Guy Baele
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Computer Science
Guy Baele's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science University of California, Berkeley
- Bachelors Computer Science University of California, Berkeley
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(Suggest an Edit or Addition)Guy Baele'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
- Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018) (4973)
- Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018) (1923)
- Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. (2012) (951)
- The genome of Tetranychus urticae reveals herbivorous pest adaptations (2011) (874)
- Considerable escape of SARS-CoV-2 Omicron to antibody neutralization (2021) (798)
- The early spread and epidemic ignition of HIV-1 in human populations (2014) (585)
- Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. (2012) (539)
- Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts (2016) (473)
- Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary (2014) (336)
- SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. (2016) (325)
- Virus genomes reveal factors that spread and sustained the Ebola epidemic (2017) (319)
- Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 (2014) (289)
- Temporal signal and the phylodynamic threshold of SARS-CoV-2 (2020) (278)
- Genomic and epidemiological monitoring of yellow fever virus transmission potential (2018) (232)
- Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies (2022) (185)
- BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics (2019) (111)
- Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution (2013) (110)
- Considerable escape of SARS-CoV-2 Omicron to antibody neutralization (2021) (102)
- Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence (2021) (96)
- Air Travel Is Associated with Intracontinental Spread of Dengue Virus Serotypes 1–3 in Brazil (2014) (96)
- Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty. (2016) (96)
- Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 (2020) (94)
- Emerging Concepts of Data Integration in Pathogen Phylodynamics (2016) (86)
- Untangling introductions and persistence in COVID-19 resurgence in Europe (2021) (85)
- Global disparities in SARS-CoV-2 genomic surveillance (2021) (82)
- The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates (2014) (81)
- Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency (2013) (78)
- A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages (2020) (76)
- Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography (2013) (71)
- Bayesian Estimation of Past Population Dynamics in BEAST 1.10 Using the Skygrid Coalescent Model (2019) (69)
- Interspecific hybridization facilitates niche adaptation in beer yeast (2019) (65)
- Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable (2020) (63)
- Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations (2019) (59)
- Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic (2019) (56)
- A screening methodology based on Random Forests to improve the detection of gene–gene interactions (2010) (56)
- Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak (2017) (56)
- Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus (2020) (55)
- Host ecology determines the dispersal patterns of a plant virus (2015) (51)
- Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. (2015) (48)
- Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions (2021) (39)
- Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST (2017) (37)
- Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates (2019) (36)
- Relation of fibrinogen to lifestyles and to cardiovascular risk factors in a working population. (1995) (36)
- Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk (2020) (34)
- Recent advances in computational phylodynamics. (2018) (33)
- Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil (2020) (33)
- A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. (2016) (29)
- Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa (2019) (29)
- Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages — Application to rabies virus spread in Iran (2019) (28)
- A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. (2008) (28)
- πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (2013) (28)
- Stability of selected chlorinated thiazide diuretics. (2009) (28)
- Open-ended on-board Evolutionary Robotics for robot swarms (2009) (27)
- On Adaptive Self-Organization in Artificial Robot Organisms (2009) (26)
- An improved statistical method for detecting heterotachy in nucleotide sequences. (2006) (26)
- Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2021) (26)
- Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. (2020) (25)
- Seroneutralization of Omicron BA.1 and BA.2 in patients receiving anti-SARS-CoV-2 monoclonal antibodies. (2022) (25)
- Perinatal hazards of chronic antenatal tocolysis with indomethacin. (1979) (23)
- Intra-individual variability of fibrinogen levels. (1997) (22)
- Phylogenetic Factor Analysis. (2017) (22)
- The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia (2017) (21)
- Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences (2010) (20)
- Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations (2016) (19)
- Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction (2020) (19)
- Snapshot of the evolution and mutation patterns of SARS-CoV-2 (2020) (19)
- Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution (2015) (18)
- Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity (2021) (18)
- Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World (2021) (18)
- Antibody escape and global spread of SARS-CoV-2 lineage A.27 (2021) (18)
- Massive Parallelization Boosts Big Bayesian Multidimensional Scaling (2019) (18)
- Interpretation of urinary concentrations of pseudoephedrine and its metabolite cathine in relation to doping control. (2009) (18)
- Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences (2010) (17)
- Gradients do grow on trees: a linear-time 𝒪 (N)-dimensional gradient for statistical phylogenetics. (2020) (17)
- Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus (2017) (17)
- Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing (2016) (16)
- Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling (2019) (16)
- Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City (2021) (16)
- nosoi: A stochastic agent‐based transmission chain simulation framework in r (2020) (16)
- Divergence dating using mixed effects clock modelling: An application to HIV-1 (2019) (16)
- Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations (2021) (15)
- PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context (2017) (15)
- SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data (2021) (13)
- Longitudinal analysis of serum neutralization of SARS-CoV-2 Omicron BA.2, BA.4, and BA.5 in patients receiving monoclonal antibodies (2022) (13)
- Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases (2019) (13)
- Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore (2021) (13)
- Identifying predictors of time-inhomogeneous viral evolutionary processes (2016) (13)
- Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2022) (12)
- Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. (2020) (12)
- The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing (2012) (11)
- In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography (2020) (11)
- Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST (2021) (11)
- Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region (2019) (10)
- Identification of the First SARS-CoV-2 Lineage B.1.1.529 Virus Detected in Europe (2022) (10)
- Efficient Bayesian inference of general Gaussian models on large phylogenetic trees (2020) (10)
- Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework (2020) (10)
- Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic (2016) (9)
- Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics (2021) (9)
- Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses (2020) (9)
- Bayesian model selection in phylogenetics and genealogy-based population genetics (2014) (8)
- Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics (2020) (8)
- Effects of a very low-estrogen oral contraceptive on clotting factors, carbohydrate metabolism and plasma lipids and lipoproteins. (1987) (7)
- Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences (2009) (7)
- Updated vaccine protects from infection with SARS-CoV-2 variants, prevents transmission and is immunogenic against Omicron in hamsters (2022) (7)
- Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST (2019) (7)
- Management of acute puerperal inversion of the uterus with beta-mimetic drugs and prostaglandins (1978) (6)
- Intrahost speciations and host switches played an important role in the evolution of herpesviruses (2021) (6)
- Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020 (2021) (6)
- Bromocriptine in an Injectable Retard Form for Puerperal Lactation Suppression: Comparison With Estandron Prolongatum (1987) (6)
- Principled, practical, flexible, fast: A new approach to phylogenetic factor analysis (2021) (6)
- Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore (2019) (6)
- Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes (2011) (6)
- Genomic evidence of co-identification with Omicron and Delta SARS-CoV-2 variants: a report of two cases (2022) (6)
- The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020 (2021) (6)
- Complex evolutionary history of felid anelloviruses. (2021) (6)
- Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review (2021) (6)
- Human Diversity of Killer Cell Immunoglobulin-Like Receptors and Human Leukocyte Antigen Class I Alleles and Ebola Virus Disease Outcomes (2021) (5)
- Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America (2015) (5)
- High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. (2019) (5)
- Scalable Bayesian divergence time estimation with ratio transformations (2021) (5)
- Antibody escape and global spread of SARS-CoV-2 lineage A.27 (2022) (4)
- Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation (2016) (4)
- Explorer Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H 3 N 2 (2017) (4)
- Development of a transcutaneous energy and data transmission system for high power applications up to 20 watts (1999) (4)
- Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution (2012) (4)
- On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study (2021) (4)
- Blood Coagulation and Platelet-function Parameters before and during Parenteral Administration of Medroxyprogesterone Acetate as a Contraceptive Agent (1974) (4)
- Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations (2022) (4)
- Scalable Bayesian phylogenetics (2022) (3)
- Molecular epidemiology of Porcine Parvovirus Type 1 (PPV1) and the reactivity of vaccine-induced antisera against historical and current PPV1 strains (2022) (3)
- Reconstruction of the origin and dispersal of the worldwide dominant Hepatitis B Virus subgenotype D1 (2022) (3)
- Management of gravidas with idiopathic thrombocytopenic purpura. (1978) (3)
- Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study (2022) (3)
- Accommodating sampling location uncertainty in continuous phylogeography (2022) (3)
- Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics (2020) (3)
- YMrCA: Improving Y‐chromosomal ancestor time estimation for DNA kinship research (2021) (3)
- Hunting alters viral transmission and evolution in a large carnivore (2022) (3)
- The phylodynamics of SARS-CoV-2 during 2020 in Finland (2021) (3)
- Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States (2023) (2)
- Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers (2022) (2)
- Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics (2019) (2)
- Phycova — a tool for exploring covariates of pathogen spread (2022) (2)
- Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants (2022) (2)
- Two Separate Clusters of SARS-CoV-2 Delta Variant Infections in a Group of 41 Students Travelling from India: An Illustration of the Need for Rigorous Testing and Quarantine (2022) (2)
- Global phylogeographical patterns in the spread of foot-and-mouth disease virus (2019) (2)
- International travelers and genomics uncover a ‘hidden’ Zika outbreak (2018) (2)
- Many-core algorithms for high-dimensional gradients on phylogenetic trees. (2023) (1)
- Establishment and early spread of the AIDS pandemic (2014) (1)
- Data Integration in Bayesian Phylogenetics (2022) (1)
- πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (2014) (1)
- Tracing foot-and-mouth disease virus phylogeographical patterns and transmission dynamics (2019) (1)
- Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters (2022) (1)
- GuyBaele/skygrid_hmc_data: First release of BEAST XML files for skygrid+HMC (2020) (1)
- Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal (2022) (1)
- Delta-Omicron recombinant escapes therapeutic antibody neutralization (2022) (1)
- Divergent Viruses Discovered in Swine Alter the Understanding of Evolutionary History and Genetic Diversity of the Respirovirus Genus and Related Porcine Parainfluenza Viruses (2022) (1)
- Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2021) (1)
- BEAGLE 3 High-performance Computational Library for Phylogenetic Inference (2020) (1)
- Faria populations The early spread and epidemic ignition of HIV-1 in human (2014) (1)
- Adaptive MCMC for multi-partite data in Bayesian Phylogenetics (2018) (1)
- Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution (2013) (1)
- SPREAD 4: online visualisation of pathogen phylogeographic reconstructions (2022) (1)
- A bio-inspired agent-based system for controlling robot behaviour (2011) (1)
- A novel approach to modelling site dependencies: biological realism and computational complexity (2006) (0)
- Stability studies of thiazide diuretics (2008) (0)
- Detecting second-order neighboring effects in primate ancestral sequences (2013) (0)
- Statistical methods for detecting heterotachy (2005) (0)
- Inferring large-scale heterogeneous evolutionary processes through time (2013) (0)
- Zoonotic risk assessment among farmed mammals (2023) (0)
- 1 Temporal signal and the phylodynamic threshold of SARS-CoV-2 2 3 (2020) (0)
- Delta-Omicron recombinant escapes therapeutic antibody neutralization (2023) (0)
- Peer Review #1 of "Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics (v0.2)" (2021) (0)
- Stability study of thiazide diuretics (2009) (0)
- Edinburgh Explorer Inferring heterogeneous evolutionary processes through time (2014) (0)
- PROSTAGLANDIN SYNTHASE INHIBITORS IN PRETERM LABOUR (1980) (0)
- Peer Review #1 of "Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics (v0.1)" (2021) (0)
- A63 Quantifying the dynamics of evolutionary rates through time (2019) (0)
- Reconciling host and pathogen trees for a large HIV transmission chain (2013) (0)
- Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak (2018) (0)
- Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City-from Alpha to Omicron. (2023) (0)
- Random-effects substitution models for phylogenetics via scalable gradient approximations. (2023) (0)
- Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework (2013) (0)
- Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution (2011) (0)
- A Forward Agent-Based Transmission Chain Simulator [R package nosoi version 1.0.3] (2020) (0)
- Accurate model selection while accommodating phylogenetic uncertainty in Bayesian phylogenetics (2012) (0)
- SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern (2022) (0)
- Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in (2015) (0)
- Software for Systematics and Evolution (2016) (0)
- Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore (2021) (0)
- Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States (2023) (0)
- Towards Realtime Bayesian Inference for Pathogen Phylodynamics (2019) (0)
- Detection of heterotachy and its influence on phylogenetic inference within Eukaryotes (2005) (0)
- Phylogenetic modelling of temporal heterogeneity in the circulation of human influenza lineages (2015) (0)
- Full protection against all four SARS-CoV-2 variants of concern (VOC) in hamsters requires revision of spike antigen used for vaccination (2021) (0)
- Detecting complex substitution patterns in non-coding sequences (2008) (0)
- Y-chromosomal kinship estimation for forensic familial searching: YMrCA to the rescue (2022) (0)
- Inferring the migration routes of hepatitis C virus subtype 1a lineages identifies a need for pan-European prevention strategies (2018) (0)
- A Relaxed Drift Diffusion Model for Phylogenetic Trait Evolution (2015) (0)
- Alternative methods to detect gene-gene interactions (2008) (0)
- Generalized Polya Urn Process Models for Bayesian Phylogenetic Inference (2019) (0)
- Multiple-trait subsampling for optimized ancestral trait reconstruction (2022) (0)
- Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes (2021) (0)
- Global disparities in SARS-CoV-2 genomic surveillance (2022) (0)
- Modeling context-dependent evolution: the influence of the immediate flanking bases (2007) (0)
- Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes (2021) (0)
- Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies (2022) (0)
- ECCB 2010 Organization (2010) (0)
- Correction: Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review (2023) (0)
- A Flexible Bayesian Framework to Study Viral Trait Evolution (2019) (0)
- Hunting alters viral transmission and evolution (2021) (0)
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What Schools Are Affiliated With Guy Baele?
Guy Baele is affiliated with the following schools:
