N. De Maio

Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations

This study evaluates how sampling bias affects viral spread inference using phylogeographic models and proposes strategies to mitigate its impact through simulation and empirical datasets.

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

The paper develops a novel phylogenomic method to detect recombination events in SARS-CoV-2 genomes, identifying 606 recombination events across 1.6M samples with 2.7% of genomes showing recombinant ancestry, primarily in the Spike protein region.

The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs

The paper identifies two highly conserved druggable sites in the SARS-CoV-2 replication-transcription complex as potential targets for broad-spectrum antiviral drugs.

Global spread and evolutionary history of HCV subtype 3a

The paper uses host and virus genomic data to trace the global spread and evolutionary history of HCV subtype 3a, finding it originated in South Asia and spread through three independent events post-World War II.

Mutation rates and selection on synonymous mutations in SARS-CoV-2

The paper analyzes mutation rates and selection pressures in SARS-CoV-2 genomes, identifying elevated G→U and C→U mutations and challenging previous findings on synonymous site selection.

Repeated global migrations on different plant hosts by the tropical pathogen Phytophthora palmivora

This study uses genetic analysis to trace the origin and migration history of the plant pathogen Phytophthora palmivora, identifying Southeast Asia as its center of diversity and a single colonization event responsible for its global spread.

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

This paper introduces a phylodynamic workflow to analyze SARS-CoV-2 lineage dispersal, showing external introductions were key in Belgium and lockdowns had limited impact on transmission.

Sampling bias and model choice in continuous phylogeography: getting lost on a random walk

The paper compares two phylogeographic models, showing that sampling bias affects Brownian Motion Phylogeography (BMP) and that the spatial Lambda-Fleming-Viot process (LambdaFV) is more robust but applicable to different scenarios.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

This study evaluates how sequencing depth affects taxonomic composition and AMR gene detection in metagenomic samples, finding that higher depth is needed for AMR gene richness.

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.

The Bacterial Sequential Markov Coalescent

This paper introduces a new model, BSMC, to approximate bacterial recombination and presents a simulation tool, FastSimBac, for efficient genomic evolution studies.