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Gene isoforms are quantified with a machine learning method that optimally integrates long and short sequencing reads.

The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.

MORC2, a chromatin remodeler involved in epigenetic silencing and DNA repair, is linked to cancer and neurological disorders when dysregulated. Here, the authors show that MORC2 binds DNA at multiple sites, clamps onto it, and induces compaction, a process regulated by its phosphorylation.

NIPBL perturbation activates long terminal repeat (LTR)-derived alternative promoters due to reorganization of chromatin’s hierarchical structure, leading to LTR co-option and oncogene activation in melanoma cell lines.

In a post-hoc analysis of circulating tumor DNA (ctDNA) features from patients with metastatic prostate cancer treated with [¹⁷⁷Lu]Lu–PSMA-617 or cabazitaxel in the randomized phase 2 TheraP trial, low ctDNA levels at baseline were predictive of clinical benefit from [¹⁷⁷Lu]Lu–PSMA-617, and PTEN or ATM alterations were identified as potential biomarkers of response.

Complex structural variations and rearrangements in cancer are identified using long-read sequencing.

Fluorescent calcium imaging reveals the firing patterns of brain cells, but microscopy in behaving animals is challenging due to brain motion. Here, the authors develop a two-photon fluorescent microscope to record from many cells in a brain volume of freely-behaving Drosophila larvae.

Analysis of whole-genome sequencing data from hematopoietic stem and progenitor cells taken from patients with myeloma shows how treatment shapes clonal architecture and sheds light on the evolution of treatment-related myeloid neoplasms.

Mesocosm experiments revealed that both phytoplankton community composition and cellular acclimation influence marine particulate C:N:P ratios, with community shifts more sensitive to nitrogen supply and acclimation to the nutrient N:P supply ratio

The authors present a chip-less wearable sensor-processor integrated neuromorphic system that combines multimodal physicochemical sensing with neuromorphic processing for real-time, autonomous physiological monitoring.

Using flow cytometry and single-cell RNA-sequencing, the authors here describe immune signatures defined by dysfunctional NK and T-cell responses that discriminate patients who develop severe dengue infection from those with uncomplicated dengue.

This analysis provides a collection of sequencing datasets generated from long-read and short-read RNA sequencing, serving as a valuable resource for transcriptome profiling.

X chromosomes evolve faster than autosomes, but confounding factors make this a difficult phenomenon to study. Utilising the unusual sex determination system of Sciaridae flies, this study finds a slower evolution of the X chromosomes which appears to be driven by strong purifying selection.

A CRISPR knock-in strategy that uses endogenous gene regulatory mechanisms can engineer ‘armoured’ CAR T cells that secrete proinflammatory cytokines directly within a tumour without causing toxicity, leading to prolonged survival in mice.

A gender gap in mathematical ability arises shortly after children begin school — irrespective of the type of school they attend and their socio-economic background.

Currently, most miRNA profiling study of complex tissues are based on bulk sample sequencing, among which the cellular heterogeneity may become an important potential confounding factor. Here, the authors developed a deconvolution method to systematically decode cellular components of complex tissues from miRNA profiling data.

This work presents ReLiC, an RNA-linked CRISPR platform that enables dissection of RNA metabolic processes by targeting over 2,000 RNA-associated genes, revealing key regulators on RNA splicing, translation and decay.

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.

Using pancreatic organoids and genetic mouse models, Antonucci et al. show that cellular stress activates an NRF2–EZH2 epigenetic axis leading to metabolic reprogramming and subsequent malignant transformation of KRAS-mutant benign lesions.

An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the identification of new species associated with the development of cancer.

Tumour evolution and heterogeneity in high grade serous ovarian cancer (HGSOC) remains poorly characterised. Here, the authors investigate the genomic landscape of HGSOC and reveal two distinct evolutionary trajectories associated with clinical outcomes.

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

DNA variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve genotyping accuracy, however this increases computational complexity. Here the authors develop an approximate haplotagging method that simplifies the process and enables state-of-the-art variant calling performance with multiple sequencing platforms.

Rashan, Bartlett and colleagues show that mammalian 4-hydroxy fatty acids are primarily catabolized by ACAD10 and ACAD11 (atypical mitochondrial and peroxisomal acyl-CoA dehydrogenases, respectively) that use phosphorylation in their reaction mechanisms.

Long-read chromatin assay reveals (1) a novel class of accessible chromatin regions, (2) accessibility within individual LTR retrotransposons and (3) the relationship between diffuse accessibility, gene body methylation and hAT transposon insertion.

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.

CMOS-based circuits can be integrated with silicon-based spin qubits and can be controlled at milli-kelvin temperatures, which can potentially help scale up these systems.

Iron has been shown to be necessary for the activation and differentiation of CD8⁺ T cells. Here the authors investigate changes in CD8⁺ T cell metabolism in iron limiting conditions and find that aspartate is increased yet downstream nucleotide synthesis is suppressed and addition of exogenous aspartate partially rescues T cell function.

The downscaling process of conventional static random-access memory (SRAM) cells has recently slowed down, posing challenges for future electronic devices. Here, the authors demonstrate ~40% reduction in cell area and improved interconnect length for 2-tier 3D-integrated SRAM cells based on 2D MoS₂ transistors.

High-resolution multi-omic profiling indicates widespread gut dysbiosis in individuals with MASLD, also affecting the virome, and reveals microbial signatures that can classify MASLD and its subtypes.

An analysis of research papers and citing patents indicates the extensive ties between computer-vision research and surveillance.

Current intracortical brain-computer interfaces are subject to recording interface instabilities that degrade decoding performance. Here, the authors present a platform for Nonlinear Manifold Alignment with Dynamics (NoMAD), which stabilizes decoding using models of dynamics for at least 3 months.

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.

Sinonasal squamous cell carcinoma (SNSCC) is an uncommon tumor, which has been associated with the human papillomavirus (HPV). Here the authors perform comprehensive genome-wide characterization of HPV-associated and HPV-independent SNSCC patient samples to reveal molecular patterns of tumorigenesis and identify HPV-driven mutational profiles.

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.

Around 1 in 136 pregnancies is lost due to a pathogenic small sequence variant genotype in the fetus.

Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molecular basis of an undiagnosed Mendelian disease case with an X;13-balanced translocation.

Authors report MagNet, a plasma extracellular vesicle (EV) enrichment strategy using magnetic beads. Proteomic interrogation of this plasma EV fraction enables the detection of proteins that are beyond the dynamic range of mass spectrometry of unfractionated plasma.

This study characterizes the three-dimensional (3D) genome architecture of 15 primary human cancer types from The Cancer Genome Atlas. The analyses identify different archetypes of enhancer usage and enhancer rewiring events due to different classes of mutations and structural variants.

Ataxia-telangiectasia mutated protein (ATM) phosphorylates CD98HC to promote neutral amino acid antiporter trafficking. Here the authors show that ATM loss impairs glutamate, cystine, and arginine transport, driving metabolic stress and ataxia telangiectasia–like phenotypes.

High-resolution, spatial transcriptomic analysis of colorectal cancers using matched sequencing- and imaging-based methods characterizes immune cells and their interactions with the tumor microenvironment.

Bacteria can undergo adaptive evolution during severe infections, leading to treatment failure. The authors use within-host evolution genomic analysis to investigate persistent Staphylococcus aureus infections and optimise antibiotic treatment.

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.

Vaccination efficiency in HIV infection is hampered by the low immunogenicity of HIV-1 Env glycoprotein (Env). Here authors optimise the neutralising antibody response to Env by stabilizing the Env trimers in the context of expressing them in a Newcastle Disease Virus-like particle and providing conditions that mimics replicating virus infection.

Sarcoma is a highly heterogeneous disease, which can be caused by a large variety of mutations. Here, the authors utilise multi-omics to characterise a cohort of 1,340 sarcoma tissue specimens to identify key somatic mutations and identify immune subtypes.

FIKK effector kinases underwent rapid evolutionary expansion and are a druggable target in Plasmodium falciparum.

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 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.

Monkeypox virus genomic data from Nigeria and Cameroon, sampled between 2018 and 2023, indicate that the virus spread through repeated zoonoses in Cameroon, whereas in Nigeria, it spread mainly through human–human transmission, predominantly originating in Rivers State.

Biller et al. use long-read sequencing of fractionated ocean nanoparticles, showing that extracellular vesicles and virus-like particles contain distinct pools of genetic information and thus may differentially contribute to horizontal gene transfer dynamics in the ocean.