

por Esquivel Gomez, Luis R, Spyrou, Maria A, Keller, Marcel, Herbig, Alexander, Bos, Kirsten I, Krause, Johannes, Kühnert, Denise
Publicado 2019

A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

por Sabin, Susanna, Herbig, Alexander, Vågene, Åshild J., Ahlström, Torbjörn, Bozovic, Gracijela, Arcini, Caroline, Kühnert, Denise, Bos, Kirsten I.
Publicado 2020

Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage

por Reh, Lucia, Magnus, Carsten, Kadelka, Claus, Kühnert, Denise, Uhr, Therese, Weber, Jacqueline, Morris, Lynn, Moore, Penny L., Trkola, Alexandra
Publicado 2018

Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up

por Arimide, Dawit Assefa, Esquivel-Gómez, Luis Roger, Kebede, Yenew, Sasinovich, Sviataslau, Balcha, Taye, Björkman, Per, Kühnert, Denise, Medstrand, Patrik
Publicado 2022

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

por Bouckaert, Remco, Heled, Joseph, Kühnert, Denise, Vaughan, Tim, Wu, Chieh-Hsi, Xie, Dong, Suchard, Marc A., Rambaut, Andrew, Drummond, Alexei J.
Publicado 2014

Phylogenetic analysis of the origin and spread of plague in Madagascar

por Esquivel Gomez, Luis Roger, Savin, Cyril, Andrianaivoarimanana, Voahangy, Rahajandraibe, Soloandry, Randriantseheno, Lovasoa Nomena, Zhou, Zhemin, Kocher, Arthur, Didelot, Xavier, Rajerison, Minoarisoa, Kühnert, Denise
Publicado 2023

Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage

por Boumasmoud, Mathilde, Dengler Haunreiter, Vanina, Schweizer, Tiziano A., Meyer, Lilly, Chakrakodi, Bhavya, Schreiber, Peter W., Seidl, Kati, Kühnert, Denise, Kouyos, Roger D., Zinkernagel, Annelies S.
Publicado 2022

Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus

por Weber de Melo, Vanessa, Sheikh Ali, Hanan, Freise, Jona, Kühnert, Denise, Essbauer, Sandra, Mertens, Marc, Wanka, Konrad M, Drewes, Stephan, Ulrich, Rainer G, Heckel, Gerald
Publicado 2015

In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance

por Dengler Haunreiter, Vanina, Boumasmoud, Mathilde, Häffner, Nicola, Wipfli, Dennis, Leimer, Nadja, Rachmühl, Carole, Kühnert, Denise, Achermann, Yvonne, Zbinden, Reinhard, Benussi, Stefano, Vulin, Clement, Zinkernagel, Annelies S.
Publicado 2019

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

por Kühnert, Denise, Kouyos, Roger, Shirreff, George, Pečerska, Jūlija, Scherrer, Alexandra U., Böni, Jürg, Yerly, Sabine, Klimkait, Thomas, Aubert, Vincent, Günthard, Huldrych F., Stadler, Tanja, Bonhoeffer, Sebastian
Publicado 2018

Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology

por Vasylyeva, Tetyana I, du Plessis, Louis, Pineda-Peña, Andrea C, Kühnert, Denise, Lemey, Philippe, Vandamme, Anne-Mieke, Gomes, Perpétua, Camacho, Ricardo J, Pybus, Oliver G, Abecasis, Ana B, Faria, Nuno R
Publicado 2019