Tavis K. Anderson

A multivalent mRNA-lipid nanoparticle vaccine containing eight hemagglutinin antigens elicited broad neutralizing antibody responses and protected against influenza A virus challenge in swine.

This paper develops a multivalent mRNA-LNP vaccine with eight swine IAV HA antigens, showing broad neutralizing antibodies and protection against viral challenge.

SmartHisto: Bayesian Active Learning for Histology Images

SmartHisto reduces annotation effort for histopathology images using Bayesian active learning, achieving higher mean IoU than competing methods.

Host type governs influenza evolutionary strategy across reservoir and spillover hosts

This study shows that influenza viruses use different evolutionary strategies in avian versus mammalian hosts, with reassortment dominating in birds and adaptation in mammals.

Quantifying Asymmetric Coevolutionary Dynamics using Normalized Phylogenetic Costs

The paper introduces normalized asymmetric phylogenetic costs to quantify coevolutionary dynamics, showing they capture complex relationships in virus-host systems and detect novel gene pairings in viral genomes.

Impact of Maternal Antibodies and Weaning Stress on the Replication and Transmission of Human H3N2 Influenza A in Piglets

This study examines how maternal antibodies and weaning stress affect piglets' susceptibility to human H3N2 influenza A virus, showing that matched maternal antibodies reduce shedding and transmission while weaning increases viral spread.

Diverse Genomic Landscape of Swine Influenza A Virus in England (2014 - 2021)

This study analyzes Swine Influenza A Virus (SwIAV) genomic diversity in England from 2014 to 2021, identifying new HA clades and genotypes within the 1B lineage.

PREMISE: A Quality-Aware Probabilistic Framework for High-Resolution Source Assignment in Metagenomic Sequencing

PREMISE improves metagenomic source assignment by using a quality-aware probabilistic framework, achieving high accuracy in both species and strain-level classification.

Splicer: Phylogenetic Placement in Sub-Linear Time

Splicer performs phylogenetic placement in sub-linear time, enabling efficient classification of large-scale genetic sequences with high accuracy.

Vaccine-induced antigenic drift of a human-origin H3N2 Influenza A virus in swine alters glycan binding and sialic acid avidity

This study shows vaccine-induced immunity drives antigenic drift in a human-origin H3N2 virus in swine, altering HA receptor binding and glycan specificity.

United States PRRSV 1-4-4 L1C.5 isolate demonstrates similar pathogenicity to a historic Chinese highly pathogenic PRRSV

This study compares the pathogenicity of PRRSV 1-4-4 L1C.5 to historical Chinese HP-PRRSV JXwn06 and US strain MN184 in weaned pigs, finding L1C.5 and JXwn06 cause more severe disease than MN184.

Sources and sinks of influenza A virus genomic diversity in swine from 2009 to 2022 in the United States

This study quantifies the sources and sinks of influenza A virus genomic diversity in U.S. swine from 2009 to 2022, showing regional hotspots and the role of swine transport in diversity spread.

Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades

The paper conducts active surveillance of influenza A virus in swine farms and nurseries, revealing within-farm reassortment, cocirculation of subtypes, and human-to-swine transmission events.

Revealing reassortment in influenza A viruses with TreeSort

TreeSort detects influenza A reassortment in thousands of genomes via clock-based tests; avian H7 reassorts most, and HA, NA, MP rarely reassort in human and H5N1.

Phylo-rs: an extensible phylogenetic analysis library in Rust

Phylo-rs provides a fast, extensible Rust library for phylogenetic analysis with WebAssembly support and open-source availability.

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle

This study identifies a reassortment event in wild birds leading to HPAI A(H5N1) infection in cattle and highlights the risk of virus spread through asymptomatic cattle to humans.

PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance

This paper introduces a dynamic classification system for PRRSV-2 genetic variants using clustering algorithms and demonstrates its effectiveness in tracking genetic diversity over time.

Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction

The paper identifies genetic signatures in influenza A viruses associated with interspecies transmission between swine and humans using phylogenetic analysis and machine learning.

Experimental reproduction of viral replication and disease in dairy calves and lactating cows inoculated with highly pathogenic avian influenza H5N1 clade 2.3.4.4b

This study experimentally reproduces HPAI H5N1 infection in dairy calves and cows, confirming clinical disease and viral transmission through respiratory and mammary routes.

Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

This study compares phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences, identifying robust approaches that improve resolution over RFLP-typing.

classLog: Logistic regression for the classification of genetic sequences

The paper introduces a logistic regression pipeline for classifying genetic sequences, achieving high accuracy even with degraded data and identifying clade-defining mutations.

Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine

This study uses machine learning to predict antigenic drift in swine influenza A viruses and validates predictions with experimental assays.

The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine

The paper develops a centralized database for swine pathogen sequences to monitor emerging pathogens and support genomic surveillance.