Sebastián Duchêne

The limits of Bayesian estimates of divergence times in measurably evolving populations

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

The phylodynamic threshold of measurably evolving populations

This study shows that determining if a population is measurably evolving or has reached the phylodynamic threshold depends on model assumptions and sampling strategies, not just data, and emphasizes prior sensitivity over tests of temporal signal.

DIANA: Deep Learning Identification and Assessment of Ancient DNA

DIANA predicts metadata categories from ancient metagenomics data, achieving high accuracy in host, community type, and material classification.

Benchmarking BEAGLE to find optimal parameters for BEAST X

The paper benchmarks BEAGLE integration in BEAST X to determine optimal parameters for different hardware configurations using Dengue Virus data and simulations.

Global evolutionary patterns of Yersinia pestis and its spread into Africa

This study analyzes the global evolutionary patterns of Yersinia pestis, revealing its introduction into Africa and key genomic adaptations contributing to its persistence.

Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal

The paper evaluates how model and prior choices affect the Bayesian temporal signal detection method BETS and provides guidelines for reliable molecular clock estimates.

ClockstaRX: testing molecular clock hypotheses with genomic data

ClockstaRX tests molecular clock hypotheses by analyzing phylogenomic data to identify rate variation patterns and influential loci.

Detecting episodic evolution through Bayesian inference of molecular clock models

This paper introduces a Bayesian method to detect episodic evolution by comparing molecular clock models and applies it to SARS-CoV-2 data, finding strong evidence for episodic evolution.

Persistence of rare Salmonella Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

This study characterizes the genomic structure and evolutionary history of Salmonella Typhi in Samoa, revealing dominant rare genotypes with low antimicrobial resistance.

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

This study identifies genome degradation and convergent mutations in Staphylococcus aureus during severe infections, linking them to adaptation and clinical outcomes.

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

SNPPar detects homoplasic SNPs in microbial genomes to identify convergent evolution and adaptive traits with high accuracy and efficiency.

Phylodynamic modelling of bacterial outbreaks using nanopore sequencing

This paper uses nanopore sequencing and Random Forest models to estimate transmission dynamics of MRSA outbreaks, showing sustained transmission with Re > 1.

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

This paper introduces BETS, a Bayesian method to evaluate temporal signal in sequence data, showing it accurately classifies datasets with or without temporal signal across various empirical examples.

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

This study finds that proportionally linking branch lengths across loci provides the best fit for phylogenetic inference compared to other models.

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

This study analyzes the population genomics of hypervirulent Klebsiella pneumoniae clonal group 23, revealing its early emergence and global spread through genomic analysis of 98 isolates.

Phylodynamic model adequacy using posterior predictive simulations

The paper introduces TreeModelAdequacy, a tool to assess phylodynamic model adequacy using posterior predictive simulations, applied to Ebola and H1N1 influenza outbreak data.

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

The paper compares fully Bayesian and hybrid methods for inferring demographic parameters in bacterial genomic data, finding hybrid methods are computationally efficient and reliable when data have strong temporal structure.

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

This study analyzes Salmonella isolates from Nepali children to assess antimicrobial resistance and inform vaccine policy.

Evolution and global transmission of a multidrug-resistant, community-associated MRSA lineage from the Indian subcontinent

This study traces the origin and global spread of a multidrug-resistant MRSA lineage from the Indian subcontinent, showing its emergence through plasmid acquisition and intercontinental transmission.