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cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

Identifying jets originating from heavy quarks plays a fundamental role in hadronic collider experiments. In this work, the ATLAS Collaboration describes and tests a transformer-based neural network architecture for jet flavour tagging based on low-level input and physics-inspired constraints.

Cardiometabolic disease and depression often co-occur, but their multi-organ basis was unclear. Here, the authors analyse UK Biobank imaging and genetics, identifying abdomen-heart-brain networks and 43 shared loci, improving multimorbidity prediction

The CMS Collaboration reports the measurement of the spin, parity, and charge conjugation properties of all-charm tetraquarks, exotic fleeting particles formed in proton–proton collisions at the Large Hadron Collider.

Systems of electron spins in nuclear-spin-rich hosts are gaining attention for quantum memory applications. Using spin ensemble studies, the authors propose transition metal ions in halide double perovskites as promising candidates, featuring long electron spin coherence and deterministic nuclear spin control.

An outstanding question about the iron-based superconductors has been whether or not their magnetic characteristics are dominated by itinerant or localized magnetic moments. Absolute measurements and calculations of the magnetic response of undoped and Ni-doped BaFe₂As₂ indicate the latter.

By combining satellite observations with ground-based data and expert validation, this analysis demonstrates considerable misestimation of grassland extent and thereby carbon stock estimates in previous global assessments based on remote sensing.

The quark structure of the f₀(980) hadron is still unknown after 50 years of its discovery. Here, the CMS Collaboration reports a measurement of the elliptic flow of the f₀(980) state in proton-lead collisions at a nucleon-nucleon centre-of-mass energy of 8.16 TeV, providing strong evidence that the state is an ordinary meson.

Native top-down proteomics reveals epidermal growth factor receptor–estrogen receptor-alpha (EGFR–ER) signaling crosstalk in breast cancer cells and dissociation of nuclear transport factor 2 (NUTF2) dimers to modulate ER signaling and cell growth.

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

A multimodal pretrained transformer uses 154,274 pairs of chest CT scans and their corresponding reports and is applied to diverse clinical tasks with multimodal data.

MultiSTAAR provides a general and flexible statistical framework for functionally informed multi-trait rare variant analysis of biobank-scale sequencing studies by jointly analyzing multiple traits and incorporating annotation information.

A single-cell epigenomic atlas of human immune cells highlights cell-type-specific features associated with genetic or environmental exposures.

Metabolite signatures were identified for subtypes of dietary carbohydrate, including added sugar, whole grain and refined grain, and showed different associations with type 2 diabetes, providing an objective measure of dietary risk.

Screening methods to predict the development of type 1 diabetes (T1D) prior to pancreatic β-cell disruption are currently lacking. Here, the authors perform proteomics analysis of cord serum samples obtained from a Swedish birth cohort and identify an inflammatory signature predictive of disease development with good accuracy, suggesting that an inflammatory stage during pregnancy predisposes to T1D.

Gas-phase actinium monofluoride (AcF) has been produced and spectroscopically studied at the CERN-ISOLDE radioactive ion beam facility; the results highlight the potential of ²²⁷AcF for exceptionally sensitive searches of CP violation.

In this study, the authors present an fMRI‑based signature of corticospinal connections, which predicts individual pain sensitivity, generalizes to patient cohorts, and tracks changes after brain stimulation, suggesting a biomarker to guide personalized pain care.

A new artificial intelligence model, DeepSeek-R1, is introduced, demonstrating that the reasoning abilities of large language models can be incentivized through pure reinforcement learning, removing the need for human-annotated demonstrations.

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.

Optimizing the crystallization of the active materials in organic solar cells is challenging. Fu et al. use an acenaphthene additive to induce a two-step crystallization of the non-fullerene acceptor, achieving a certified 20.5% power conversion efficiency.

Patients with primary mitochondrial disease manifesting cardiomyopathy are twice as likely to die compared to those without cardiomyopathy. Here, the authors show that a modest increase in cardiac mitochondrial energetics via gene therapy can significantly improve cardiac function and is effective in treating mitochondrial cardiomyopathy.

While Bell inequalities have been violated several times—mostly in photonic systems—their violations within particle physics experiments are less explored. Here, the BESIII Collaboration showcases Bell-violating nonlocal correlations between entangled hyperon pairs.

Previous structural studies of T cell recognition of SARS-CoV-2 have been confined to spike epitopes. Here the authors assess T cell recognition of SARS-CoV-2 nucleocapsid epitopes, which are more conserved than spike epitopes, providing structural insights into recognition of two epitopes.

Ion diffusion region is an indicator of active magnetic reconnection, but it had not been detected in Jupiter’s magnetosphere previously. Here, the authors show a magnetic reconnection event in Jupiter’s inner magnetosphere that presents the detection of an ion diffusion region.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

The Einstein Probe has discovered a fast X-ray transient, EP240414a, associated with a broad-lined type Ic supernova. Its unusually soft spectrum and weak jet add to the diversity of stellar deaths and suggest a previously unknown Wolf–Rayet star explosion mechanism.

Chemoautotrophic carbon fixation is vital for evaluating permafrost carbon-climate feedback, but has been largely ignored. Here the authors find that dark carbon fixation predominates ~1/3 of the investigated thermokarst lakes on the Tibetan Plateau.

In this study, authors use molecular dynamics simulations to explore why Tantalum (Ta) and Zirconium (Zr) have different glass-forming abilities. It is shown that Ta’s lower critical cooling rate is due to stronger competing ordering effects and local icosahedral structures, which influence crystallisation pathways.

scTranslator is a large-scale generative model that translates single-cell transcriptomic data to proteomic data and can assess the impact of gene perturbation on protein levels.

Here the authors use a genome-wide approach to identify genetic variants associated with RNA isoform variation, uncovering new links between transcriptional regulation and complex traits. The findings can advance understanding of disease mechanisms.

By reconstituting and visualizing mammalian transcription elongation at the single-molecule level, Wang et al. dissected the effects of individual elongation factors on the speed of RNA polymerase II, which is found to operate as a multi-gear molecular machine.

Improved vaccines and antivirals are needed for many enveloped viruses. Here, the authors identify sulfur-based small molecules that disrupt viral membrane properties, inhibiting fusion and entry, and safely inactivate influenza virus. The resulting inactivated influenza vaccine is protective in mice.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Entanglement was observed in top–antitop quark events by the ATLAS experiment produced at the Large Hadron Collider at CERN using a proton–proton collision dataset with a centre-of-mass energy of √s  = 13 TeV and an integrated luminosity of 140 fb⁻¹.

Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.

Experimental measurements of high-order out-of-time-order correlators on a superconducting quantum processor show that these correlators remain highly sensitive to the quantum many-body dynamics in quantum computers at long timescales.

Spatial transcriptomic studies and lineage tracing reveal that, after brain injury, transient profibrotic fibroblasts develop from existing brain fibroblasts, infiltrate lesions, regulate the local immune response and lead to beneficial scar tissue formation.

The semileptonic decay channels of the Λc baryon can give important insights into weak interaction, but decay into a neutron, positron and electron neutrino has not been reported so far, due to difficulties in the final products’ identification. Here, the BESIII Collaboration reports its observation in e+e- collision data, exploiting machine-learning-based identification techniques.

The CMS Collaboration reports evidence for off-shell Higgs boson contributions in the production of Z boson pairs, and measures the width of the Higgs boson, which is inversely related to its lifetime.

This work presents a deep learning model that predicts white matter tracts from anatomical MRI without diffusion data. It enables faster, accessible mapping of white-matter connections for research and clinical use.

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.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

A reinforcement learning-based virtual reality system, implementing a series of sport sessions with coaching, was as effective as standard physical activity in reducing fat mass in adolescents, with positive effects on cognition.

The ALICE Collaboration provides details on the microscopic mechanism that ends up creating antideuteron in high-energy proton–proton collisions at the Large Hadron Collider.

Investigating the inner structure of baryons is important to further our understanding of the strong interaction. Here, the BESIII Collaboration extracts the absolute value of the ratio of the electric to magnetic form factors and its relative phase for e + e − → J/ψ → ΛΣ decays, enhancing the signal thanks to the vacuum polarisation effect at the J/ψ peak.

In this study, the authors combine interpolation techniques and deep learning methods, introducing Interpolating Neural Networks (INNs) to model complex systems with high accuracy and low computational cost.

Getting a picture of a d or f atomic orbital has been a challenge, but the X-ray scattering technique reported here enables direct transition from core s orbitals to the d orbitals so that their spatial shape can be mapped with no need for modelling.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Unlike the other iron-based superconductors, the parent compounds of the alkaline iron selenide superconductors are insulators. Dai and colleagues examine the spin-wave excitations in these materials and uncover evidence for a common magnetic origin for all iron-based superconductors.