Search

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

Nylon-11 is a common and durable polymer but possess low piezoelectric properties. Here, the authors use mechanical accelerations and strong electric fields to induce crystallization, hydrogen-bonding and dipole alignment in Nylon-11 films, achieving high piezoelectricity.

A M5 earthquake triggered the 2018 Sierra Negra eruption after 10 hours. Subsequent microseismicity revealed a cryptic fluid phase facilitated magma intrusion, highlighting that cascading processes are potentially essential for eruption initiations.

HIV-1 integrase forms an RNA-binding module on the luminal side of the mature capsid lattice.

Estimates from the Global Burden of Disease study reveal declines in chronic respiratory disease mortality between 1990 and 2023—especially during the COVID-19 pandemic—but the burdens on people affected remain substantial.

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.

Lung adenocarcinoma is often curable when diagnosed at an early stage, but a subsection of patients will progress. Here, the authors use multi-omics profiling to show that gene expression data can predict clinical outcome.

Global Burden of Disease estimates show that between 1990 and 2023, the prevalence and burden of drug use disorders, inclusive of amphetamine, cannabis, cocaine and opioid use, have been increasing in high-income countries, particularly in the USA.

Jupiter’s radiation belt exhibits complex electron distributions shaped by wave–particle interactions and moon absorption. Here, the authors identify an electron slot region and quantify its formation driven by whistler waves via Juno mission data and simulations.

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.

Human impacts on marine ecosystems are increasing the likelihood of pathogenic outbreaks, harmful algal blooms and coral stress. Here the authors develop a CRISPR biomonitoring tool that can help detect key marine species that are important to public health, the aquaculture sector and marine ecosystems.

Atomic force microscopy is used to investigate the adsorption and organization of ions on charged surfaces. Trivalent ions adopt complex networks, clusters and layers associated with overcharging, whereas divalent ions follow classical predictions.

Spatial transcriptomics (ST) technologies link tissue morphology with gene expression, but remain expensive to use; furthermore, models that predict ST data from histopathology images possess considerable limitations. Here, the authors develop STimage, a deep learning probabilistic framework for ST prediction from histopathology images while prioritising robustness and interpretability.

The growth of a biofilm—a bacterial colony attached to a surface—is governed by a trade-off between horizontal and vertical expansion. Now, it is shown that this process significantly depends on the contact angle at the biofilm’s edge.

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.

The authors employ a 3D printing technique to induce a triple-twinned martensitic microstructure in a commercial titanium alloy, achieving both high strength and enhanced strain hardening.

In this study, Yang et al. compile a global dataset to uncover the degree to which plants coordinate root and seed traits. They report a global positive correlation between root diameter and seed size, driven by dual roles of arbuscular mycorrhiza in phosphorus uptake and pathogen defence.

STAARpipeline is a comprehensive framework for flexible and scalable rare-variant association analysis using whole-genome sequencing data and annotation information.

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.

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.

Parity induces an accumulation of CD8⁺ T cells, including cells with a tissue-resident-memory-like phenotype within human normal breast tissue, offering long-term protection against triple-negative breast cancer.

The authors create a distributed sensor array that achieves optical super-resolution without lenses, using computational synchronization to combine multiple sensors and expand imaging areas 16-fold beyond physical sensor dimensions.

There has been significant interest in using spin-waves or magnons for information processing, due to their low energy dissipation and short wavelength at terahertz frequencies, however, manipulating magnons can be challenging. Here, Kim et al show that magnons in Sr2IrO4 are extremely strain sensitive, with small applied strains leading to large variation in the magnon energy.

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.

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.

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.

Amorphous films with tunable thermal conductivity are needed for semiconductor/aerospace fields. Amorphous Al(Ti)N nanoparticles have negligible effect on thermal conductivity of Si₃N₄ 2 W m⁻¹K⁻¹, while incorporating crystal TiN phases increases to 15 W m⁻¹K⁻¹.

During poxvirus-induced shutoff, certain cellular and viral mRNAs continue to be translated through distinct modes of non-canonical initiation, in part due to altered ribosome activity, to produce host and viral proteins that support virus spread.

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

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.

The accretion geometry of X-ray binary Cygnus X-3 is determined here from IXPE observations. X-ray polarization reveals a narrow funnel with reflecting walls, which focuses emission, making Cyg X-3 appear as an ultraluminous X-ray source.

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.

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.

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.

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.

Despite extensive structural studies elucidating how antigens are anchored to antigen-presenting molecules and presented to T cells, little is known about the display mechanism of the lipid-antigen-presenting molecule CD1c. Here, by combining structural immunology, lipidomics, and biophysical analysis, the authors reveal that the CD1c binding cleft accommodates two different lipids, one of them with a bulky headgroup positioned sideways for display to T cells, rather than upwards, different from the conventional upright antigen-presentation mode

Understanding the keyhole porosity formation is important in laser powder bed fusion. Here the authors reveal the dynamics of keyhole fluctuation, and collapse that induces bubble formation with three main stages of evolution; growth, shrinkage, and being captured by the solidification front.

Delay lines are a critical part of future optical communications. Here, the authors create a delay line in free space by tuning the group velocities of multiple inline space-time wavepackets to introduce different delays.

A stacked series of lithographed polymer disks could provide a lightweight and modular optics system for a future hard X-ray telescope, retaining the angular resolution of current telescopes, but improving on effective area.

The ability to imprint phase shifts on light lie at the basis of several classical and quantum light-based information processing primitives. Here, the authors demonstrate the phase shift of an optical field by a single quantum emitter in a waveguide, at the single photon level.