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Authors use metagenomic environmental surveillance in Cambodian live-bird markets and found that air sampling captured the greatest diversity of poultry viruses. It outperformed traditional swabs, identifying undetected H5N1 clades.

Embryonic patterning requires generation of positional information that defines where cells reside within the embryo. Here, Azambuja, Rothstein and colleagues report that the epigenome is spatially patterned during early development, showing that chromatin organization reflects the embryo’s emerging body plan.

Omnivores like bears can switch between plant and animal diets, potentially helping them respond to changing conditions. By combining modern and fossil data, this study shows that bears shift toward carnivory in harsher climates and toward herbivory in more productive environments.

DBiTplus represents an integrated experimental and computational workflow that unifies sequencing-based and imaging-based spatial omics, demonstrated by combining transcriptomic profiling and multiplexed protein imaging on the same tissue section.

Advancements in sequencing technologies and assemblers have enabled us to generate a complete, haplotype-resolved X chromosome in cattle. This study discovers the cattle X centromere is a natural neocentromere and characterises its genetic and epigenetic structure.

Vertebra lengths differ from the neck to the tail tip and differ between species, evidenced by extreme differences in mouse and jerboa tails. Here, Weber and colleagues identify cellular mechanisms and candidate genes that shape vertebral proportion.

This study applies magnetic fields in selected in-plane directions to disentangle the mechanisms underlying the anomalous Hall effect in a representative noncollinear antiferromagnet.

ESPRESSO leverages functional information obtained from organelles for deep spatiotemporal phenotyping of single cells.

Spatial transcriptomics technologies are still too restrictive for widespread clinical use, and methods that have been designed to bridge them with histopathology carry important limitations. Here, the authors develop MISO, a deep learning framework that allows inferring tissue spatial organisation and gene expression with near single-cell resolution from histopathology images.

Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks and generating reports even in data-scarce scenarios, such as rare cancer diagnosis and survival prediction, without requiring further fine-tuning.

Understanding the mechanisms underlying the survival of drug tolerant persister cells following chemotherapy remains elusive. Here, multi-omics analysis and experimental approaches show that the germ-cell-specific H3K4 methyltransferase PRDM9 promotes metabolic rewiring in glioblastoma stem cells.

Regeneration varies dramatically even between closely related species. Here they show that the evolutionary loss of foot regeneration observed in Hydra oligactis stems from weak Wnt activation after injury. Transient Wnt activation restores foot regeneration and the expression of foot transcription factor dlx2.

The authors report a meta-analysis of methylome-wide association studies, identifying 15 significant CpG sites linked to major depression, revealing associations with inflammatory markers and suggesting potential causal relationships through Mendelian randomization analysis.

Here, the authors provide evidence of the biotherapeutic potential of Klebsiella ARO112 for gut inflammatory conditions by showing it accelerates pathobiont clearance and recovery of microbiota diversity, boosting intestinal butyrate, and preventing inflammation and colitis in IBD models.

Low- and middle-income countries face unique challenges when it comes to balancing growing energy needs with broader, long-term development needs. This Perspective argues for innovative, context-specific modelling practices to support these goals.

We examine the historical development and underlying principles of foundation models realized in language and vision, and propose how physics-infused machine learning interaction potentials could dramatically transform at scale to create transformative foundation models for chemistry and materials science.

Stratified medicine promises to tailor treatment for individual patients, however it remains a major challenge to leverage genetic risk data to aid patient stratification. Here the authors introduce an approach to stratify individuals based on the aggregated impact of their genetic risk factor profiles on tissue-specific gene expression levels, and highlight its ability to identify biologically meaningful and clinically actionable patient subgroups, supporting the notion of different patient ‘biotypes’ characterized by partially distinct disease mechanisms.

Complexes of the transcription factor Ume6 bridge morphogenesis, adherence and hypoxic genes that determine biofilm architecture in the human fungal pathogen Candida albicans.

AI copilots are integrated into brain–computer interfaces, enabling a paralysed participant to achieve improved control of computer cursors and robotic arms. This shared autonomy approach offers a promising path to increase BCI performance and clinical viability.

An analysis of rare genetic variants identifies three genes—MAP1A, ANO8 and ANK2—that have a role in attention deficit hyperactivity disorder (ADHD) and investigates the potential underlying biological mechanisms.

DNA affinity purification and sequencing (DAP-seq) allows genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, Lax et al. use this technique to characterize 58 TFs encoded by genes regulated by adenine methylation, and provide insights into the regulatory mechanisms of gene expression in an opportunistic pathogenic fungus.

Dense calcium imaging combined with co-registered high-resolution electron microscopy reconstruction of the brain of the same mouse provide a functional connectomics map of tens of thousands of neurons of a region of the primary cortex and higher visual areas.

This work presents GōMartini 3, an improved coarse-grained protein model combining physics- and structure-based approaches. It boosts computational efficiency and accuracy for structured soluble and membrane as well as disordered peptides/proteins.

Authors show that all individuals have asymmetrically glycosylated IgGs—the glycans on each of the Fc protomers are not identical. Asymmetrically monofucosylated IgGs drive dengue disease and are functionally similar to afucosylated IgGs.

The pathophysiology of epilepsy is unclear. Here, the authors present single-nuclei transcriptomic profiling of human temporal lobe epilepsy from patients. They identified epilepsy-associated neuronal subtypes, and a panel of dysregulated genes, predicting neuronal circuits contributing to epilepsy.

High near-surface nitrogen-fixation rates that promoted the recent growth of the Great Atlantic Sargassum Belt were tied to greater upwelling of phosphorus from the equatorial Atlantic, according to coral-bound nitrogen isotope records from the Caribbean.

GO monolayers are presumed to invariably contain a large density of nanoscale pinholes. Here the authors present gas and proton transport measurements which show that GO monolayers can be pinhole-free over micrometer-scale areas.

HIV infection and substance use disorders converge in human midbrain. Here, authors show transcriptional impacts using single-nucleus RNA sequencing, linking dopaminergic vulnerability and microglial dysregulation, and in viremia, GABAergic deficits.

Artificial intelligence (AI) can greatly improve healthcare delivery and outcomes, but potential embedded biases can affect fairness in clinical deployment. Here, the authors develop a simulation-based approach to explore which formalisations of AI algorithmic fairness translate into long-term outcome fairness, with a focus on breast cancer.

As Nature Aging celebrates its fifth anniversary, the journal asks some of the researchers who contributed to the journal early on to reflect on the past and the future of aging and age-related disease research, the impact of the field on human health now and in the future, and what challenges need to be addressed to ensure sustained progress.

Classes of autism are uncovered with a generative mixture modeling approach leveraging matched phenotypic and genetic data from a large cohort, revealing different genetic programs underlying their phenotypic and clinical traits.

Powering single organic electrochemical transistor (OECT) device is challenging as power reductions can cause unstable device outputs. Wu et al. report a wearable, self-powered biosensor with a dual-OECT amplifier powered by an organic solar cell for monitoring physiological signals under varying light conditions.

This study reveals that phosphorus and nitrogen deficiency alters the abundance and profiles of extrachromosomal circular DNA in rice, underscoring its crucial role in genome plasticity and stress adaptation, which has implications for agricultural performance.

Martínez-Molina et al. utilized fMRI, EEG-TMS, and cognitive modeling to reveal the mechanisms behind expectation and adaptation to upcoming conflicting events, demonstrating the causal role of theta oscillations in the lateral prefrontal cortex.

Yeo and Zhou et al. profile whole-genome chromatin accessibility in different cell types of the adult neurogenic niche, which reveals a reversible decrease in the migration of proliferative neural stem cells in aged mice.

Here the authors report NiGa₂O_4–x(OH)_y for light-driven CO₂ hydrogenation to methanol. The surface Lewis acid–base pairs and -OH groups act as conduits for H^- /H⁺ transport to active sites, enhancing photocatalytic methanol production.

Anode materials used for sodium-ion batteries often suffer from poor stability and rate capability in electrochemical reactions. Yu et al.report a nanocomposite anode consisting of stibnite and reduced graphene oxide, which exhibits excellent cycle stability and rate performance.

This work presents a fully implantable wireless optogenetic device that delivers spatiotemporally patterned cortical stimulation through the skull and generates artificial perception in mice.

Lysosomes are vital for cellular health and linked to many diseases. Here, authors use cryo-ET to image intact lysosomes and resolve lysosomal protein structures, providing a platform to advance the study of lysosome biology.

The oocyte-to-embryo transition marks the beginning of development but the mechanisms underlying this process are incompletely described. Here they show that PRDM10 activates Septin11 and is required for progression through the oocyte-to-embryo transition.

The molecular etiology of hypertensive disorders of pregnancy is largely unknown. Here the authors show from a prospective study of diverse pregnancies that the disease can be split into molecular subtypes based on RNA data and validated a classifier for individuals with no preexisting high risk factors.

Timothy Frayling, Joel Hirschhorn, Peter Visscher and colleagues report a meta-analysis of genome-wide association studies for adult height in 253,288 individuals. They identify 697 variants in 423 loci significantly associated with adult height and find that these variants cluster in pathways involved in growth and together explain one-fifth of the heritability for this trait.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Huang and colleagues report that TIM4–AMPK signaling induces downregulation of the mitochondrial HSP90 chaperone TRAP1 in tumor-associated macrophages, thereby enhancing their immunoinhibitory function and promoting immune evasion and tumorigenesis.

Perineural invasion and cancer-induced nerve injury of tumour-associated nerves are associated with poor response to anti-PD-1 therapy, which can be reversed by combining anti-PD-1 therapy with anti-inflammatory interventions.

A strongly lensed galaxy at redshift z ≈ 6 is resolved into at least 15 star-forming clumps embedded in a rotating disk. Clump formation in this system, which is not predicted by cosmological zoom-in simulations, may be driven by disk instabilities with weak feedback, rather than past mergers.