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Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

A long- and short-read barley pan-transcriptome assembled from 20 diverse barley genotypes offers insights into genotype- and tissue-dependent gene expression and function.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

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.

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.

Long non-coding RNAs are implicated in multiple aspects of tumourigenesis. Here, the authors generate a landscape of these macromolecules in a wide array of cancer types and examine which RNAs are transcriptionally altered in relation to somatic driver mutations in established coding cancer genes.

Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

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.

Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evolutionary comparisons.

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

The clinical significance of inferring cell spatial profiles from histology images from cancer patients remains to be explored. Here, the authors develop a weakly-supervised deep-learning method, HistoCell, for the direct prediction of super-resolution cell spatial profiles from histology images at the single-nucleus-level.

Battery recyclability presents a sustainability challenge in materials design. Now it has been shown that aramid amphiphile self-assembly yields solid-state electrolytes with fast ion conductivity and electrochemical stability, which disassemble to the monomeric state upon solvent exposure, enabling inherently recyclable, molecularly engineered battery designs.

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.

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.

A population genomic analysis of 1,854 Listeria soil isolates collected across the contiguous United States identifies geographically prevalent phylogroups with increased pangenome openness and recombination, as a result of adaptation to variable environments.

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.

Managing power exhaust in fusion reactors is a key challenge, especially in compact designs for cost-effective commercial energy. This study shows how alternative divertor configurations improve exhaust control, enhance stability, absorb transients and enable independent plasma regulation.

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.

The authors report that the metallic spin-1/2 chain compound Ti₄MnBi₂ forms near a quantum critical point with inherent frustration. They identify strong 1D spin and 3D electron coupling that should stimulate the search for materials exhibiting a 1D Kondo effect and heavy fermions.

The efficacy of CAR-T cells against solid tumors is still limited by immunosuppressive factors. Here, the authors show that engineering of CAR T cells with A1R enhances their efficacy against solid tumors in vitro and in vivo.

Barocaloric materials, undergoing thermal changes in response to applied pressure, may provide energy efficient and zero-emission solid-state cooling. Here the authors report a mechanism for achieving large reversible barocaloric effects near ambient temperature, leveraging volume and conformational entropy changes within the organic bilayers of two-dimensional metal–halide perovskites.

The death of massive stars has traditionally been discovered by explosive events in the gamma-ray band. Liu et al. show that the sensitive wide-field monitor on board Einstein Probe can reveal a weak soft-X-ray signal much earlier than gamma rays.

Integrating incomplete multi-omics data remains a key challenge in precision oncology. IntegrAO, an unsupervised framework that integrates diverse omics, enables accurate patient classification even with incomplete datasets.

A combination of adenovirus-vectored and subunit protein intranasal vaccine enhances immune response against SARS-CoV-2 variants in animal models and humans.

Aligned 2D assembled fibres have been developed by drawing like 1D polymers, yet with disorders in cross-section. Here, the authors bidirectionally promote assembly order of graphene fibres, achieving high modulus and highly thermal conductivity.

Multi-ancestry genome-wide analyses identify 95 loci associated with post-traumatic stress disorder and implicate candidate genes, pathways and neurobiological systems underlying its pathophysiology.

Replacing animal feathers and wool with synthetic materials can ameliorate the ethical and environmental issues associated with the production of clothing designed to retain warmth. Here the authors present synthetic nanofibre textiles that combine wearability, comfort, lightness and thermal insulation.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Study shows PTSD predisposition shares distinct genes and genomic regions with several cardiovascular conditions. Here the findings reveal neuronal, immune, and metabolic pathways, and repurposed drug targets that further the understanding of the comorbidity.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Prostate cancers (PCa) are characterized by an immunosuppressive tumor microenvironment. Here the authors identify a subset of iron-loaded cancer-associated fibroblasts secreting myeloid cell-associated proteins and driving immunosuppression in PCa.

This study identifies and characterizes evolutionarily conserved cytosine methylation patterns related to age across mammals and establishes pan-mammalian epigenetic clocks.

Xue et al. report self-powered photoelectrochemical photodetectors based on CuOx decorated AlGaN nanowires with staggered energy band structure. High-energy photons can be absorbed by CuOx to trigger the multiexciton generation effect, enabling an external quantum efficiency of 131.5% at 255 nm.

Collective behavior plays an important role in predator evasion, but its neurogenetic basis is poorly understood. Here, Sato and Takahashi show that genetic diversity within groups of fruit flies enhances collective antipredator performance.

Patient-derived xenograft models (PDX) have been extensively used to study the molecular and clinical features of cancers. Here the authors present a cohort of 536 PDX models from 25 cancers, as well as their genomic and evolutionary profiles and their suitability for clinical trials.

A giant planet candidate roughly the size of Jupiter but more than 14 times as massive is observed by TESS and other instruments to be transiting the white dwarf star WD 1856+534.

The regenerative capacity of the lung in response to injury deteriorates with aging. Here, Raslan et al. discover that aging-associated progressive lung fibrosis is accompanied by persistent activation of blood vessels. The authors identified the vascular YAP/TrkB axis as a putative driver of this process and potential therapeutic target.

Alzheimer’s disease is associated with changes in astrocytes. Here the authors investigated the astrocyte translatome associated with amyloid-ß and tau pathology.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

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.

The seasonal lake dynamics in sub-Sahelian Africa are shaped by climate and human activities, revealing shared ecological vulnerabilities, according to a climatological analysis of 137 lakes.

Opsins are responsible for light perception across the animal kingdom. Here the authors show cryo-EM structures of an activated bistable opsin, shedding light on the activation mechanism of this class of bidirectional photoswitches.

Protein serial crystallography at X-ray free-electron lasers (XFELs) is a powerful technique for structure determination. Here, authors present a device for sample delivery designed to abate challenges to non-specialists allowing for compound screening.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.