Works by Duchêne, Sebastián

Results: 34

Bayesian molecular dating: opening up the black box.

Published in:

Biological Reviews, 2018, v. 93, n. 2, p. 1165, doi. 10.1111/brv.12390

By:

Bromham, Lindell;
Hua, Xia;
Duchêne, David A.;
Duchêne, Sebastián;
Ritchie, Andrew M.;
Ho, Simon Y. W.

Publication type:

Article

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

Published in:

PLoS Genetics, 2019, v. 15, n. 4, p. 1, doi. 10.1371/journal.pgen.1008114

By:

Wyres, Kelly L.;
Wick, Ryan R.;
Judd, Louise M.;
Froumine, Roni;
Tokolyi, Alex;
Gorrie, Claire L.;
Lam, Margaret M. C.;
Duchêne, Sebastián;
Jenney, Adam;
Holt, Kathryn E.

Publication type:

Article

Infectious disease phylodynamics with occurrence data.

Published in:

Methods in Ecology & Evolution, 2021, v. 12, n. 8, p. 1498, doi. 10.1111/2041-210X.13620

By:

Featherstone, Leo A.;
Di Giallonardo, Francesca;
Holmes, Edward C.;
Vaughan, Timothy G.;
Duchêne, Sebastián

Publication type:

Article

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Published in:

Genome Biology & Evolution, 2024, v. 16, n. 4, p. 1, doi. 10.1093/gbe/evae064

By:

Duchêne, David A;
Duchêne, Sebastián;
Stiller, Josefin;
Heller, Rasmus;
Ho, Simon Y W

Publication type:

Article

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Published in:

BMC Evolutionary Biology, 2016, v. 16, p. 1, doi. 10.1186/s12862-016-0688-y

By:

Duchêne, Sebastián;
Duchêne, David A.;
Di Giallonardo, Francesca;
Eden, John-Sebastian;
Geoghegan, Jemma L.;
Holt, Kathryn E.;
Ho, Simon Y. W.;
Holmes, Edward C.

Publication type:

Article

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

Published in:

BMC Evolutionary Biology, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12862-015-0312-6

By:

Duchêne, Sebastián;
Ho, Simon Y. W.;
Holmes, Edward C.

Publication type:

Article

Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing.

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 3, p. 1, doi. 10.1093/molbev/msac040

By:

Steinig, Eike;
Duchêne, Sebastián;
Aglua, Izzard;
Greenhill, Andrew;
Ford, Rebecca;
Yoannes, Mition;
Jaworski, Jan;
Drekore, Jimmy;
Urakoko, Bohu;
Poka, Harry;
Wurr, Clive;
Ebos, Eri;
Nangen, David;
Manning, Laurens;
Laman, Moses;
Firth, Cadhla;
Smith, Simon;
Pomat, William;
Tong, Steven Y C;
Coin, Lachlan

Publication type:

Article

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

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 4, p. 1202, doi. 10.1093/molbev/msz291

By:

Duchêne, David A;
Tong, K Jun;
Foster, Charles S P;
Duchêne, Sebastián;
Lanfear, Robert;
Ho, Simon Y W

Publication type:

Article

Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes.

Published in:

Molecular Biology & Evolution, 2019, v. 36, n. 5, p. 942, doi. 10.1093/molbev/msz021

By:

Yuen, Lilly K W;
Littlejohn, Margaret;
Duchêne, Sebastián;
Edwards, Rosalind;
Bukulatjpi, Sarah;
Binks, Paula;
Jackson, Kathy;
Davies, Jane;
Davis, Joshua S;
Tong, Steven Y C;
Locarnini, Stephen

Publication type:

Article

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

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 7, p. 1895, doi. 10.1093/molbev/msv056

By:

Duchêne, Sebastián;
Duchêne, David;
Holmes, Edward C.;
Ho, Simon Y.W.

Publication type:

Article

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

Published in:

Molecular Ecology, 2015, v. 24, n. 24, p. 6007, doi. 10.1111/mec.13450

By:

Ho, Simon Y. W.;
Duchêne, Sebastián;
Molak, Martyna;
Shapiro, Beth

Publication type:

Article

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

Published in:

Molecular Ecology, 2015, v. 24, n. 15, p. 3964, doi. 10.1111/mec.13284

By:

Morin, Phillip A.;
Parsons, Kim M.;
Archer, Frederick I.;
Ávila‐Arcos, María C.;
Barrett‐Lennard, Lance G.;
Dalla Rosa, Luciano;
Duchêne, Sebastián;
Durban, John W.;
Ellis, Graeme M.;
Ferguson, Steven H.;
Ford, John K.;
Ford, Michael J.;
Garilao, Cristina;
Gilbert, M. Thomas P.;
Kaschner, Kristin;
Matkin, Craig O.;
Petersen, Stephen D.;
Robertson, Kelly M.;
Visser, Ingrid N.;
Wade, Paul R.

Publication type:

Article

Molecular-clock methods for estimating evolutionary rates and timescales.

Published in:

Molecular Ecology, 2014, v. 23, n. 24, p. 5947, doi. 10.1111/mec.12953

By:

Ho, Simon Y. W.;
Duchêne, Sebastián

Publication type:

Article

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 4, p. 688, doi. 10.1111/1755-0998.12320

By:

Ho, Simon Y. W.;
Duchêne, Sebastián;
Duchêne, David

Publication type:

Article

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

Published in:

Systematic Biology, 2018, v. 67, n. 3, p. 400, doi. 10.1093/sysbio/syx076

By:

DUCHÊNE, DAVID A.;
BRAGG, JASON G.;
DUCHÊNE, SEBASTIÁN;
NEAVES, LINDA E.;
POTTER, SALLY;
MORITZ, CRAIG;
JOHNSON, REBECCA N.;
HO, SIMON Y. W.;
ELDRIDGE, MARK D. B.

Publication type:

Article

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 4, p. 1, doi. 10.1371/journal.pcbi.1006650

By:

Bouckaert, Remco;
Vaughan, Timothy G.;
Barido-Sottani, Joëlle;
Duchêne, Sebastián;
Fourment, Mathieu;
Gavryushkina, Alexandra;
Heled, Joseph;
Jones, Graham;
Kühnert, Denise;
De Maio, Nicola;
Matschiner, Michael;
Mendes, Fábio K.;
Müller, Nicola F.;
Ogilvie, Huw A.;
du Plessis, Louis;
Popinga, Alex;
Rambaut, Andrew;
Rasmussen, David;
Siveroni, Igor;
Suchard, Marc A.

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 1017

By:

Duchêne, Sebastián;
Molak, Martyna;
Ho, Simon Y. W.

Publication type:

Article

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

Published in:

Virologica Sinica (16740769), 2019, v. 34, n. 1, p. 1, doi. 10.1007/s12250-018-0078-2

By:

Hu, Tao;
Li, Juan;
Carr, Michael J.;
Duchêne, Sebastián;
Shi, Weifeng

Publication type:

Article

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

Published in:

BMC Evolutionary Biology, 2018, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12862-018-1192-3

By:

Tong, K. Jun;
Duchêne, David A.;
Duchêne, Sebastián;
Geoghegan, Jemma L.;
Ho, Simon Y. W.

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3375, doi. 10.1093/bioinformatics/btw421

By:

Duchêne, Sebastián;
Geoghegan, Jemma L.;
Holmes, Edward C.;
Ho, Simon Y. W.

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 9, p. 1281, doi. 10.1093/bioinformatics/btw005

By:

Duchêne, Sebastián;
Foster, Charles S. P.;
Ho, Simon Y. W.

Publication type:

Article

Phylogenetics: Mammalian genome evolution is governed by multiple pacemakers.

Published in:

Bioinformatics, 2015, v. 31, n. 13, p. 2061, doi. 10.1093/bioinformatics/btv121

By:

Duchêne, Sebastián;
Ho, Simon Y. W.

Publication type:

Article

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

Published in:

2016

By:

Liu, Wenjun;
Pickering, Paul;
Duchêne, Sebastián;
Holmes, Edward C;
Aaskov, John G

Publication type:

journal article

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

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-20235-8

By:

Geoghegan, Jemma L.;
Ren, Xiaoyun;
Storey, Matthew;
Hadfield, James;
Jelley, Lauren;
Jefferies, Sarah;
Sherwood, Jill;
Paine, Shevaun;
Huang, Sue;
Douglas, Jordan;
Mendes, Fábio K.;
Sporle, Andrew;
Baker, Michael G.;
Murdoch, David R.;
French, Nigel;
Simpson, Colin R.;
Welch, David;
Drummond, Alexei J.;
Holmes, Edward C.;
Duchêne, Sebastián

Publication type:

Article

Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats.

Published in:

Viruses (1999-4915), 2021, v. 13, n. 2, p. 252, doi. 10.3390/v13020252

By:

Bergner, Laura M.;
Mollentze, Nardus;
Orton, Richard J.;
Tello, Carlos;
Broos, Alice;
Biek, Roman;
Streicker, Daniel G.;
Eden, John-Sebastian;
Duchêne, Sebastián;
Shi, Mang

Publication type:

Article

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

Published in:

Viruses (1999-4915), 2019, v. 11, n. 5, p. 482, doi. 10.3390/v11050482

By:

Di Giallonardo, Francesca;
Pinto, Angie N.;
Keen, Phillip;
Shaik, Ansari;
Carrera, Alex;
Salem, Hanan;
Telfer, Barbara;
Cooper, Craig;
Price, Karen;
Selvey, Christine;
Holden, Joanne;
Bachmann, Nadine;
Lee, Frederick J.;
Dwyer, Dominic E.;
Duchêne, Sebastián;
Holmes, Edward C.;
Grulich, Andrew E.;
Kelleher, Anthony D.

Publication type:

Article

The Temporal Evolution and Global Spread of <i>Cauliflower mosaic virus</i>, a Plant Pararetrovirus.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0085641

By:

Yasaka, Ryosuke;
Nguyen, Huy D.;
Ho, Simon Y. W.;
Duchêne, Sebastián;
Korkmaz, Savas;
Katis, Nikolaos;
Takahashi, Hideki;
Gibbs, Adrian J.;
Ohshima, Kazusato

Publication type:

Article

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0055336

By:

Nguyen, Huy D.;
Tomitaka, Yasuhiro;
Ho, Simon Y. W.;
Duchêne, Sebastián;
Vetten, Heinrich-Josef;
Lesemann, Dietrich;
Walsh, John A.;
Gibbs, Adrian J.;
Ohshima, Kazusato

Publication type:

Article

Phylogeography and Sex-Biased Dispersal across Riverine Manatee Populations (Trichechus inunguis and Trichechus manatus) in South America.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0052468

By:

Satizábal, Paula;
Mignucci-Giannoni, Antonio A.;
Duchêne, Sebastián;
Caicedo-Herrera, Dalila;
Perea-Sicchar, Carlos M.;
García-Dávila, Carmen R.;
Trujillo, Fernando;
Caballero, Susana J.

Publication type:

Article

Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation.

Published in:

PLoS ONE, 2011, v. 6, n. 11, p. 1, doi. 10.1371/journal.pone.0027138

By:

Duchêne, Sebastián;
Archer, Frederick I.;
Vilstrup, Julia;
Caballero, Susana;
Morin, Phillip A.

Publication type:

Article

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

Published in:

2018

By:

Geoghegan, Jemma L.;
Saavedra, Aldo F.;
Duchêne, Sebastián;
Sullivan, Sheena;
Barr, Ian;
Holmes, Edward C.

Publication type:

Correction Notice

Continental synchronicity of human influenza virus epidemics despite climactic variation.

Published in:

PLoS Pathogens, 2018, v. 14, n. 1, p. 1, doi. 10.1371/journal.ppat.1006780

By:

Geoghegan, Jemma L.;
Saavedra, Aldo F.;
Duchêne, Sebastián;
Sullivan, Sheena;
Barr, Ian;
Holmes, Edward C.

Publication type:

Article

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

Published in:

PLoS Pathogens, 2017, v. 13, n. 2, p. 1, doi. 10.1371/journal.ppat.1006215

By:

Geoghegan, Jemma L.;
Duchêne, Sebastián;
Holmes, Edward C.

Publication type:

Article

Region‐specific diversification dynamics and biogeographic history of one of the most diverse families of insects.

Published in:

Systematic Entomology, 2025, v. 50, n. 1, p. 206, doi. 10.1111/syen.12651

By:

Ghanavi, Hamid Reza;
Chazot, Nicolas;
Sanmartín, Isabel;
Murillo‐Ramos, Leidys;
Duchêne, Sebastián;
Sihvonen, Pasi;
Brehm, Gunnar;
Wahlberg, Niklas

Publication type:

Article