Tanya Golubchik

COSMOS integrates vector-pathogen metagenomics to monitor mosquito-borne diseases, detecting pathogens and mosquito communities in field samples with high accuracy.

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

The paper identifies and masks artefactual variants in SARS-CoV-2 sequencing data to improve the accuracy of within-host diversity and transmission analysis.

The paper identifies a bias in phylogenetic branch lengths when using the discrete Gamma model and recommends replacing it with the FreeRate model.

The paper analyzes SFTSV intra-host diversity in patients with varying disease severity, finding lower diversity in severe cases despite higher viral loads and identifying iSNVs linked to replication and immunity.

Castanet is a pipeline for analyzing multi-pathogen enrichment sequencing data, providing accurate consensus sequences and metrics for pathogen detection and quantification.

This study compares metagenomics and targeted approaches for virus detection, finding that targeted methods improve sensitivity while untargeted ONT offers better specificity.

The paper evaluates two tools for HIV transmission direction prediction using short and long-read sequencing data from serodiscordant couples, showing long reads improve phylogenetic resolution and transmission prediction accuracy.

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

This paper describes a method to generate full-length HBV genome data using isothermal amplification and sequencing with Nanopore and Illumina, achieving high consensus accuracy and resolving intra-sample variants.

This paper introduces veSEQ-HIV, a cost-effective, high-throughput sequencing method for HIV that recovers complete genomes and quantifies viral load, enabling drug resistance monitoring and transmission analysis.

This study examines HHV-6 prevalence in clinical samples using PCR and NGS, finding 33% positivity in hematology patients and 20% detection via NGS in CSF and respiratory samples.

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.

Severe S. aureus infections arise from the nasal microbiome through adaptive evolution, with specific mutations enriched in infecting bacteria compared to colonizing ones.

This paper develops a tool to predict antibiotic resistance in S. aureus and M. tuberculosis from genome sequences with high accuracy and speed.