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Polyploidy and subsequent post-polyploid diploidization (PPD) contribute to evolutionary success of plant species. Here, using 11 genomes from all nine subfamilies of Malvaceae as an example, the authors provide evidence to support the “polyploidy for survival and PPD for success” hypothesis.

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.

The tumor microenvironment influences the metabolic behavior of cancer cells. Here, using Dual Ribosome Profiling, the authors uncover a cancer-stromal cell interaction under glucose starvation that increases nutrient availability, in response to type I interferon. In addition, in vivo, immune checkpoint blockade triggers metabolic constraints in T cells, reducing their proliferation and cytotoxicity.

The tumour microenvironment often suppresses immune cell function and cancer-associated fibroblasts (CAF) are involved in the process. Here authors show in human tumours and in mouse models that AEBP1 is highly expressed in CAFs, and via autocrine stimulation of its receptor CKAP4, it induces the upregulation of PD-L1, which inhibits the anti-tumor T cell response.

Federated learning (FL) algorithms have emerged as a promising solution to train models for healthcare imaging across institutions while preserving privacy. Here, the authors describe the Federated Tumor Segmentation (FeTS) challenge for the decentralised benchmarking of FL algorithms and evaluation of Healthcare AI algorithm generalizability in real-world cancer imaging datasets.

Sequencing the genome and microbiome of about 1,500 tick samples from regions across China revealed host–microbe associations in ticks that could have implications for controlling ticks and tick-borne diseases.

Spin defects in 2D materials offer practical advantages for quantum sensing over their 3D counterparts. Here, the authors demonstrate quantum sensing under high pressure using boron vacancy centers in hBN placed inside a diamond anvil cell and use it to detect both stress gradient inside the pressure chamber and pressure-induced magnetic phase transitions.

Chronic care manages long-term, progressive conditions, while acute care handles short-term ones. Here, authors show chronic conditions account for most of the global health burden, with 68% of DALYs and 93% of YLDs attributed to chronic care needs.

Isotope engineering can enhance spin coherence of solid-state defects, such as NV centers in diamond but progress for defects in hBN has been limited. Gong et al. report the optimization of isotopes in hBN and demonstrate improved coherence and relaxation times for the negatively charged boron vacancy centers.

Identifying an immunologic marker as a correlate of protection (CoP) for RSV vaccination is important. Here, the authors demonstrate RSV neutralizing antibodies and RSV prefusion IgG binding antibodies as CoP for mRNA vaccination against RSV disease.

Blue QD-LEDs suffer from poor operational stability due to the carrier accumulation at transport layers. Here, the authors propose a strategy to mitigate the hole accumulation driven oxidation in hole transport layer, effectively elongating the operational lifetime of blue QD-LEDs.

Multiyear analysis of antibody responses in recipients of the dengue vaccine Dengvaxia in the Philippines supports their utility as a predictor of protection against disease, and reveals that Dengvaxia efficacy declines 3 years after complete vaccination.

Gastric Squamous Cell Carcinoma (GSCC) is a rare subtype of gastric cancer with unknown etiology. Here, the authors identify frequent mutations in epigenetic regulation genes including EZH2 in twenty GSCC patient samples, and demonstrate that EZH2 loss, along with TP53 and PTEN loss, leads to GSCC in mouse models.

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.

An icing forecast hydrogel device encapsulating ice-nucleating proteins colorimetrically predicts ice formation with high accuracy. The device successfully activated a wind turbine deicing system 70 min before ice accumulation.

The pentazolate anion shows great promise for high energy density materials, but has only been isolated alongside non-energetic counter ions that impede its energetic properties. Here, the authors synthesize a silver cyclo-N₅-complex devoid of stabilizing ions, as well as a complementary [Ag(NH₃)₂]⁺[Ag₃(N₅)₄]⁻ 3D framework.

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.

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.

Adenoids and tonsils in children can become hypertrophic because of multiple infections. Here the authors use single cell transcriptomics to assess the immune cell composition of these hypertrophic organs and find B, T and NK cells and exhausted memory CD4 T cells indicating immune changes in these organs associated with respiratory infection.

A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

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.

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.

Building liquid devices from solid enclosing walls can be costly and lack reconfigurability. Now the rapid construction and reconfiguration of diverse liquid devices is demonstrated through assembly and disassembly of droplet arrays in a pillared substrate.

DICER1 syndrome is associated with a predisposition to multiple tumor types. Here, the authors identify and characterize 3 molecular subgroups of mesenchymal tumors with DICER1 mutations.

Species genomes are important for analyses of genetic variation. Wu et al. assembled a T2T genome of a male cashmere goat, including 288.5 Mb of previously unresolved regions, and identified selective variants and genes associated with domestication and cashmere traits.

Using a longitudinal dataset, the authors investigated the effects of maternal positive mental health during pregnancy on offspring’s structural brain morphology and functional brain connectivity.

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.

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.

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.

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.

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.

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.

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.

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

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 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.

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.

A biosynthetic enzyme that mediates ligand-protein NOS chemistry allowing addition and decarboxylation alongside noncanonical FAD-dependent reactions to implement the N-formimidoylation/-iminoacetylation modification in aminoglycosides was uncovered.

Functional characterization of genetic alterations is a prerequisite for pancreatic cancer precision medicine. Here, using in vivo CRISPR screens, the authors integrate human cancer genomics and mouse models, identifying that loss of USP15 or SCAF1 accelerates tumor development and leads to reduced inflammatory responses and increased sensitivity to PARP inhibition and Gemcitabine.

The use of metal clusters to construct artificial protein-mimic structures with adaptable cavities has potential for simulating the dynamics and functionality of natural proteins. Here, the authors develop a family of chiral metal-peptide assemblies using {Ni3} clusters and flexible peptides, resulting in structures such as octahedral cages, trigonal prisms, and capsules.

All-thermal evaporation enables the fabrication of green perovskite LEDs with a peak external quantum efficiency of 16.4%, and active-matrix displays with high resolution and continuous greyscale information.

Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here, the authors present the largest FL study to-date to generate an automatic tumor boundary detector for glioblastoma.