virus

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

Development of a Pan-Proteome Multi-Epitope Vaccine Candidate Against Nipah Virus Using Reverse Vaccinology and Immunoinformatics Approaches

This paper designs a multi-epitope vaccine candidate against Nipah virus using immunoinformatics and reverse vaccinology, identifying VC033_V6_BD_L03 as a lead candidate with high global and regional population coverage.

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Decoding the molecular cues regulating the transition of Influenza virus polymerase from transcriptase to replicase.

This study identifies interdomain interactions in PB2 that regulate Influenza virus polymerase conformational transitions and transcription-replication balance, revealing a phosphomimetic adaptation mechanism in bat influenza viruses.

Provenance-aware handling of identical dengue genome records alters inferred envelope-protein variation in Bangladesh DENV-3

The paper evaluates how handling identical dengue genome records affects inferred envelope-protein variation in a Bangladesh DENV-3 dataset, showing that exclusion strategies can lead to loss of variation.

Prokaryotic homologs of the major vault protein form engineerable vault nanocapsules

The paper identifies prokaryotic homologs of the major vault protein that assemble into vault nanocapsules, revealing structural and size variability.

MicrobeRT: A Framework and Suite of Fine-tuned Language Models for Genomic Sequences

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

Identification of cis-Acting Elements that Regulate Influenza A Virus Segment 7 Differential mRNA Splicing

This study identifies cis-acting elements that regulate splicing balance between influenza A virus segment 7 mRNA1 and mRNA2, revealing key sequences that influence M1 and M2 protein expression.

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

This study shows H5N5 viruses have been repeatedly introduced across the Atlantic by high latitude seabirds, with more frequent introductions in fall and spring, and a distinct ecology from H5N1.

Hic sunt dracones: ancient DNA from the extinct palaeofauna of the tiny Mediterranean archipelago of Columbretes and its implications for human visitation

This study recovers ancient DNA from extinct species and human remains on Columbretes Island, revealing biogeographic origins and human-mediated introductions.

Stochastic population growth and its implications for mutation dynamics under carrying capacity constraints

This study introduces a stochastic logistic growth model with carrying capacity to analyze mutation dynamics in microbial populations, showing that random fluctuations significantly impact population variability near carrying capacity.

Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites

This study maps SARS-CoV-2 protein-RNA interactions using eCLIP, revealing new regulatory sites for viral replication and translation.

Assembly of minimally fragmented metagenomic pangenome graphs

The paper introduces PANIMaSTA, a method to construct minimally fragmented metagenomic pangenome graphs for highly diverse viral genomes, improving graph topology for comparative analysis.

Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

This paper evaluates H5Nx influenza virus genotyping tools and finds they often group viruses with distinct evolutionary histories due to reassortment and reference bias.

Ablation of a maternal Cryptosporidium mRNA-binding protein results in sterile sporozoites

The paper identifies an RNA-binding protein essential for female gamete development and sporozoite infectivity in Cryptosporidium by analyzing single-cell data and conducting conditional ablation experiments.

Inferring the multi-host fitness landscape of endive necrotic mosaic virus from cross-inoculation experiments

The paper infers a multi-host fitness landscape of endive necrotic mosaic virus using cross-inoculation experiments and a Bayesian model linked to Fisher's geometrical model.

Isoform-Resolved Temporal Remodeling of Transcriptome Architecture in Monkeypox Virus

The paper reanalyzes sequencing data to reconstruct full-length monkeypox virus transcripts and shows temporal changes in gene regulation and transcript structure.

Sequence-structured fitness landscapes predict influenza evolution

This study develops a generative framework to infer influenza virus fitness landscapes from sequence data, revealing antigenic determinants and improving evolutionary predictions.

A maximum entropy model for m6A prediction: from human transcripts to influenza A viral segments

The paper introduces MEMAR, a Maximum Entropy model for predicting m6A methylation in human transcripts and influenza A viral segments, showing improved performance over existing methods.

Endophytic colonization pathways of Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 in grapevine following stem injection

This study compares the colonization patterns of Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 in grapevine after stem injection, showing distinct movement and persistence behaviors.

Genetic analysis of grapevine wood composition identifies glycosyltransferases involved in the biosynthesis of stilbene glycosides

The paper identifies glycosyltransferases involved in the biosynthesis of stilbene glycosides in grapevine wood through metabolomic and genetic analyses.

Mathematical AI Predicts 40% and 57% Influenza Vaccine Effectiveness Against H1N1 and H3N2, Respectively, for the 2026--2027 U.S. Season

The paper uses mathematical distances from HA sequences to forecast influenza vaccine effectiveness for the 2026--2027 season, predicting 40% and 57% effectiveness against H1N1 and H3N2, respectively.

Presumptive detection of Giardia lamblia cysts in borehole water in Gombe metropolis, north-eastern Nigeria: a two-round cross-sectional study with implications for water safety

The paper detects Giardia lamblia cysts in borehole water in Nigeria using light microscopy, finding 20% positivity in two rounds with no significant difference between rounds.

Structure and antigenicity of the 2026 Bundibugyo virus glycoprotein

This study determines the structure of the 2026 Bundibugyo virus glycoprotein and identifies conserved epitopes for antibody therapeutics and pan-ebolavirus vaccines.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

Development of a Synthetic Genomics-Based Venezuelan Equine Encephalitis Virus Expressing Secreted Gaussia Luciferase for High-Throughput Antiviral Screening

This paper develops a synthetic VEEV reporter virus for high-throughput antiviral screening, identifying inhibitors of VEEV replication using FDA-approved compounds.

Mapping the Fragment-Binding Landscape of SARS-CoV-2 nsp14 for Antiviral Drug Discovery

The paper maps the fragment-binding landscape of SARS-CoV-2 nsp14, identifies promising sites for antiviral drug development, and provides a prioritized resource for future inhibitors.

Sodium nitrophenolates as a potential tool for the management of grapevine trunk diseases

This study evaluates the antifungal and defence-modulating effects of sodium nitrophenolate product Atonik against fungal trunk diseases in grapevines, showing reduced lesion length and increased defence gene expression.

Indigenous generalist pollinators shape plant-insect interaction networks across a land-use gradient on an oceanic island

The paper examines how plant-pollinator networks reorganize across a land-use gradient on Terceira Island, finding that plant species turnover drives network reshuffling and that indigenous generalist pollinators maintain network resilience.

Evolution of multidrug-resistant IncC plasmids in the seventh pandemic Vibrio cholerae O1 El Tor lineage between 1979 and 2024

The paper analyzes IncC plasmids from Vibrio cholerae O1 El Tor isolates between 1979 and 2024, revealing their evolution and antimicrobial resistance gene diversity.