ETH - Theoretical Biology - Publications Tanja Stadler

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ETH Zurich - D-UWIS - Theoretical Biology - Publications

Publications

Publications Tanja Stadler

2012

Stadler, T, Degnan, J
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
ALGORITHMS FOR MOLECULAR BIOLOGY (2012) in press:-

Bokma, F, van den Brink, V, Stadler, T
Unexpectedly high extinction rate in recent hominins
EVOLUTION (2012) doi:10.1111/j.1558-5646.2012.01660.x:-

Cusimano, N, Stadler, T, Renner, S
A new method for handling missing species in diversification analysis applicable to randomly or non-randomly sampled phylogenies
SYSTEMATIC BIOLOGY (2012) doi:10.1093/sysbio/sys031:-

Leventhal, G, Kouyos, R, Stadler, T, von Wyl, V, Yerly, S, Boni, J, Cellerai, C, Klimkait, T, Gunthard, HF, Bonhoeffer, S
Inferring Epidemic Contact Structure from Phylogenetic Trees
PLOS COMPUTATIONAL BIOLOGY (2012) 8:-

Etienne, RS, Haegeman, B, Stadler, T, Aze, T, Pearson, PN, Purvis, A, Phillimore, AB
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2012) 279:1300-1309

Mooers, A, Gascuel, O, Stadler, T, Li, H, Steel, M
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity
SYSTEMATIC BIOLOGY (2012) 61:195-203

Stadler, T, Steel, M
Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models
JOURNAL OF THEORETICAL BIOLOGY (2012) 297:33-40

Degnan, JH, Rosenberg, NA, Stadler, T
The probability distribution of ranked gene trees on a species tree
MATHEMATICAL BIOSCIENCES (2012) 235:45-55
Abstract

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
Estimating the Basic Reproductive Number from Viral Sequence Data
MOLECULAR BIOLOGY AND EVOLUTION (2012) 29:347-357
Abstract

2011

Meredith, RW, Janecka, JE, Gatesy, J, Ryder, OA, Fisher, CA, Teeling, EC, Goodbla, A, Eizirik, E, Simao, TLL, Stadler, T, Rabosky, DL, Honeycutt, RL, Flynn, JJ, Ingram, CM, Steiner, C, Williams, TL, Robinson, TJ, Burk-Herrick, A, Westerman, M, Ayoub, NA, Springer, MS, Murphy, WJ
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
SCIENCE (2011) 334:521-524
Abstract

Stadler, T
Simulating Trees with a Fixed Number of Extant Species
SYSTEMATIC BIOLOGY (2011) 60:676-684
Abstract

Stadler, T
Inferring speciation and extinction processes from extant species data
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011) 108:16145-16146

Hohna, S, Stadler, T, Ronquist, F, Britton, T
Inferring Speciation and Extinction Rates under Different Sampling Schemes
MOLECULAR BIOLOGY AND EVOLUTION (2011) 28:2577-2589
Abstract

Stadler, T
Inferring Epidemiological Parameters on the Basis of Allele Frequencies
GENETICS (2011) 188:663-672
Abstract

Stadler, T
Mammalian phylogeny reveals recent diversification rate shifts
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011) 108:6187-6192
Abstract

Hoorn, C, Wesselingh, FP, Ter Steege, H, Bermudez, MA, Mora, A, Sevink, J, Sanmartin, I, Sanchez-Meseguer, A, Anderson, CL, Figueiredo, JP, Jaramillo, C, Riff, D, Negri, FR, Hooghiemstra, H, Lundberg, J, Stadler, T, Sarkinen, T, Antonelli, A
Origins of Biodiversity Response
SCIENCE (2011) 331:399-400

2010

Stadler, T
Sampling-through-time in birth-death trees
JOURNAL OF THEORETICAL BIOLOGY (2010) 267:396-404
Abstract

Hoorn, C, Wesselingh, FP, ter Steege, H, Bermudez, MA, Mora, A, Sevink, J, Sanmartin, I, Sanchez-Meseguer, A, Anderson, CL, Figueiredo, JP, Jaramillo, C, Riff, D, Negri, FR, Hooghiemstra, H, Lundberg, J, Stadler, T, Sarkinen, T, Antonelli, A
Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity
SCIENCE (2010) 330:927-931
Abstract

Linz, S, Semple, C, Stadler, T
Analyzing and reconstructing reticulation networks under timing constraints
JOURNAL OF MATHEMATICAL BIOLOGY (2010) 61:715-737
Abstract

Alizon, S, von Wyl, V, Stadler, T, Kouyos, RD, Yerly, S, Hirschel, B, Boni, J, Shah, C, Klimkait, T, Furrer, H, Rauch, A, Vernazza, PL, Bernasconi, E, Battegay, M, Burgisser, P, Telenti, A, Gunthard, HF, Bonhoeffer, S
Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load
PLOS PATHOGENS (2010) 6:-
Abstract Request reprint

Hartmann, K, Wong, D, Stadler, T
Sampling Trees from Evolutionary Models
SYSTEMATIC BIOLOGY (2010) 59:465-476
Abstract

Trajanovski, S, Albrecht, C, Schreiber, K, Schultheiss, R, Stadler, T, Benke, M, Wilke, T
Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus Dina (Hirudinea: Erpobdellidae) in Lake Ohrid
BIOGEOSCIENCES (2010) 7:3387-3402
Abstract

2009

Stadler, T
On incomplete sampling under birth-death models and connections to the sampling-based coalescent
JOURNAL OF THEORETICAL BIOLOGY (2009) 261:58-66
Abstract

Ford, D, Matsen, FA, Stadler, T
A Method for Investigating Relative Timing Information on Phylogenetic Trees
SYSTEMATIC BIOLOGY (2009) 58:167-183
Abstract

2008

Stadler, T
Lineages-through-time plots of neutral models for speciation
MATHEMATICAL BIOSCIENCES (2008) 216:163-171
Abstract

Gernhard, T, Hartmann, K, Steel, M
Stochastic properties of generalised Yule models, with biodiversity applications
JOURNAL OF MATHEMATICAL BIOLOGY (2008) 57:713-735
Abstract

Gernhard, T
The conditioned reconstructed process
JOURNAL OF THEORETICAL BIOLOGY (2008) 253:769-778
Abstract

Gernhard, T
New analytic results for speciation times in neutral models
BULLETIN OF MATHEMATICAL BIOLOGY (2008) 70:1082-1097
Abstract

2006

Gernhard, T, Ford, D, Vos, R, Steel, M
Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny
EVOLUTIONARY BIOINFORMATICS (2006) 2:285-293
Abstract

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