Alexei J. Drummond
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Computational biologist in New Zealand
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Alexei J. Drummondcomputer-science Degrees
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Alexei J. Drummondbiology Degrees
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Computer Science Biology
Alexei J. Drummond's Degrees
- PhD Computational Biology University of Auckland
- Bachelors Computer Science University of Auckland
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Why Is Alexei J. Drummond Influential?
(Suggest an Edit or Addition)Alexei J. Drummond'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
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data (2012) (14597)
- BEAST: Bayesian evolutionary analysis by sampling trees (2007) (11768)
- Bayesian Phylogenetics with BEAUti and the BEAST 1.7 (2012) (8908)
- Relaxed Phylogenetics and Dating with Confidence (2006) (5634)
- Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018) (4973)
- BEAST 2: A Software Platform for Bayesian Evolutionary Analysis (2014) (4854)
- Bayesian coalescent inference of past population dynamics from molecular sequences. (2005) (2792)
- Bayesian Inference of Species Trees from Multilocus Data (2009) (2328)
- Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018) (1923)
- BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018) (1760)
- Bayesian Phylogeography Finds Its Roots (2009) (1452)
- Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. (2005) (990)
- Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. (2002) (968)
- Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. (2006) (695)
- Bayesian inference of population size history from multiple loci (2008) (668)
- Rise and Fall of the Beringian Steppe Bison (2004) (647)
- Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement (2009) (617)
- Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. (2012) (539)
- Mapping the Origins and Expansion of the Indo-European Language Family (2012) (522)
- bModelTest: Bayesian phylogenetic site model averaging and model comparison (2016) (495)
- Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) (2012) (404)
- Bayesian random local clocks, or one rate to rule them all (2010) (389)
- Measurably evolving populations (2003) (370)
- Bayesian Evolutionary Analysis with BEAST (2015) (350)
- Rates of Evolution in Ancient DNA from Adélie Penguins (2002) (314)
- StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016) (309)
- Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation (2011) (284)
- Evidence for time dependency of molecular rate estimates. (2007) (276)
- The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. (2003) (260)
- Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins (2015) (255)
- mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. (2008) (255)
- Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration (2014) (251)
- Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus (2007) (217)
- Estimating the basic reproductive number from viral sequence data. (2012) (197)
- Inference of viral evolutionary rates from molecular sequences. (2003) (181)
- Bayesian coestimation of phylogeny and sequence alignment (2005) (176)
- Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics (2007) (174)
- PAL: an object-oriented programming library for molecular evolution and phylogenetics (2001) (173)
- Guided tree topology proposals for Bayesian phylogenetic inference. (2012) (171)
- Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis (2003) (165)
- The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography (2009) (158)
- Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. (2005) (155)
- A Virus Reveals Population Structure and Recent Demographic History of Its Carnivore Host (2006) (144)
- Evaluating a multigene environmental DNA approach for biodiversity assessment (2015) (140)
- Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. (2007) (139)
- The Molecular Population Genetics of HIV-1 Group O (2004) (138)
- Bayesian Inference of Species Networks from Multilocus Sequence Data (2017) (133)
- Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. (2005) (132)
- A Bayesian phylogenetic method to estimate unknown sequence ages. (2011) (123)
- Epidemic dynamics revealed in dengue evolution. (2010) (115)
- Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics (2011) (114)
- Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model (2013) (110)
- Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand (2020) (107)
- Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods (2015) (105)
- Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data (2016) (102)
- Efficient Bayesian inference under the structured coalescent (2014) (99)
- Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B (2006) (98)
- Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. (2000) (96)
- Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa (2009) (94)
- Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars (2003) (88)
- Influenza A Virus Migration and Persistence in North American Wild Birds (2013) (88)
- The Phylogenetic Handbook: Bayesian evolutionary analysis by sampling trees (2009) (84)
- The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates (2014) (81)
- The Evolutionary Genetics of Viral Emergence (2007) (80)
- Phylogenetic and epidemic modeling of rapidly evolving infectious diseases (2011) (79)
- Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1 (2006) (78)
- Divergence time estimates for major cephalopod groups: evidence from multiple genes (2006) (78)
- Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection (2006) (69)
- Taming the BEAST—A Community Teaching Material Resource for BEAST 2 (2017) (66)
- Accommodating the effect of ancient DNA damage on inferences of demographic histories. (2009) (64)
- The inference of stepwise changes in substitution rates using serial sequence samples. (2001) (63)
- The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes (2017) (60)
- Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference (2013) (57)
- A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics (2013) (56)
- Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo (2011) (53)
- Statistical Alignment: Recent Progress, New Applications, and Challenges (2005) (52)
- Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing (2021) (48)
- Explorer BEAST : Bayesian evolutionary analysis by sampling trees (2017) (46)
- Simulating gene trees under the multispecies coalescent and time-dependent migration (2013) (46)
- Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity (2018) (41)
- The founding charter of the Genomic Observatories Network (2014) (40)
- How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships? (2010) (40)
- Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments (2012) (39)
- DRAFT - Bayesian Evolutionary Analysis with BEAST 2 (2015) (38)
- The space of ultrametric phylogenetic trees. (2014) (37)
- Clock-constrained tree proposal operators in Bayesian phylogenetic inference (2008) (34)
- BEAST2: Bayesian evolutionary analysis sampling trees (2014) (34)
- Estimating Epidemic Incidence and Prevalence from Genomic Data (2018) (33)
- Neotenous origins for pelagic octopuses (2004) (33)
- Inferring Ancestral Recombination Graphs from Bacterial Genomic Data (2016) (33)
- How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? (2015) (32)
- Fully Bayesian tests of neutrality using genealogical summary statistics (2008) (30)
- Bayesian phylogenetic estimation of fossil ages (2016) (30)
- Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models (2014) (28)
- Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model (2003) (26)
- Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA (2005) (25)
- Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. (2019) (24)
- Phylodynamic Model Adequacy Using Posterior Predictive Simulations (2018) (21)
- Extinction times in autocatalytic systems. (2010) (20)
- Ancient DNA: Would the Real Neandertal Please Stand up? (2004) (20)
- Inferring evolutionary rates using serially sampled sequences from several populations. (2003) (20)
- SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination (2018) (19)
- Improving the performance of Bayesian phylogenetic inference under relaxed clock models (2020) (18)
- Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand (2021) (18)
- Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations (2021) (18)
- Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene (2020) (15)
- A case study of extended in-flight transmission of SARS-CoV-2 en route to Aotearoa New Zealand (2020) (13)
- Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration (2019) (12)
- Recursive algorithms for phylogenetic tree counting (2013) (12)
- Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations (2020) (11)
- Inferring Species Trees Using Integrative Models of Species Evolution (2018) (10)
- Genealogies from Time-Stamped Sequence Data (2004) (10)
- Inference of species histories in the presence of gene flow (2018) (9)
- Inferring host roles in bayesian phylodynamics of global avian influenza A virus H9N2. (2019) (8)
- Within-host demographic fluctuations and correlations in early retroviral infection. (2012) (8)
- Tree measures and the number of segregating sites in time-structured population samples (2005) (6)
- Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales (2021) (6)
- Computational statistical inference for molecular evolution and population genetics. (2002) (6)
- Joint inference of microsatellite mutation models, population history and genealogies using trans-dimensional MCMC (2011) (5)
- Faculty Opinions recommendation of Distribution of fitness and virulence effects caused by single-nucleotide substitutions in Tobacco Etch virus. (2008) (5)
- The evolutionary analysis of measurably evolving populations using serially sampled gene sequences (2007) (5)
- Bayesian inference and comparison of stochastic transcription elongation models (2020) (4)
- Estimating species trees from multilocus data (2015) (4)
- EVOLUTION OF THE HIV-1 ENVELOPE GENE IS DOMINATED BY PURIFYING SELECTION (2006) (4)
- Directly Estimating Epidemic Curves From Genomic Data (2017) (4)
- The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand (2020) (3)
- Bayesian Coalescent Epidemic Inference: Comparison of Stochastic and Deterministic SIR Population Dynamics (2014) (3)
- Bayesian Evolutionary Analysis with BEAST: Evolutionary trees (2015) (3)
- A brief introduction to the Phylogenetic Analysis Library version 1.5 (2004) (3)
- Bayesian phylodynamics of avian influenza virus H9N2 in Asia with time-dependent predictors of migration (2018) (3)
- Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. (2014) (3)
- Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia (2022) (2)
- Joint inference of species histories and gene flow (2018) (2)
- Posterior analysis and post-processing (2015) (2)
- Phylogenetic analysis reveals coincidence of the expansion of very virulent Infectious Bursal Disease Virus and the reassortment of its genome segment B (2006) (2)
- Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution (2022) (2)
- Scalable total-evidence inference from molecular and continuous characters in a Bayesian framework (2021) (2)
- Recursive algorithms for phylogenetic tree (2013) (2)
- Field validation of phylodynamic analytical methods for inference on epidemiological processes in wildlife (2020) (1)
- Approximate Bayesian computation of transcriptional pausing mechanisms (2019) (1)
- Substitution and site models (2015) (1)
- Bayesian inference of ancestral recombination graphs for bacterial populations (2016) (1)
- Extinction in a self-regulating population with demographic and environmental noise (2008) (1)
- Inferring phylogenies: an instant classic (2004) (1)
- Recursive algorithms for phylogenetic tree counting (2013) (1)
- Bayesian inference and comparison of transcription elongation stochastic models (2018) (1)
- Ignoring errors causes inaccurate timing of single-cell phylogenies (2021) (1)
- Molecular Clock (2021) (1)
- LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses (2022) (1)
- Evaluation of proposal distributions on clock-constrained trees in Bayesian phylogenetic inference (2008) (1)
- Structured trees and phylogeography (2015) (1)
- Simulating gene trees under the multispecies coalescent and time-dependent migration (2013) (1)
- For consideration as a Research Article (2010) (0)
- Sifting Through Tangled Trees: Bayesian Reconstruction of Cophylogenies (2015) (0)
- Bayesian inference of the climbing grade scale (2021) (0)
- Getting started with BEAST 2 (2015) (0)
- TreeFlow: probabilistic programming and automatic differentiation for phylogenetics (2022) (0)
- A new method for tackling the stochastic dynamics of viral infection (2008) (0)
- Exploring phylogenetic tree space (2015) (0)
- A retrodictive stochastic simulation algorithm (2010) (0)
- Extinction in a canonical self-regulating population with demographic and environmental noise (2008) (0)
- Estimating Mutation Parameters and Population History Simultaneously from Temporally-Spaced Genome Data (2016) (0)
- Coding and design patterns (2015) (0)
- Reconciling host and pathogen trees for a large HIV transmission chain (2013) (0)
- ADVANCES IN PARASITOLOGY, VOL 54 (2003) (0)
- Manuscript Type: Letter (2008) (0)
- Supplementary Data Files (2015) (0)
- A Brief Introduction to the Phylogentics Analysis Library V1.5 (2004) (0)
- Exploring viral infection dynamics using the Poisson representation (2009) (0)
- MBE methodology became available allowing for sequences being sampled sequentially through time ( Rambaut 2000 ) , allowing for changing population sizes through time ( (2018) (0)
- Accounting for errors in data improves timing in single-cell cancer evolution (2022) (0)
- Setting up and running a phylogenetic analysis (2015) (0)
- Tracing virus migration using Bayesian phylogeographic inference (2007) (0)
- 21 st New Zealand Phylogenomics Meeting (2017) (0)
- bModelTest: Bayesian phylogenetic site model averaging and model comparison (2017) (0)
- Combined inference of epidemic trajectories, parameters and phylogenetic trees from viral genomes (2016) (0)
- Explorer Bayesian Phylogeography Finds Its Roots (2017) (0)
- Evidences of the Recombinant Origin of a Bat SARS-like Coronavirus and its 2 Implications on the Direct Ancestor of SARS Coronavirus 3 4 Running title: 5 (2007) (0)
- Improving the performance of Bayesian phylogenetic inference under relaxed clock models (2020) (0)
- Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework (2013) (0)
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