Viacheslav Y. Fofanov

MetaTracer: A nucleotide alignment-based framework for high-resolution taxonomic and transcript assignment in metatranscriptomic data

MetaTracer assigns taxonomic and gene expression to metatranscriptomic reads using nucleotide alignment, achieving high accuracy in simulated and real datasets.

Longitudinal prevalence and co-carriage of pathogens associated with nursing home acquired pneumonia in three long-term care facilities

This study tracks prevalence and co-carriage of respiratory pathogens in nursing home residents, finding distinct colonization patterns and persistence differences.

High-throughput targeted amplicon screening tool for characterizing intrahost diversity in Staphylococcus aureus directly from sample

This paper develops a low-cost amplicon sequencing assay to rapidly characterize Staphylococcus aureus intrahost diversity directly from samples, enabling transmission analysis without whole-genome sequencing.

Population sequencing for diversity and transmission analyses

This paper introduces and validates population sequencing methods to analyze phylogenetic diversity in bacterial populations without haplotype reconstruction, demonstrating applications in tracking transmission and understanding pathogen dynamics.

Biological Drivers of Early Childhood Caries in Preschool Children of Northern Arizona and Hawaii

This study investigates the relationship between demographic factors, S. mutans colonization, and early childhood caries risk in preschool children from northern Arizona and Hawaii.

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

The paper investigates leptospirosis transmission among brown rats in Boston, finding high genetic structure and limited dispersal, with Leptospira clades linked to specific rat populations and a human case linked to rats.

Sample pooling methods for efficient pathogen screening: Practical implications

This paper evaluates sample pooling methods for pathogen screening, finding that existing methods excel in some areas but not others, and introduces a new method that performs well across multiple criteria.

Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location

This study links a soil microbiome from a suspect's sock to a crime scene location, showing potential for forensic use.

Phylogenetic Analysis of St. Louis Encephalitis Virus within Two Southwestern United State Counties: a case for a bulk introduction event into the southwest United States

The paper uses phylogenetic analysis to determine if St. Louis Encephalitis Virus (SLEV) in Arizona and California originated from local cycling or new imports, finding evidence of annual imports in California and local cycling in Arizona.