Lucy van Dorp

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

The paper identifies 18 mitochondrial variants associated with climate adaptation using a large dataset of human mtDNA and climate variables.

This study analyzes ancient DNA to reveal the 2500-year evolutionary history of human betaherpesviruses 6A and 6B, showing established diversity by the 14th century and ancient integration into the human genome.

This study uses nanopore metagenomic sequencing to analyze the microbiomes of HAP patients, revealing high fungal prevalence and multi-drug-resistant microbes.

The paper analyzes ancient Borrelia genomes to document the evolutionary transition from tick-borne to louse-borne transmission and shows rapid reductive evolution.

The paper uses SARS-CoV-2 genomic data to predict the fitness of viral mutations by analyzing intrahost diversity and genetic linkage patterns, showing improved forecasting with machine learning models.

The paper investigates the evolutionary origins of the BA.2.86 SARS-CoV-2 variant, finding it evolved through multiple transmission chains and recombination, not a single chronic infection.

This study investigates the evolutionary drivers of viral host jumps using genomic data, finding that humans can be both sources and sinks for viral spillover and that adaptation varies across viral families.

The paper screens bat samples for coronaviruses, identifies novel strains, and assesses their potential to infect humans.

The paper presents ancient HSV-1 genomes from Europe, estimates mutation rates, and suggests lineage replacement during the Bronze Age.

The paper analyzes SARS-CoV-2 genomic mutations in mink and deer to identify potential host-specific adaptations and assess spillover risks.

This study identifies microbial hallmarks of sepsis using metagenomic data and shows that polymicrobial communities, not single pathogens, are key in sepsis diagnosis.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

This study examines the genetic structure of Ethiopians, linking cultural and geographic factors to genetic diversity and intermixing across 68 ethnic groups.

The paper analyzes SARS-CoV-2 genomic data to determine if genetic recombination is occurring, finding no detectable evidence of it.

This study tests if recurrent mutations in SARS-CoV-2 are linked to increased transmissibility and finds no significant association.

This study analyzes SARS-CoV-2 genomes from Palestine to trace the virus's introduction and circulation, finding at least nine independent introductions and a locally predominant lineage introduced before the first reported cases.

The paper identifies pre-existing bedaquiline resistance variants in Mycobacterium tuberculosis genomes before clinical use of the drug, highlighting the need for rapid susceptibility testing.

The paper predicts SARS-CoV-2 spike protein interactions with ACE2 orthologues across 215 vertebrates, finds mutations in ACE2 are more detrimental, and shows human strains are present in animals.

This study uses network analysis of over 10,000 bacterial plasmids to uncover population structure, gene content correlations, and drivers of horizontal gene transfer.

The paper analyzes metagenomic data from a blood stain on a newspaper linked to Jean-Paul Marat to investigate potential infectious agents of his skin condition.

The paper generates a genome from a historical European Plasmodium vivax strain, revealing its evolutionary relationship to American strains and the presence of drug resistance variants predating their use.

The paper demonstrates how to assess the reliability of genetic clustering results from STRUCTURE/ADMIXTURE using simulated and real data with badMIXTURE.

This study analyzes genetic data from Zoroastrians in Iran and India to explore population structure, gene flow, and selection, revealing patterns of endogamy, admixture timing, and disease-related selection.

This study shows early European farmers descended directly from Neolithic Aegeans, linking Mediterranean and Central European farmers to southwestern Asia.