Tanja Stadler
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German-Swiss mathematician and professor of computational evolution at the Swiss Federal Institute of Technology in Zurich
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Tanja Stadlermathematics Degrees
Mathematics
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Measure Theory
#1996
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Mathematics
Tanja Stadler's Degrees
- PhD Mathematics University of Zurich
Why Is Tanja Stadler Influential?
(Suggest an Edit or Addition)According to Wikipedia, Tanja Stadler is a mathematician and professor of computational evolution at the Swiss Federal Institute of Technology . She’s the current president of the Swiss Scientific Advisory Panel COVID-19.
Tanja Stadler's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018) (1760)
- Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity (2010) (1745)
- Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification (2011) (1238)
- The fossilized birth–death process for coherent calibration of divergence-time estimates (2013) (511)
- Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix (2012) (432)
- Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) (2012) (404)
- Mammalian phylogeny reveals recent diversification rate shifts (2011) (379)
- On incomplete sampling under birth-death models and connections to the sampling-based coalescent. (2009) (347)
- Sampling-through-time in birth-death trees. (2010) (344)
- Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record (2012) (307)
- Practical considerations for measuring the effective reproductive number, Rt (2020) (271)
- Total-Evidence Dating under the Fossilized Birth–Death Process (2015) (256)
- Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins (2015) (255)
- Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration (2014) (251)
- Simulating trees with a fixed number of extant species. (2011) (232)
- Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 (2021) (229)
- Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020 (2020) (222)
- Estimating the basic reproductive number from viral sequence data. (2012) (197)
- Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 (2020) (163)
- Practical considerations for measuring the effective reproductive number, Rt (2020) (159)
- The contrasting phylodynamics of human influenza B viruses (2015) (159)
- Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. (2021) (145)
- Inferring speciation and extinction rates under different sampling schemes. (2011) (145)
- Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load (2010) (133)
- Bayesian Inference of Species Networks from Multilocus Sequence Data (2017) (133)
- Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods (2013) (117)
- Recovering speciation and extinction dynamics based on phylogenies (2013) (115)
- Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model (2013) (110)
- Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. (2013) (106)
- Epiphytic leafy liverworts diversified in angiosperm-dominated forests (2014) (104)
- Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data (2016) (102)
- CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants (2021) (102)
- Inferring Epidemic Contact Structure from Phylogenetic Trees (2012) (96)
- The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology (2018) (91)
- Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data (2014) (87)
- Sampling trees from evolutionary models. (2010) (85)
- Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure (2017) (81)
- How can we improve accuracy of macroevolutionary rate estimates? (2013) (76)
- The Structured Coalescent and Its Approximations (2016) (76)
- Using an Epidemiological Model for Phylogenetic Inference Reveals Density Dependence in HIV Transmission (2013) (75)
- Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples (2021) (72)
- The origin and early spread of SARS-CoV-2 in Europe (2020) (70)
- Reproductive number of the COVID-19 epidemic in Switzerland with a focus on the Cantons of Basel-Stadt and Basel-Landschaft. (2020) (67)
- Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies (2015) (67)
- Taming the BEAST—A Community Teaching Material Resource for BEAST 2 (2017) (66)
- A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies. (2012) (64)
- Dating phylogenies with sequentially sampled tips. (2013) (63)
- Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable (2020) (63)
- Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. (2010) (62)
- FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS, GENERIC DIVERSITY, AND TURNOVER RATES ARE DISCONNECTED (2014) (61)
- Inferring speciation and extinction processes from extant species data (2011) (61)
- MASCOT: parameter and state inference under the marginal structured coalescent approximation (2017) (60)
- The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes (2017) (60)
- Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations (2019) (59)
- Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2 (2021) (59)
- Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models (2014) (58)
- Closing the gap between palaeontological and neontological speciation and extinction rate estimates (2018) (55)
- Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam (2015) (54)
- Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch (2021) (53)
- Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison (2016) (52)
- Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus Dina (Hirudinea: Erpobdellidae) in Lake Ohrid (2010) (51)
- Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models. (2011) (47)
- On the Need for Mechanistic Models in Computational Genomics and Metagenomics (2013) (46)
- On Age and Species Richness of Higher Taxa (2014) (43)
- Lineages-through-time plots of neutral models for speciation. (2008) (43)
- Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process (2018) (43)
- The abrupt climate change at the Eocene-Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages. (2013) (43)
- Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo (2020) (43)
- Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics (2018) (42)
- Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2 (2020) (41)
- Estimating speciation and extinction rates for phylogenies of higher taxa. (2013) (41)
- Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland (2021) (40)
- A method for investigating relative timing information on phylogenetic trees. (2008) (38)
- Impact of the tree prior on estimating clock rates during epidemic outbreaks (2018) (37)
- Getting to the root of epidemic spread with phylodynamic analysis of genomic data. (2015) (35)
- Comparison of methods for phylogenetic B‐cell lineage inference using time‐resolved antibody repertoire simulations (AbSim) (2017) (34)
- Estimating Epidemic Incidence and Prevalence from Genomic Data (2018) (33)
- How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? (2015) (32)
- Phylodynamics for cell biologists (2021) (32)
- The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic (2018) (31)
- The probability distribution of ranked gene trees on a species tree. (2012) (31)
- Quantifying Age-dependent Extinction from Species Phylogenies (2015) (30)
- Bayesian phylogenetic estimation of fossil ages (2016) (30)
- Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland (2021) (29)
- Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models (2014) (28)
- Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection. (2020) (28)
- Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models (2019) (27)
- A Multitype Birth–Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates (2020) (26)
- Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1 (2016) (26)
- Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses (2019) (25)
- Origins of biodiversity: response (2011) (25)
- Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC (2022) (25)
- Detection and surveillance of SARS-CoV-2 genomic variants in wastewater (2021) (25)
- Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. (2019) (24)
- Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland. (2014) (24)
- Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland (2018) (24)
- Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective. (2016) (24)
- Inferring Epidemiological Parameters on the Basis of Allele Frequencies (2011) (24)
- A Practical Guide to Estimating the Heritability of Pathogen Traits (2018) (21)
- Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates (2020) (21)
- Phylodynamic Model Adequacy Using Posterior Predictive Simulations (2018) (21)
- Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth–death model (2017) (21)
- A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees (2012) (21)
- Tuberculosis outbreak investigation using phylodynamic analysis (2017) (20)
- Tracing Antibody Repertoire Evolution by Systems Phylogeny (2018) (20)
- Exact vs. Approximate Computation: Reconciling Different Estimates of Mycobacterium tuberculosis Epidemiological Parameters (2014) (19)
- TreeSimGM: Simulating phylogenetic trees under general Bellman–Harris models with lineage‐specific shifts of speciation and extinction in R (2017) (19)
- Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa (2018) (18)
- A transmissible cancer shifts from emergence to endemism in Tasmanian devils (2020) (18)
- Within-patient genetic diversity of SARS-CoV-2 (2020) (18)
- Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference (2020) (18)
- Finding the best resolution for the Kingman–Tajima coalescent: theory and applications (2015) (18)
- Phylodynamics on local sexual contact networks (2016) (17)
- Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics (2020) (17)
- Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations (2018) (16)
- Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics. (2013) (16)
- UNEXPECTEDLY MANY EXTINCT HOMININS (2012) (16)
- SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing (2021) (16)
- Improved multi-type birth-death phylodynamic inference in BEAST 2 (2020) (15)
- Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data (2020) (14)
- Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times? (2016) (14)
- Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium (2019) (14)
- Analyzing and reconstructing reticulation networks under timing constraints (2010) (14)
- The Heritability of Pathogen Traits - Definitions and Estimators (2017) (13)
- Mathematical and computational evolutionary biology (2013). (2015) (13)
- A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree (2012) (13)
- On the statistical analysis of single cell lineage trees (2018) (13)
- Testing the spatial and temporal framework of speciation in an ancient lake species flock (2010) (12)
- Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models (2019) (12)
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences (2020) (12)
- Exploring the power of Bayesian birth‐death skyline models to detect mass extinction events from phylogenies with only extant taxa (2019) (11)
- A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates (2018) (10)
- Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data (2020) (10)
- Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models (2018) (10)
- The probability distribution of the reconstructed phylogenetic tree with occurrence data (2019) (10)
- Inferring Species Trees Using Integrative Models of Species Evolution (2018) (10)
- Inference of species histories in the presence of gene flow (2018) (9)
- The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data (2020) (9)
- Quantifying transmission fitness costs of multi-drug resistant tuberculosis. (2021) (8)
- Estimating shifts in diversification rates based on higher-level phylogenies (2016) (8)
- Evolving Trees - Models for Speciation and Extinction in Phylogenetics (2008) (8)
- Fast likelihood evaluation for multivariate phylogenetic comparative methods: the PCMBase R package (2018) (7)
- Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library (2018) (7)
- Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. (2019) (7)
- The probability distribution of the reconstructed phylogenetic tree with occurrence data. (2019) (6)
- Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales (2021) (6)
- SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination (2021) (5)
- Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study (2019) (5)
- Extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can be spread in the absence of selection (2019) (5)
- External introductions helped drive and sustain the high incidence of HIV-1 in rural KwaZulu-Natal, South Africa (2017) (5)
- POUMM: An R-package for Bayesian Inference of Phylogenetic Heritability (2017) (5)
- Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies (2013) (5)
- A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences (2020) (5)
- Asymmetric division events promote variability in cell cycle duration in animal cells and Escherichia coli (2019) (4)
- Directly Estimating Epidemic Curves From Genomic Data (2017) (4)
- Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data (2021) (4)
- Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes (2020) (4)
- Phylodynamic Analyses based on 93 genomes (2020) (4)
- Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes (2021) (4)
- Branch lengths on Yule trees and the expected loss of phylogenetic diversity (2010) (3)
- IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status (2020) (3)
- LAPIS is a fast web API for massive open virus sequencing databases (preprint) (2022) (3)
- TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data (2022) (3)
- The ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data (2019) (3)
- DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 (2021) (3)
- Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations (2022) (3)
- The Occurrence Birth–Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology (2022) (3)
- Bayesian Coalescent Epidemic Inference: Comparison of Stochastic and Deterministic SIR Population Dynamics (2014) (3)
- Fast and Robust Inference of Phylogenetic Ornstein-Uhlenbeck Models Using Parallel Likelihood Calculation (2017) (3)
- Species-specific diversification (2019) (2)
- Fast Bayesian Inference of Phylogenetic Models Using Parallel Likelihood Calculation and Adaptive Metropolis Sampling (2017) (2)
- A unified multi-resolution coalescent: Markov lumpings of the Kingman-Tajima n-coalescent (2009) (2)
- High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters (2020) (2)
- Joint inference of migration and reassortment patterns for viruses with segment genomes (2021) (2)
- What can phylodynamics bring to animal health research? (2021) (2)
- The methodologies to assess the effectiveness of non-pharmaceutical interventions during COVID-19: a systematic review (2022) (2)
- Joint inference of species histories and gene flow (2018) (2)
- Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example (2022) (2)
- Inferring epidemiological parameters based on allele frequencies (2011) (2)
- Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland (2023) (1)
- The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies (2021) (1)
- Running Title: AGE-DEPENDENT SPECIATION (2015) (1)
- Response to Comment on “Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification” (2012) (1)
- Mathematical Models for the Epidemiology and Evolution of Mycobacterium tuberculosis. (2017) (1)
- Identification of a Cluster of Extended-spectrum Beta-Lactamase–Producing Klebsiella pneumoniae Sequence Type 101 Isolated From Food and Humans (2020) (1)
- Ignoring fossil age uncertainty leads to inaccurate topology and divergence times in time calibrated tree inference (2020) (1)
- Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe (2021) (1)
- On the reliability of approximate Bayesian computation: epidemiological parameter estimates from Mycobacterium tuberculosis genotypes (2014) (1)
- Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study. (2022) (1)
- A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits (2021) (0)
- 576 What have the Fagales been up to for the last 65 My? : A synthesis of fossils, phylogeny & plant functional traits (2012) (0)
- Information for Members and Subscribers - Subscriptions. (2016) (0)
- Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human–live bird market interface in China (2023) (0)
- Correction: Practical considerations for measuring the effective reproductive number, Rt (2021) (0)
- Asymmetric division events promote variability in cell cycle duration in animal cells and Escherichia coli (2019) (0)
- Redescription of the type material of Eubrachiella antarctica (Quidor, 1906) (Copepoda, Lernaeopodidae) (1986) (0)
- The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection (2020) (0)
- CONSTRAINING THE LATE TRIASSIC MASS EXTINCTION USING THE FOSSILIZED BIRTH-DEATH RANGE MODEL (2018) (0)
- Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania (2022) (0)
- Erratum to “On the statistical analysis of single cell lineage trees” [J. Theor. Biol. 439 (2018) 160–165] (2020) (0)
- Estimating Mutation Parameters and Population History Simultaneously from Temporally-Spaced Genome Data (2016) (0)
- Estimating disease spread using structured coalescent and birth-death models: A quantitative comparison (2020) (0)
- Closing the gap between palaeontological and neontological speciation and extinction rate estimates (2018) (0)
- Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection (2020) (0)
- The fossilised birth-death chronospecies model: a coherent modelling framework for the fossil record & extant species samples (2017) (0)
- ON THE IMPORTANCE OF INCOMPLETE SAMPLING IN PALAEONTOLOGICAL AND PHYLOGENETIC APPROACHES TO ESTIMATING SPECIATION AND EXTINCTION RATES (2017) (0)
- Finding the best resolution for the Kingman–Tajima coalescent: theory and applications (2014) (0)
- OP-MOLB160219 185..203 (2016) (0)
- Talk outline ! The ‘ shape ’ of evolutionary trees " rates and balance " the problem with existing models ! Our approach ! (2013) (0)
- Effectiveness assessment of non-pharmaceutical interventions: lessons learned from the COVID-19 pandemic (2023) (0)
- MBE methodology became available allowing for sequences being sampled sequentially through time ( Rambaut 2000 ) , allowing for changing population sizes through time ( (2018) (0)
- A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree (2012) (0)
- Systematic Biology - Editorial Board. (2016) (0)
- The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot (2023) (0)
- Data for: Tuberculosis outbreak investigation using phylodynamic analysis (2018) (0)
- TOTAL-EVIDENCE BAYESIAN INFERENCE OF PAST DIVERSITY: THE OCCURRENCE BIRTH-DEATH PROCESS (2020) (0)
- Correction to: ‘TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data’ (2022) by Seidel & Stadler (2023) (0)
- Species-specific diversification (2019) (0)
- Software for Systematics and Evolution the Community Teaching Material Resource for BEAST 2 (2017) (0)
- Combined inference of epidemic trajectories, parameters and phylogenetic trees from viral genomes (2016) (0)
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