S. Weaver

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

Broad intraspecies killing activity in Pseudomonas syringae due to the combinatorial action of LPS-interacting bacteriocins

The paper shows Pseudomonas syringae pv. aptata uses multiple bacteriocins to kill a wide range of intraspecific strains by targeting different LPS conformations.

Potential of Ilheus virus to emerge

This study develops murine models of Ilheus virus infection and shows Aedes mosquitoes are highly susceptible, suggesting ILHV is poised for emergence in the neotropics.

Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama

This study examines seroprevalence of Madariaga and Venezuelan equine encephalitis viruses in rodents across Eastern and Western Panama, revealing spatial and species-specific patterns.

The influence of the larval microbiome on susceptibility to Zika virus is mosquito genotype dependent

This study shows that mosquito genotype interacts with larval microbiome to influence Zika virus susceptibility in Aedes aegypti.

Pantailocins: Phage-derived Bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes

The paper identifies and characterizes tailocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes, showing they are derived from Myoviridae phages and exhibit killing activity against phytopathogens.

Genomic Correlates of Tailocin Sensitivity in Pseudomonas syringae

This study identifies genomic factors associated with tailocin sensitivity in Pseudomonas syringae through genome-wide association analysis, revealing LPS-related gene clusters and rfbD as key predictors.

Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection

This study identifies the N679K mutation in Omicron variants as reducing spike protein expression and attenuating SARS-CoV-2 infection, while showing a replication advantage in the upper airway.

SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3

This paper shows that SARS-CoV-2's NSP16 protein helps evade immune detection by methylating viral mRNA, and disrupting this function reduces viral replication and disease in hamsters.

Peptide and protein alphavirus antigens for broad spectrum vaccine design

The paper designs and tests peptide and protein antigens from alphavirus envelope proteins to create broad-spectrum vaccines effective against multiple alphavirus species.

Antibody escape and cryptic cross-domain stabilization in the SARS CoV-2 Omicron spike protein

This study examines the molecular effects of Omicron spike mutations on ACE2 binding and antibody escape, revealing compensatory stabilizing mutations that enable high mutation counts.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

QTQTN motif upstream of the furin-cleavage site plays key role in SARS-CoV-2 infection and pathogenesis.

This study shows that deleting the QTQTN motif reduces SARS-CoV-2 replication and disease by affecting spike processing and glycosylation.

Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis.

This study shows that mutations in the SARS-CoV-2 nucleocapsid protein enhance viral replication and pathogenesis by increasing phosphorylation and resisting kinase inhibition.

BNT162b2-Elicited Neutralization of Delta Plus, Lambda, and Other Variants

The paper assesses the neutralization ability of BNT162b2-elicited sera against SARS-CoV-2 variants, finding that all sera neutralize variants to titers of ≥80, indicating vaccine effectiveness against emerging strains.

Distinct neutralizing kinetics and magnitudes elicited by different SARS-CoV-2 variant spikes

This study shows that immunization with different SARS-CoV-2 variant spikes leads to varying neutralizing kinetics and magnitudes against other variants, with significant differences in titers between homologous and heterologous variants.

Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant

This study identifies the P681R mutation in the Delta variant's spike protein as critical for enhanced viral replication compared to the Alpha variant through increased furin cleavage of the spike protein.

Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera

The paper evaluates the neutralization effect of BNT162b2 vaccine-elicited sera against SARS-CoV-2 variants with specific spike mutations.

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

The paper reconstructs the progenitor SARS-CoV-2 genome and traces its evolution and spread globally, showing multiple dominant strains and lineage replacements in different regions.

Prophylactic Application of Tailocins Prevents Infection by Pseudomonas syringae

This study shows that tailocins can prevent Pseudomonas syringae infection in Nicotiana benthamiana by targeting specific strains and demonstrates that heritable resistance mutations do not explain tailocin failure.

Furin Cleavage Site Is Key to SARS-CoV-2 Pathogenesis

This study shows that removing the furin cleavage site from SARS-CoV-2 increases replication in Vero cells but reduces replication in respiratory cells and pathogenesis in hamsters, while also decreasing neutralization susceptibility.

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

The paper shows SARS-CoV-2's ability to infect humans stems from its evolutionary history in bats, not human adaptation, with evidence of positive selection in bat viruses and weak purifying selection in SARS-CoV-2.

Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient

The paper isolates and characterizes SARS-CoV-2 from the first US COVID-19 patient, showing high replication in Vero cells and depositing the strain for public use.

Evidence for rapid phenotypic and behavioral change in a recently established cavefish population

This study compares phenotypic and behavioral traits between a recently established cavefish population and its surface counterpart, finding significant differences in morphology and behavior.