virus

This paper identifies data leakage in pre-trained pLLMs used for protein-protein interaction inference and shows their limitations in generalization.

The paper evaluates grapevine genotypes with single or pyramided resistance loci against downy mildew during a severe epidemic, showing that pyramiding improves resistance effectiveness.

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

This study shows that optimized irrigation during heat events improves grapevine physiology and fruit production, while excessive or insufficient irrigation harms plant function and yield.

This study identifies the dimerization mechanism of HIV-1 RNA hairpins to extended duplex structures using simulations, revealing intermediates and ion-dependent pathways.

This study identifies RNA secondary structures in influenza A virus gene segments and shows that mutations in packaging signal structures reduce viral replication.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

This study identifies genomic adaptations in group B Streptococcus (GBS) following intrapartum antibiotic prophylaxis, showing increased mutation rates and biofilm production in persistent colonizers.

Whole-genome sequencing and geolocation tracking indicate that high pathogenicity avian influenza H5N1 reached Tristan skuas on remote Gough Island via sub-Antarctic marine networks linked to South Georgia rather than Africa.

The paper identifies and classifies 163 putative Type IV IRESs from diverse viruses, revealing structural variations that correlate with functional differences.

The paper develops a multiplex qPCR assay to differentiate monkeypox virus clades, showing high sensitivity and specificity in clinical samples.

This study investigates the structural plasticity of the Lassa virus fusion domain and its interaction with BMP lipids during membrane fusion.

This study identifies PTSP as a ligand that induces proteolytic degradation of SmcR, controlling quorum sensing state transitions in Vibrio species.

This study uses haplotype-resolved genomics to show GRBV induces distinct genetic and epigenetic responses in grapevines, revealing asymmetric antiviral strategies and epigenetic reprogramming.

This study shows that PIP2;1 aquaporin promotes earlier stomatal closure during water stress in grapevines without affecting leaf hydraulic conductance.

The paper uses CRISPR-Cas9 to edit MLO genes in grapevine, revealing their roles in powdery mildew resistance and plant development.

This study uses topological data analysis and deep learning to show that grapevine leaf blade and vasculature shapes are predictively linked, suggesting a one-to-one relationship between the two tissues.

FoldMason uses Foldseek's 3Di+AA alphabet for progressive multiple structure alignment, beating structure aligners' LDDT on AlphaFold DB clusters at near sequence-aligner speed, scaling to 100,000 structures.

The paper links protease sequence variation to biochemical parameters and viral fitness using high-throughput enzymology and replication assays.

The paper evaluates the effectiveness of single and pyramided resistance loci in grapevine against Plasmopara viticola, finding that defeated loci can reduce resistance efficacy.

The paper validates a single reaction amplicon sequencing approach for generating high-quality WNV genomes and characterizes transmission dynamics during a 2023 outbreak in Nebraska.

This study reveals ATP-dependent coupling between nucleotide and RNA affinity in WNV NS3h, showing how motif VIL residues modulate RNA binding through conformational changes.

Cryo-ET of Langat virus-infected cells shows replication organelle size set by a membrane coat plus RNA pressure, with virion budding and maturation occurring beside the organelles.

This study uses ultra-deep sequencing to analyze intra-host SARS-CoV-2 diversity and co-infection-driven evolution in Chilean patients, finding increased genetic diversity and positive selection in the Spike gene during co-infections.

This study investigates how the two active sites of SARS-CoV-2 Mpro communicate and cooperate in catalysis using enzymatic assays, crystal structures, and engineered mutations.

Cattle B3.13 H5N1 polymerase gained PB2 M631L and PA K497R, boosting replication in bovine and human cells via better bovine ANP32A use; later PB2 E627K and D740N add activity.

This study uses Bayesian analysis of TSWV genome sequences to estimate its evolutionary origin, divergence date, and demographic history, finding it originated in South Korea around 1768 CE and expanded with agricultural development.

This study examines genome rearrangement dynamics in bacteria and archaea, finding variable rates and mobile elements as key drivers of genomic changes.

The paper determines the structure of the portal vertex and neck complex in the hyperthermophilic phage Oshimavirus, revealing a pressure-sensitive mechanism for terminating DNA packaging and triggering tail attachment.