Search filters

List of works by Sebastian Duchene

17th Century Variola Virus Reveals the Recent History of Smallpox.

scientific article published on 5 December 2016

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection

scientific article published in 2022

A comparison of methods for estimating substitution rates from ancient DNA sequence data.

scientific article

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates.

scientific article published in July 2014

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

scientific article published on 22 September 2017

Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology

publication published on 03 January 2022

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 27 May 2019

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 1 August 2019

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

scientific article published on 08 April 2019

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 21 October 2019

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 06 July 2020

Bayesian molecular dating: opening up the black box.

scientific article published on 15 December 2017

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

scientific article published on 10 August 2016

Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

scientific article published on 16 April 2019

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis

scientific article published on 14 November 2013

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

scientific article (publication date: 8 February 2017)

Continental synchronicity of human influenza virus epidemics despite climactic variation.

scientific article published on 11 January 2018

Correction: Continental synchronicity of human influenza virus epidemics despite climactic variation

scientific article published on 7 February 2018

Correction: The paradox of HBV evolution as revealed from a 16th century mummy.

scientific article published on 9 February 2018

Cross-validation to select Bayesian hierarchical models in phylogenetics

scientific article published on 26 May 2016

Dating the emergence of human pathogens

scientific article published on 01 June 2020

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models.

scientific article

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy.

scientific article published in June 2018

Direct RNA sequencing and early evolution of SARS-CoV-2

scientific article (preprint)

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

article

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

scientific article published on 15 April 2019

Estimating evolutionary rates in giant viruses using ancient genomes.

scientific article

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods

scientific article

Estimating the number and assignment of clock models in analyses of multigene datasets.

scientific article published on 6 January 2016

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

scientific article published on 10 July 2015

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

scientific article published on 26 November 2019

Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster

scientific article

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

scientific article published on 09 August 2021

Evolutionary stasis of viruses?

scientific article published on 01 May 2019

Genome Analysis of Coxsackievirus A4 Isolates From Hand, Foot, and Mouth Disease Cases in Shandong, China

article

Genome-scale rates of evolutionary change in bacteria

Genome-scale rates of evolutionary change in bacteria.

scientific article published on 30 November 2016

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

scientific article published on 14 December 2020

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

scientific article published on 11 December 2020

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

scientific article published on 19 June 2015

Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia

scientific article published on December 2016

INSECT PHYLOGENOMICS. Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

scientific article published on July 2015

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

scholarly article published 18 September 2017

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

scientific article published on 19 June 2018

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes

scientific article

Laboratory and Molecular Surveillance of Paediatric Typhoidal Salmonella in Nepal: Antimicrobial Resistance and Implications for Vaccine Policy

scholarly article published 18 January 2018

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

scientific article published on 23 April 2018

Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia.

scientific article

Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

scientific article published on 01 April 2020

Mammalian genome evolution is governed by multiple pacemakers

scientific article

Millennia of genomic stability within the invasive Para C Lineage ofSalmonella enterica

article published in 2017

Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation

scientific article (publication date: 2011)

Molecular-clock methods for estimating evolutionary rates and timescales

scientific article published on 30 October 2014

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

scientific article

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity

scientific article

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

scientific article published on 19 July 2018

PhyloMAd: efficient assessment of phylogenomic model adequacy

scientific article published on 01 July 2018

Phylodynamic Model Adequacy Using Posterior Predictive Simulations

scientific article published in 2018

Phylodynamic model adequacy using posterior predictive simulations

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods

scientific article published on 14 July 2015

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

scientific article published in Nature Communications

Real-Time and Remote MCMC Trace Inspection with Beastiary

scientific article published in 2022

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

scientific article published on 12 September 2014

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales

scientific article published on 28 September 2015

Temporal signal and the phylodynamic threshold of SARS-CoV-2

scientific article published on 05 May 2020

Temporal signal and the phylodynamic threshold of SARS-CoV-2

scientific article published on 01 July 2020

The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas

article

The International Virus Bioinformatics Meeting 2022

publication published on 05 May 2022

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

scientific article

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

scientific article published on 01 October 2020

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant

scientific article published on 30 September 2021

The impact of calibration and clock-model choice on molecular estimates of divergence times

scientific article published on 6 June 2014

The impacts of drift and selection on genomic evolution in insects

scientific article published on 27 April 2017

The molecular clock of Mycobacterium tuberculosis

scientific article published on 12 September 2019

The paradox of HBV evolution as revealed from a 16th century mummy.

scientific article published on 4 January 2018

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

scientific article published in Nature Communications

The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus

scientific article

Time-dependent estimates of molecular evolutionary rates: evidence and causes

scientific article published in December 2015

Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes

scientific article published on 01 May 2019

Tracking the COVID-19 pandemic in Australia using genomics

scientific article published on 17 May 2020

Tracking the COVID-19 pandemic in Australia using genomics

scientific article published on 01 September 2020

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

scientific article published on 16 December 2014

Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago.

scientific article

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.

scientific article

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data

scientific article

Paulina is supported by:

About Paulina

Help