S. Duchene

Genetic heterogeneity in the Salmonella Typhi Vi capsule locus: A population genomic study from Fiji

This study examines genetic diversity in the Vi capsule locus of Salmonella Typhi in Fiji, identifying convergent evolution of tviE mutations globally and highlighting the need for further functional analysis.

Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

Clockor2 is a web application for RTT regression that fits global and local molecular clocks, handling large datasets efficiently while keeping data on the client-side.

Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference

This paper introduces a method to quantify plasmid movement in Shigella species over time, finding higher transfer rates for small plasmids and recent dissemination of a multidrug-resistant plasmid.

Decoding the fundamental drivers of phylodynamic inference

This paper introduces a formal method to quantify the impact of genome sequences and sampling times on phylodynamic inference, using simulations and real outbreak data to identify trade-offs and guidelines for analysis.

Real-time and remote MCMC trace inspection with Beastiary

Beastiary provides real-time and remote inspection of MCMC traces from Bayesian phylogenetic analysis software.

Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis

This study examines gene loss and selection changes in plastid genomes during secondary endosymbiosis in three lineages, finding constrained gene loss and temporary relaxation of purifying selection.

Phylodynamic signatures in the emergence of community-associated MRSA

This study uses phylodynamic methods to analyze the emergence and spread of community-associated MRSA lineages globally, identifying common patterns of epidemic growth and transmission.

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

The study investigates typhoid dynamics in Kenya, finding high multidrug-resistant H58 S. Typhi prevalence in both cases and controls, suggesting carriers contribute to community spread.

Infectious disease phylodynamics with occurrence data

The paper shows that incorporating occurrence data with birth-death models improves estimates of the basic reproductive number in phylodynamic analyses, while coalescent models are less affected by sampling biases but cannot use occurrence data.

Temporal signal and the phylodynamic threshold of SARS-CoV-2

This study assesses the phylodynamic threshold of SARS-CoV-2 by analyzing genome sequences over time to determine when reliable evolutionary rate and outbreak timing estimates became possible.

Direct RNA sequencing and early evolution of SARS-CoV-2

The paper presents the first native RNA sequence of SARS-CoV-2, detailing its transcriptome and epitranscriptome, and infers genetic features and evolutionary rate.

The molecular clock of Mycobacterium tuberculosis

This study systematically analyzes the molecular clock of Mycobacterium tuberculosis using 6,285 strains, finding wide variation in clocklike structure and SNP accumulation rates independent of calibration time.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

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.

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

The paper compares the evolutionary dynamics of horizontal gene transfer in drug-resistant and virulent Klebsiella pneumoniae clones to assess the risk of gene convergence.

A Comparison of Methods for Estimating Substitution Rates from Ancient DNA Sequence Data

This study compares three methods for estimating substitution rates from ancient DNA data and finds they perform reliably under specific conditions but vary when rate variation and phylo-temporal clustering are present.

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

The study analyzes an 800-year-old Paratyphi C genome to show its origin from swine pathogens and its long history as a human pathogen.