Alexei J. Drummond

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All published works

Action	Title	Year	Authors
+ PDF Chat	Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia	2022	Cinthy L. Jiménez-Silva Ricardo Rivero Jordan Douglas Remco Bouckaert Julian Villabona-Arenas Katherine E. Atkins Bertha Gastelbondo Alfonso Calderón Camilo Guzmán Daniel Echeverri-De la Hoz
+	TreeFlow: probabilistic programming and automatic differentiation for phylogenetics	2022	Christiaan Swanepoel Mathieu Fourment Ji Xiang Hassan Nasif Marc A. Suchard F. A. Matsen Alexei J. Drummond
+	Bayesian inference of the climbing grade scale.	2021	Alexei J. Drummond Alex Popinga
+ PDF Chat	Bayesian inference of the climbing grade scale	2021	Alexei J. Drummond Alex Popinga
+	Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	2021	Jordan Douglas Fábio K. Mendes Remco Bouckaert Dong Xie Cinthy L. Jiménez-Silva Christiaan Swanepoel Joep de Ligt Xiaoyun Ren Matt Storey James Hadfield
+	Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing	2021	Tara Swadi Jemma L. Geoghegan Tom Devine Caroline McElnay Jillian Sherwood Phil Shoemack Xiaoyun Ren Matt Storey Sarah Jefferies Erasmus Smit
+	Bayesian inference of the climbing grade scale	2021	Alexei J. Drummond Alex Popinga
+ PDF Chat	Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand	2020	Jemma L. Geoghegan Xiaoyun Ren Matthew Storey James Hadfield Lauren Jelley Sarah Jefferies Jill Sherwood Shevaun Paine Q. Sue Huang Jordan Douglas
+	A case study of extended in-flight transmission of SARS-CoV-2 en route to Aotearoa New Zealand	2020	Tara Swadi Jemma L. Geoghegan Tom Devine Caroline McElnay Phil Shoemack Xiaoyun Ren Matt Storey Sarah Jefferies Jillian Sherwood Erasmus Smit
+	Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand	2020	Jemma L. Geoghegan Xiaoyun Ren Matthew Storey James Hadfield Lauren Jelley Sarah Jefferies Jill Sherwood Shevaun Paine Q. Sue Huang Jordan Douglas
+	Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations	2020	Jordan Douglas Fábio K. Mendes Remco Bouckaert Dong Xie Cinthy L. Jiménez-Silva Christiaan Swanepoel Joep de Ligt Xiaoyun Ren Matt Storey James Hadfield
+ PDF Chat	Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration	2019	Jing Yang Nicola F. Müller Remco Bouckaert Bing Xu Alexei J. Drummond
+ PDF Chat	Estimating Epidemic Incidence and Prevalence from Genomic Data	2019	Timothy G. Vaughan Gabriel E. Leventhal David A. Rasmussen Alexei J. Drummond David Welch Tanja Stadler
+	Directly Estimating Epidemic Curves From Genomic Data	2017	Timothy G. Vaughan Gabriel E. Leventhal David A. Rasmussen Alexei J. Drummond David Welch Tanja Stadler
+	Estimating epidemic incidence and prevalence from genomic data	2017	Timothy G. Vaughan Gabriel E. Leventhal David A. Rasmussen Alexei J. Drummond David Welch Tanja Stadler
+	The fossilized birth-death model for the analysis of stratigraphic range data under different speciation concepts	2017	Tanja Stadler Alexandra Gavryushkina Rachel C. M. Warnock Alexei J. Drummond Tracy A. Heath
+ PDF Chat	Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins	2016	Alexandra Gavryushkina Tracy A. Heath Daniel T. Ksepka Tanja Stadler David Welch Alexei J. Drummond
+ PDF Chat	Bayesian phylogenetic estimation of fossil ages	2016	Alexei J. Drummond Tanja Stadler
+	The space of ultrametric phylogenetic trees	2016	Alex Gavryushkin Alexei J. Drummond
+ PDF Chat	Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods	2016	Huw A. Ogilvie Joseph Heled Dong Xie Alexei J. Drummond
+	Bayesian phylogenetic estimation of fossil ages	2016	Alexei J. Drummond Tanja Stadler
+	Bayesian phylogenetic estimation of fossil ages	2016	Alexei J. Drummond Tanja Stadler
+ PDF Chat	Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models	2014	Alex Popinga Tim Vaughan Tanja Stadler Alexei J. Drummond
+ PDF Chat	Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration	2014	Alexandra Gavryushkina David Welch Tanja Stadler Alexei J. Drummond
+	Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference	2014	Joseph Heled Alexei J. Drummond
+	Bayesian Coalescent Epidemic Inference: Comparison of Stochastic and Deterministic SIR Population Dynamics	2014	Alex Popinga Tim Vaughan Tanja Stadler Alexei J. Drummond
+ PDF Chat	Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model	2014	Denise Kühnert Tanja Stadler Timothy G. Vaughan Alexei J. Drummond
+	Calibrated birth-death phylogenetic time-tree priors for Bayesian inference	2013	Joseph Heled Alexei J. Drummond
+	Calibrated birth-death phylogenetic time-tree priors for Bayesian inference	2013	Joseph Heled Alexei J. Drummond
+	Phylogenetic and epidemic modeling of rapidly evolving infectious diseases	2011	Denise Kühnert Chieh‐Hsi Wu Alexei J. Drummond
+ PDF Chat	Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation	2011	Joseph Heled Alexei J. Drummond
+	Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation	2011	Joseph Heled Alexei J. Drummond
+	Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation	2011	Joseph Heled Alexei J. Drummond
+	Exploring viral infection dynamics using the Poisson representation	2009	Timothy G. Vaughan P. D. Drummond Alexei J. Drummond
+	Extinction in a canonical self-regulating population with demographic and environmental noise	2008	Alexei J. Drummond P. D. Drummond
+	Extinction in a self-regulating population with demographic and environmental noise	2008	Alexei J. Drummond P. D. Drummond
+	A new method for tackling the stochastic dynamics of viral infection	2008	Timothy G. Vaughan P. D. Drummond Alexei J. Drummond

Common Coauthors

Coauthor	Papers Together
Tanja Stadler	12
David Welch	11
Joseph Heled	7
Jemma L. Geoghegan	6
Timothy G. Vaughan	6
Xiaoyun Ren	6
Joep de Ligt	6
James Hadfield	6
Colin R Simpson	6
Alex Popinga	5
Jordan Douglas	5
Q. Sue Huang	4
Lauren Jelley	4
Edward C. Holmes	4
P. D. Drummond	4
Sarah Jefferies	4
Matt Storey	4
Fábio K. Mendes	4
Andrew Sporle	4
Nigel French	4
Alexandra Gavryushkina	3
Remco Bouckaert	3
Cinthy L. Jiménez-Silva	3
Dong Xie	3
Gabriel E. Leventhal	3
David A. Rasmussen	3
Tara Swadi	2
Denise Kühnert	2
Jillian Sherwood	2
Michael G. Baker	2
Caroline McElnay	2
Kip Mouldey	2
Gerard J.B. Sonder	2
Tom Devine	2
Aoife Kenny	2
Jill Sherwood	2
Sebastián Duchêne	2
Andrea McNeill	2
David R. Murdoch	2
Christiaan Swanepoel	2
Shevaun Paine	2
Phil Shoemack	2
G. Edwin Reynolds	2
Erasmus Smit	2
Tracy A. Heath	2
Tim Vaughan	2
Matthew Storey	2
Lindsay Lowe	2
Juan David Ramírez	1
Rachel C. M. Warnock	1

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration	2014	Alexandra Gavryushkina David Welch Tanja Stadler Alexei J. Drummond	8
+ PDF Chat	The conditioned reconstructed process	2008	Tanja Gernhard	7
+ PDF Chat	Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins	2016	Alexandra Gavryushkina Tracy A. Heath Daniel T. Ksepka Tanja Stadler David Welch Alexei J. Drummond	6
+ PDF Chat	Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation	2011	Joseph Heled Alexei J. Drummond	6
+ PDF Chat	Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model	2014	Denise Kühnert Tanja Stadler Timothy G. Vaughan Alexei J. Drummond	6
+ PDF Chat	Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series	2011	David A. Rasmussen Oliver Ratmann Katia Koelle	6
+	A contribution to the mathematical theory of epidemics	1927	W. O. Kermack A. G. McKendrick	5
+ PDF Chat	Particle Markov Chain Monte Carlo Methods	2010	Christophe Andrieu Arnaud Doucet Roman Holenstein	5
+ PDF Chat	Phylodynamic Inference for Structured Epidemiological Models	2014	David A. Rasmussen Erik Volz Katia Koelle	5
+ PDF Chat	Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing	2020	Luca Ferretti Chris Wymant Michelle Kendall Lele Zhao Anel Nurtay Lucie Abeler‐Dörner Michael Parker David Bonsall Christophe Fraser	4
+ PDF Chat	The fossilized birth–death process for coherent calibration of divergence-time estimates	2014	Tracy A. Heath John P. Huelsenbeck Tanja Stadler	4
+	Exact stochastic simulation of coupled chemical reactions	1977	Daniel T. Gillespie	4
+	Modeling Infectious Diseases in Humans and Animals	2011	Matt J. Keeling Pejman Rohani	3
+ PDF Chat	Virus genomes reveal factors that spread and sustained the Ebola epidemic	2017	Gytis Dudas Luiz Max Carvalho Trevor Bedford Andrew J. Tatem Guy Baele Nuno R. Faria Daniel J. Park Jason T. Ladner Armando Arias Danny Asogun	3
+ PDF Chat	Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone	2015	Daniel J. Park Gytis Dudas Shirlee Wohl Augustine Goba Shannon Whitmer Kristian G. Andersen Rachel Sealfon Jason T. Ladner Jeffrey R. Kugelman Christian B. Matranga	3
+ PDF Chat	Coalescent inference for infectious disease: meta-analysis of hepatitis C	2013	Bethany L. Dearlove Daniel J. Wilson	3
+	Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference	2014	Joseph Heled Alexei J. Drummond	3
+ PDF Chat	GISAID: Global initiative on sharing all influenza data – from vision to reality	2017	Yuelong Shu John W. McCauley	3
+	The pseudo-marginal approach for efficient Monte Carlo computations	2009	Christophe Andrieu Gareth O. Roberts	3
+ PDF Chat	Temporal dynamics in viral shedding and transmissibility of COVID-19	2020	Xi He Eric H. Y. Lau Peng Wu Xilong Deng Jian Wang Xinxin Hao Yiu Chung Lau Jessica Y. Wong Yujuan Guan Xinghua Tan	2
+	Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies	2013	Peter J. Wagner Jonathan D. Marcot	2
+	Estimating the Cumulative Incidence of COVID-19 in the United States Using Four Complementary Approaches	2020	Fred Lu André T. Nguyen Nicholas Link Jessica T. Davis Matteo Chinazzi Xinyue Xiong Alessandro Vespignani Marc Lipsitch Mauricio Santillana	2
+ PDF Chat	Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China	2020	Joseph T. Wu Kathy Leung Mary Bushman Nishant Kishore René Niehus Pablo M. De Salazar Benjamin J. Cowling Marc Lipsitch GM Leung	2
+ PDF Chat	Covid-19: identifying and isolating asymptomatic people helped eliminate virus in Italian village	2020	Michael Day	2
+ PDF Chat	Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020	2020	Kenji Mizumoto Katsushi Kagaya Alexander E. Zarebski Gerardo Chowell	2
+	Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2)	2020	Ruiyun Li Sen Pei Бин Чэн Yimeng Song Zhang Tao Wan Yang Jeffrey Shaman	2
+	The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak	2020	Hussin A. Rothan Siddappa N. Byrareddy	2
+ PDF Chat	Covid-19: four fifths of cases are asymptomatic, China figures indicate	2020	Michael Day	2
+ PDF Chat	Estimate of the Basic Reproduction Number for COVID-19: A Systematic Review and Meta-analysis	2020	Yousef Alimohamadi Maryam Taghdir Mojtaba Sepandi	2
+	Estimates of the severity of coronavirus disease 2019: a model-based analysis	2020	Robert Verity Lucy Okell Ilaria Dorigatti Peter Winskill Charles Whittaker Natsuko Imai Gina Cuomo-Dannenburg Hayley Thompson Patrick Walker Han Fu	2
+ PDF Chat	Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020	2020	Timothy Russell Joel Hellewell Christopher I Jarvis Kevin van Zandvoort Sam Abbott Ruwan Ratnayake Stefan Flasche Rosalind M. Eggo W. John Edmunds Adam J. Kucharski	2
+	What settings have been linked to SARS-CoV-2 transmission clusters?	2020	Quentin J. Leclerc Naomi M. Fuller Lisa E. Knight Sebastian Funk Gwenan M. Knight	2
+ PDF Chat	Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic	2016	Gytis Dudas Luiz Max Carvalho Trevor Bedford Andrew J. Tatem Guy Baele Nuno R. Faria Daniel J. Park Jason T. Ladner Armando Arias Danny Asogun	2
+	The expected length of pendant and interior edges of a Yule tree	2010	Mike Steel Arne Ø. Mooers	2
+ PDF Chat	The reproductive number of COVID-19 is higher compared to SARS coronavirus	2020	Ying Liu Alberto Alexander Gayle Annelies Wilder‐Smith Joacim Rocklöv	2
+ PDF Chat	Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography	2014	Filip Bielejec Philippe Lemey Guy Baele Andrew Rambaut Marc A. Suchard	2
+	Geometry of the space of phylogenetic trees	2000	Louis J. Billera Susan Holmes Karen Vogtmann	2
+ PDF Chat	Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts	2020	Joel Hellewell Sam Abbott Amy Gimma Nikos I Bosse Christopher I Jarvis Timothy Russell James D. Munday Adam J. Kucharski W. John Edmunds Sebastian Funk	2
+ PDF Chat	Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data	2014	Daniele Silvestro Jan Schnitzler Lee Hsiang Liow Alexandre Antonelli Nicolas Salamin	2
+ PDF Chat	A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data	2011	Heng Li	2
+ PDF Chat	A Fast Algorithm for Computing Geodesic Distances in Tree Space	2010	Megan Owen J. Scott Provan	2
+	The Mathematics of Infectious Diseases	2000	Herbert W. Hethcote	2
+	Contributions to the mathematical theory of epidemics. II. —The problem of endemicity	1932	W. O. Kermack A. G. McKendrick	2
+ PDF Chat	Rates of coalescence for common epidemiological models at equilibrium	2011	Katia Koelle David A. Rasmussen	2
+	Monte Carlo sampling methods using Markov chains and their applications	1970	W. Keith Hastings	2
+ PDF Chat	Evolution of discrete populations and the canonical diffusion of adaptive dynamics	2007	Nicolas Champagnat Amaury Lambert	2
+	Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans	2006	Katia Koelle Sarah Cobey Bryan T. Grenfell Mercedes Pascual	2
+ PDF Chat	Mathematical models of infectious disease transmission	2008	Nicholas C. Grassly Christophe Fraser	2
+ PDF Chat	The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak	2020	Matteo Chinazzi Jessica T. Davis Marco Ajelli Corrado Gioannini Maria Litvinova Stefano Merler Ana Pastore y Piontti Kunpeng Mu Luca Rossi Kaiyuan Sun	2
+	Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2	2020	Alessia Lai Annalisa Bergna Carla Acciarri Massimo Galli Gianguglielmo Zehender	2