Cedric C.S. Tan

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.

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

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.

This paper introduces a capture-based method to purify whole viral native RNA genomes, achieving high purification and mapping efficiency in direct RNA sequencing.