virus

This study evaluates Vitis germplasm diversity to predict adventitious rooting traits, identifying genetic loci and developing genomic prediction models for improved grapevine rootstock breeding.

The paper introduces evoPLM-Tree, a tree-aware language model that predicts viral mutations by incorporating phylogenetic context, showing it captures mutational patterns and functional constraints in SARS-CoV-2 spike protein evolution.

This paper investigates the interaction between influenza HA's cytoplasmic tail domain and PIP2 using MD and FPALM, finding electrostatic and hydrophobic contributions to HA-PIP2 binding.

The paper predicts and validates the global RNA structure of CMV satRNA T1 using AlphaFold3 and experimental methods, revealing conformational switching at the 3' terminus.

This paper develops a CRISPR-Cas3-based diagnostic platform for emerging RNA viruses, enabling rapid assay design and deployment with high sensitivity and portability.

The paper profiles the nuclear proteome of Trypanosoma cruzi using mass spectrometry and identifies protein interactions and modifications, providing a resource for further studies.

The paper estimates lynx population density in Valais, Switzerland, showing it is lower than politically cited figures, highlighting the need for science-based management.

The paper investigates how intraspecific variation in physiological strategies affects susceptibility to esca in grapevine cultivars, finding that conservative water use strategies reduce susceptibility while metabolic responses vary with disease symptoms.

This study uses machine learning to predict avian influenza zoonosis risk based on viral genome sequence features, finding that a multi-model approach outperforms individual models.

A >50,000-element viral smORF library screened by growth, MHC-I, ER stress, Perturb-seq and mass spectrometry yields >2,000 active microproteins and shows EBV BNLF2b inhibits PKA by mimicry.

This study identifies promoter-dependent nuclear export as a mechanism for influenza A virus to select its genome for packaging into virions.

This study shows how Vibrio cholerae pellicles form through planktonic cell recruitment mediated by extracellular matrix factors and quorum-sensing.

This study compares MALDI-TOF MS and whole-genome sequencing for identifying Vibrio parahaemolyticus strains from oysters, finding MALDI-TOF MS provides comparable resolution to WGS for strain tracking.

The paper identifies ligands that bind beyond a known hydrophobic pocket at the HBV core protein interface using molecular dynamics and fragment mapping.

The paper identifies molecular signatures and endotypes in severe dengue by integrating clinical and proteomic data, revealing immune pathways associated with severe disease.

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

This study uses molecular dynamics simulations to investigate how HIV-1 Env proteins reorganize during viral maturation, revealing clustering mechanisms and implications for antibody accessibility.

This paper develops a high-throughput platform to rapidly adapt DNA aptamers against evolving SARS-CoV-2 variants, identifying mutants with improved binding affinity and specificity.

This study tracks vampire bat movement in response to human disturbance, finding rapid roost switching and altered flight patterns that may influence rabies spread.

This paper introduces vhPPIpred, a machine learning method for predicting virus-human PPIs that outperforms existing methods and provides a benchmark dataset.

This paper introduces a method to estimate mutation rates as a distribution rather than a single number, using sequencing data from a single viral replication cycle.

This study improves platypus behavior classification using accelerometry by incorporating frequency-domain features, achieving higher accuracy for rhythmic behaviors like diving and foraging.

This study compares how two Vibrio species respond to different inorganic nitrogen sources, revealing distinct metabolic strategies and ecological adaptations.

The paper develops PhyCD to detect contamination in SARS-CoV-2 genomes, identifying 10,942 putative contamination events across nearly 5 million genomes.

This study uses single-molecule force spectroscopy to resolve the multi-domain architecture of Orsay virus δ protein by creating a 2D mechano-structural signature map.

This paper introduces Vir3D, a structure-aware deep learning model that predicts influenza antigenicity and improves vaccine strain selection by incorporating 3D structural information from amino acid sequences.

This paper presents a standardized whole-genome variant dataset of 547 grapevine accessions, including domesticated and wild Vitis species, for genetic and genomic research.

This study determines the structure of Bap1 bound to VPS and shows how it facilitates biofilm adhesion and VPS organization through a conserved β-propeller interaction.

The paper shows that TPS gene expression, not copy number, explains aroma diversity in grapevine cultivars by analyzing haplotype-resolved genomes and validating enzyme activity through functional assays.

The paper uses machine learning-augmented virtual screening to discover a novel series of Mac1 inhibitors for SARS-CoV-2 NSP3, validated by experimental assays and crystallography.