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Blue light promotes DNA repair in plants via cryptochrome signalling. Here the authors report that this occurs via suppression of COP1 mediated degradation of the repair factor ADA2b and propose that together photoreceptors and COP1 balance genome stability with growth under fluctuating light.

Extremely quantum-confined Cd₃P₂ magic-size clusters exhibit linearly polarized excitons with large oscillator strength, allowing observation of a Mollow-like lineshape under resonant coherent driving by laser pulses.

A single-crystalline aluminum nitride seed layer improves crystal alignment in scandium-doped aluminum nitride films, and subsequent removal eliminates polarity mismatch, enabling high-performance film bulk acoustic resonators and wideband filters.

The authors demonstrate that targeted protein degradation of the dengue virus capsid suppresses infection through capsid-dependent pathways rather than classical inhibition, revealing a new antiviral strategy effective against resistant viral variants.

Here the authors introduce a radical-based approach for the generation of allylic copper(III) complexes, enabling the efficient synthesis of allylic amines in the presence of alkyl/aryl amines.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

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

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.

Messenger RNA therapeutics hold great promise but are limited by suboptimal protein expression. Here, the authors develop RiboDecode, a deep learning framework that generates optimized mRNA codon sequences to significantly enhance translation efficiency and therapeutic efficacy in both vaccines and protein replacement therapies.

The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

Evolution of accretion disk and corona during outbursts in black hole binary systems is still unclear. Here, the authors show spectral analysis of MAXI J1820+070 and propose a scenario of a dynamical corona to explain the evolution of the reflection fraction observed by Insight-HXMT.

The ALPK1 agonist UDSP-Hep stimulates tumour-cell antigen presentation, macrophage–DC cross-priming and differentiation of protective memory T cells.

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.

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.

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.

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.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

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 characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

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.

A circular economy approach applied to the global lithium-ion battery supply chain shows that combining cross-regional cooperation on technology and trade with regionally tailored domestic circular economy policies yields the highest global emission reduction.

Direct reduction of unactivated alkyl halides for C(sp3)-N couplings under mild conditions presents a significant challenge in organic synthesis. Here the authors introduce an in situ formed pyridyl carbene-ligated copper (I) catalyst that is capable of abstracting halide atom and generating alkyl radicals for general C(sp3)-N couplings under visible light.

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.

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.

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.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

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.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

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.

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.

Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.

The interplay of electronic correlations and topology has been a forefront topic in condensed matter physics. Wang et al. present evidence of a correlated topological edge state supporting the Luttinger liquid behaviour in the candidate quadrupole topological insulator Ta₂Pd₃Te₅.

Energy density and cyclability are often a trade-off for lithium-ion batteries. The authors develop cobalt- and nickel-free cathodes with both good cycling stability and high energy density through the integration of polyanion units into rocksalt structures.

Environmental transmission electron microscopy reveals distinct atomistic pathways for the reduction of NiO to metallic nickel by CO and H₂, with H₂ more effective in transforming the entire bulk material.

The authors investigate the response of Archaea to experimental warming in a tallgrass prairie ecosystem. Warming was linked to reduced diversity and convergent succession, with further links to changed ecosystem function. Stochastic processes dominated community changes but decreased over time.

Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

Inflammatory immune cells are found in the synovial fluid of patients with rheumatoid arthritis (RA). Here the authors use scRNA sequencing of synovial fluid cells from RA patients before and after treatment with adalimumab/tofacitinib and find changes in inflammatory SPP1+ macrophages and explore the function of these cells in mouse models.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

Crystal structures of the Legionella effector SdeA in a ligand-free state and in complex with ubiquitin and NADH provide insight into SdeA-mediated phosphoribosyl-linked ubiquitination.

Assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation strategies. Sang et al. assemble a reference genome for Populus koreana and combine population genomics and modelling to predict spatiotemporal responses to climate change.

The authors show that bulk brittle semiconductors can be plastically manufactured like metals by warm metalworking into free-standing, metre-scale films with decent physical properties.

Arabidopsis blue-light photoreceptor cryptochromes interact with ADA2b and SMC5 in a blue-light-dependent manner, which enhances ADA2b–SMC5 interaction and promotes ADA2b-mediated recruitment of SMC5 to DNA double-strand breaks, leading to break repair.

Recent studies have reported the exceptional plasticity of InSe van der Waals crystals, but their deformation-correlated lattice dynamics remains unexplored. Here, the authors investigate the correlations of plastic interlayer slip, lattice anharmonicity and thermal transport in β-InSe crystals via neutron scattering techniques.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.