Epidemiology; Evolution; Bayesian methods; Inference; HIV
Gavryushkina Alexandra, Welch David, Stadler Tanja, Drummond Alexei J. (2014), Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration, in PLoS computational biology
, 10(12), 1003919-1003919.
Feldberg Kathrin, Schneider Harald, Stadler Tanja, Schaefer-Verwimp Alfons, Schmidt Alexander R., Heinrichs Jochen (2014), Epiphytic leafy liverworts diversified in angiosperm-dominated forests, in Scientific Reports
, 4, 1.
Aandahl R. Zachariah, Stadler Tanja, Sisson Scott A., Tanaka Mark M. (2014), Exact vs. approximate computation: Reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters, in GENETICS
, 196(4), 1227-1230.
Xing Yaowu, Onstein Renske E., Carter Richard J., Stadler Tanja, Linder H. Peter (2014), FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS, GENERIC DIVERSITY, AND TURNOVER RATES ARE DISCONNECTED, in Evolution
, 68(10), 2821-2832.
Boskova Veronika, Bonhoeffer Sebastian, Stadler Tanja (2014), Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models, in Plos Computational Biology
, 10(11), 1.
Stadler Tanja, Kuhnert Denise, Rasmussen David, DuPlessis Louis (2014), Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data, in PLoS Currents: Outbreaks
, 1(1), 1.
Stadler Tanja, Rabosky Daniel L., Ricklefs Robert E., Bokma Folmer (2014), On Age and Species Richness of Higher Taxa, in American Naturalist
, 184(4), 447-455.
Lambert Amaury, Alexander Helen K., Stadler Tanja (2014), Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics, in JOURNAL OF THEORETICAL BIOLOGY
, 352, 60-70.
Kuehnert Denise, Stadler Tanja, Vaughan Timothy G., Drummond Alexei J. (2014), Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model, in JOURNAL OF THE ROYAL SOCIETY INTERFACE
, 11(94), 1.
Avila Dorita, Keiser Olivia, Egger Matthias, Kouyos Roger, Boeni Juerg, Yerly Sabine, Klimkait Thomas, Vernazza Pietro L., Aubert Vincent, Rauch Andri, Bonhoeffer Sebastian, Guenthard Huldrych F., Stadler Tanja, Spycher Ben D. (2014), Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland, in AMERICAN JOURNAL OF EPIDEMIOLOGY
, 179(12), 1514-1525.
Heath Tracy A., Huelsenbeck John P., Stadler Tanja (2014), The fossilized birth-death process for coherent calibration of divergence-time estimates, in Proceedings of the National Academy of Sciences of the United States of America
, 111(29), 2957-2966.
Leventhal Gabriel E., Guenthard Huldrych F., Bonhoeffer Sebastian, Stadler Tanja (2014), Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission, in MOLECULAR BIOLOGY AND EVOLUTION
, 31(1), 6-17.
Lambert Amaury, Stadler Tanja (2013), Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies, in THEORETICAL POPULATION BIOLOGY
, 90, 113-128.
Stadler Tanja, Kuehnert Denise, Bonhoeffer Sebastian, Drummond Alexei J. (2013), Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
, 110(1), 228-233.
Stadler Tanja, Yang Ziheng (2013), Dating Phylogenies with Sequentially Sampled Tips, in SYSTEMATIC BIOLOGY
, 62(5), 674-688.
Stadler Tanja, Bokma Folmer (2013), Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa, in SYSTEMATIC BIOLOGY
, 62(2), 220-230.
Stadler Tanja (2013), How Can We Improve Accuracy of Macroevolutionary Rate Estimates?, in SYSTEMATIC BIOLOGY
, 62(2), 321-329.
Liberles David A., Teufel Ashley I., Liu Liang, Stadler Tanja (2013), On the Need for Mechanistic Models in Computational Genomics and Metagenomics, in GENOME BIOLOGY AND EVOLUTION
, 5(10), 2008-2018.
Stadler T. (2013), Recovering speciation and extinction dynamics based on phylogenies, in JOURNAL OF EVOLUTIONARY BIOLOGY
, 26(6), 1203-1219.
Buerki Sven, Forest Felix, Stadler Tanja, Alvarez Nadir (2013), The abrupt climate change at the Eocene-Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages, in ANNALS OF BOTANY
, 112(1), 151-160.
Stadler Tanja, Bonhoeffer Sebastian (2013), Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods, in PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
, 368(1614), 20120198.
Degnan James H., Rosenberg Noah A., Stadler Tanja (2012), A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees, in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
, 9(6), 1558-1568.
Cusimano N, Stadler T, Renner SS (2012), A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies, in SYSTEMATIC BIOLOGY
, 61(5), 785-792.
Stadler Tanja, Degnan James H. (2012), A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree, in Algorithms for Molecular Biology
, 7(1), 1.
Mooers A, Gascuel O, Stadler T, Li HY, Steel M (2012), Branch Lengths on Birth-Death Trees and the Expected Loss of Phylogenetic Diversity, in SYSTEMATIC BIOLOGY
, 61(2), 195-203.
Stadler T, Steel M (2012), Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models, in JOURNAL OF THEORETICAL BIOLOGY
, 297, 33-40.
Etienne RS, Haegeman B, Stadler T, Aze T, Pearson PN, Purvis A, Phillimore AB (2012), Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record, in PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
, 279(1732), 1300-1309.
Stadler T, Kouyos R, von Wyl V, Yerly S, Boni J, Burgisser P, Klimkait T, Joos B, Rieder P, Xie D, Gunthard HF, Drummond AJ, Bonhoeffer S (2012), Estimating the Basic Reproductive Number from Viral Sequence Data, in MOLECULAR BIOLOGY AND EVOLUTION
, 29(1), 347-357.
Leventhal GE, Kouyos R, Stadler T, von Wyl V, Yerly S, Boni J, Cellerai C, Klimkait T, Gunthard HF, Bonhoeffer S (2012), Inferring Epidemic Contact Structure from Phylogenetic Trees, in PLOS COMPUTATIONAL BIOLOGY
, 8(3), -.
Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janecka JE, Fisher CA, Murphy WJ (2012), Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix, in PLOS ONE
, 7(11), -.
Murphy WJ, Janecka JE, Stadler T, Eizirik E, Ryder OA, Gatesy J, Meredith RW, Springer MS (2012), Response to Comment on "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification", in SCIENCE
, 337(6090), 34.
Degnan JH, Rosenberg NA, Stadler T (2012), The probability distribution of ranked gene trees on a species tree, in MATHEMATICAL BIOSCIENCES
, 235(1), 45-55.
Bokma F, van den Brink V, Stadler T (2012), UNEXPECTEDLY MANY EXTINCT HOMININS, in EVOLUTION
, 66(9), 2969-2974.
RNA viruses are characterized by short generation time and high mutation rates. Therefore even over relatively short time spans epidemiological processes leave a fingerprint in the genetic structure of viral sequences sampled from the host population. As a consequence, both epidemiological and evolutionary processes can be inferred from virus sequences. However, until now epidemiological virus sequence data have been analyzed without assuming explicit epidemiological models, and therefore the quantification of key epidemiological parameters was not possible. The objective of this research proposal is to merge epidemiological and evolutionary models, so that both epidemiological and evolutionary parameters can be estimated on the basis of viral sequence data. The methodology will be available both as a Bayesian phylogenetic inference method and as a maximum likelihood phylogenetic method. The epidemiological models need to be formulated and analyzed in a stochastic framework rather than in the common deterministic framework as used by epidemiologists. Using the developed methodology, I will quantify epidemiological and evolutionary processes in HIV epidemics, followed by a large scale comparison of different viral epidemics. I will first investigate which treatment and intervention strategies had a significant impact on the epidemic spread of HIV in the past. In particular, I will apply the methods to sequence data of the Swiss HIV epidemic to identify to what extent different population groups (risk groups such as homosexuals, heterosexuals and intravenous drug users; or geographic groups) drive the HIV epidemics. The results will have the potential to support the efforts to design improved intervention strategies in the future. Second, I will address a key empirical paradox challenging our understanding of HIV evolutionary biology, namely the apparent incompatibility between the observed fast evolutionary rates obtained from within-host data and slow evolutionary rates obtained from between-host data. Applying the developed phylogenetic methods to HIV sequence data from the Swiss epidemic, I will quantify the risk group specific within- and between-host evolutionary rates. The quantification will allow me to support or reject alternative hypotheses explaining the rate differences. Third, the methodology will be applied to a variety of viral epidemics in order to recover the specific epidemiological dynamics. I plan to study Influenza virus, Dengue virus, Hepatitis C virus and Rhinovirus, viruses for which enough data is available to do phylogenetic analyses.