400 papers
This study challenges the notion that Shiga toxin-producing *Escherichia coli* O157:H7 does not persist at the farm level by identifying 15 locally persistent lineages in Minnesota that have endured for up to 8.6 years and account for over a third of reported cases, thereby highlighting the critical role of ecosystem-level persistence in the disease burden.
A mutation accumulation study in the marine phytoplankton *Bigelowiella natans* reveals that integrated viral sequences undergo extreme, regulated hypermutation characterized by T/A-to-C/G transitions on TpA dinucleotides, suggesting the existence of a conserved eukaryotic immune system that targets invading DNA through localized genome editing.
The authors introduce Genotyping in Fixed Transcriptomes (GIFT), a scalable single-cell assay that simultaneously profiles whole transcriptomes and targeted somatic mutations with high accuracy, enabling the resolution of genotype-to-phenotype relationships and clonal heterogeneity in large cohorts and FFPE tissues.
This study characterizes 296.5 Mb of African Pan Genome contigs to reveal that functionally relevant, ancestry-enriched genomic sequences, including disease-associated genes and nonrepetitive regions, remain absent from current human reference frameworks, thereby highlighting critical gaps in biomedical discovery and precision medicine for underrepresented populations.
By leveraging pre-colonial palaeogenomes to correct biases in existing methods, this study establishes a scalable framework for accurately estimating European dog admixture in dingoes, thereby revealing ancient population structures and enabling more effective, regionally informed conservation management.
This study reveals that a segmental duplication-mediated deletion of a 3.6 Mbp region on orangutan chromosome 10 removed the canonical centromere's higher-order repeat array, triggering the formation of a neocentromere and demonstrating the remarkable plasticity of centromere identity through structural variation and epigenetic reprogramming.
This study reveals that the crop microbiomes of replete honeypot ants are dominated by two distinct evolutionary lineages of *Fructilactobacillus* closely related to *F. fructivorans*, with one lineage exhibiting unique phylogenetic and metabolic characteristics that may underpin the convergent evolution of ant repletism.
This study presents a chromosome-scale genome assembly and salt gland transcriptome analysis of the saline-tolerant mosquito *Aedes togoi*, revealing novel genomic features and identifying key ion-transport mechanisms that enable its larvae to thrive in hyper-saline coastal environments.
This study reveals that the intrinsic sequence preference of the DNMT1-UHRF1 complex for specific flanking DNA hexanucleotides dictates the stability of CpG methylation during cell division, thereby driving the cumulative loss of methylation that serves as a molecular marker for biological aging and cancer progression.
This study demonstrates that while the yeast helicase Ded1 is critical for translating mRNAs with structured 5'UTRs, its primary mechanism of action is the unwinding of secondary structures rather than the widespread suppression of upstream ORF translation.
This paper introduces EVEE, an interactive web resource that leverages embeddings from the Evo 2 genomic foundation model to achieve state-of-the-art, interpretable pathogenicity predictions for diverse genetic variants across a unified framework, transforming interpretability from a trade-off into a complementary product of learned biological structure.
This study utilizes genomic epidemiology and phylodynamic modeling to track the 2017–2023 *Mycoplasma bovis* outbreak in New Zealand, demonstrating how movement restrictions and culling successfully reduced transmission and eliminated major lineages by 2020, while highlighting the critical role of integrated genomic surveillance in guiding eradication efforts.
This study reveals that the drought tolerance of *Dianthus inoxianus* relies primarily on constitutive gene expression, with phenotypic plasticity limited to specific traits and driven by targeted transcriptomic adjustments in key molecular pathways rather than broad genomic reprogramming.
This study presents a comprehensive joint promoterome-proteome atlas of 75 human skeletal muscles, revealing extensive molecular diversity driven by tissue-specific transcription factors and allele-specific variants, while providing an interactive resource to advance the understanding of muscle gene regulation and heritable pathologies.
This paper describes the novel plant-associated yeast genus *Aimea* within the Microbotryomycetes, characterizing three new species through physiological, genomic, and phylogenetic analyses while providing high-quality genome resources and a genetic transformation protocol to facilitate future research on their ecological interactions.
This study presents high-quality genome assemblies of the *Palythoa* genus to investigate palytoxin biosynthesis and algal symbiosis, revealing that the toxin's production likely involves the modification of existing fatty acid synthase and bacterial-like polyketide synthase pathways rather than unique gene expansions, while also identifying genomic adaptations related to the genus's unique morphology and symbiotic states.
This study introduces Ribo-ITP, a low-input ribosome profiling method that expands the translatome of scarce samples like microdissected tissues and single embryos, enabling the discovery, validation, and machine learning-based prediction of thousands of functional non-canonical translons.
This study establishes high-quality genomic and transcriptomic resources for the invasive tunicate *Ascidiella aspersa* and conducts a comprehensive comparative analysis across 35 other tunicate species to reveal class-level genomic features, evolutionary diversification patterns, and a new phylogenetic hypothesis, all accessible through the newly constructed TUNOME database.
Deep-Plant is a supervised foundation model trained on diverse plant chromatin data that outperforms self-supervised language models in speed, accuracy, and interpretability for predicting regulatory genomic activity across species like Arabidopsis and rice.
The authors introduce DiffDriver, a powerful statistical method that overcomes limitations of current tools to detect context-dependent selection on cancer driver genes, revealing that individual-specific factors significantly modulate selection strength for a substantial proportion of driver genes.