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Here, as part of the Sherlock-Lung study, the authors profile the microbiomes of 940 lung cancers in never smokers finding no significant associations with demographic and clinical features, suggesting lung bacteria are unlikely to have a sizable role in lung cancer.

Neural basis of decision-making is not fully understood. Here authors show that mouse prefrontal neurons encode history-specific rewards and choices. However, their influence is gated by task structure and timing, affecting decisions primarily in variable interval tasks and when temporal delays separate events.

Vaziri et al. examined how humans detect changes in auditory pitch, revealing that listeners rely on correlations in sound intensity over frequency and time, processing that is reminiscent of visual motion detection.

Prior hypoglycemia alters the paracrine interaction between islet α and δ cells, leading to impaired counter-regulatory glucagon secretion through somatostatin hypersecretion, increasing the risk of recurrent hypoglycemia.

Chemical language models trained on known metabolites can identify previously unknown metabolites from mass spectrometry-based metabolomics data with high accuracy.

Protein language models capture single proteins but struggle with interactions. Here, authors present MINT, trained on large PPI datasets, which outperforms existing PLMs in predicting binding, mutations, and immune interactions, advancing biomedical discovery.

While alternative splicing is known to drive oncogenesis and be a source of potential therapeutic targets, identifying such drivers on a genome-wide scale has proven difficult. Here, the authors present a computational approach to identify potential cancer-driver exons and evaluate applicability as therapeutic targets.

The way in which the brain processes language from a collection of sounds to meaningful concepts remains poorly understood. Here, the authors show that the brain’s temporal responses to speech closely follow the layer-by-layer progression of LLMs, revealing shared computational principles.

Here, the authors examine the mechanisms behind cheatgrass’s successful invasion of North American ecosystems. Their genetic analyses and common garden experiments demonstrate that multiple introductions and migrations facilitated cheatgrass local adaptation.

This study shows that during the first wave of SARS-CoV-2 infection in England, residents of long-term care facilities who survived infection developed a robust and stable immunity against the virus that did not negatively impact responses to other seasonal viruses.

Zhao et al. generated models from whole blood gene expression to predict amyotrophic lateral sclerosis case-control status and combined gene features with clinical variables to predict survival, both validated in an external independent dataset.

Mapping of the neutrophil compartment using single-cell transcriptional data from multiple physiological and patological states reveals its organizational architecture and how cell state dynamics and trajectories vary during health, inflammation and cancer.

To enable a sensed RNA to activate diverse RNA effectors, the authors engineer a programmable dual-site ribozyme that, upon RNA trigger binding, self-cleaves to release an embedded RNA. It enables trigger-dependent release of diverse ncRNAs and controls CRISPR-Cas9 editing in zebrafish and human cells.

A combination of high-resolution spatial imaging, spatial proteomics and transcriptional data reveals sparse and heterogeneous bacterial signals in gliomas and brain metastases.

A dictionary of human-to-mouse variants aids the design of mouse models of disease.

In this work, authors utilise comparative transcriptomics to reveal lncRNAs that distinguish pathogen-specific from core macrophage responses. They identify a Q fever-specific AHR-regulated CYP1B1-AS1/CYP1B1 axis that modulates mitochondrial homeostasis and survival of Coxiella burnetii.

Spatial and single-nucleus analyses in human postmortem Alzheimer’s disease (AD) brain tissues at early and late stages from individuals with and without Down syndrome, as well as in AD mouse models, show sex and species-specific phenotypic changes.

High-depth sequencing of non-cancerous tissue from patients with metastatic cancer reveals single-base mutational signatures of alcohol, smoking and cancer treatments, and reveals how exogenous factors, including cancer therapies, affect somatic cell evolution.

Profiling host RNA shed in feces reveals disease states in the gut.

Human host-associated cellular products may act as induction agents for bacteriophages.

Chronic stress is a risk factor for depression, yet the mechanisms are unclear. Here, the authors show in mice that stress drives interferon-mediated neutrophil recruitment from the skull to the brain’s outer membranes, contributing to depressive behaviors.

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.

Base editors can inactivate splice sites or introduce stop codons into a gene sequence. Here the authors present SpliceR to design, rank, and test sgRNAs for efficient gene disruption in T cells.

Aligning electrocorticography data into a shared space improves how large language models predict brain activity during language comprehension, enhancing encoding accuracy, cross-participant generalization and denoising—especially in language-selective regions.

Here, using a genome-wide CRISPR screen, Bitew et al. identify GRA38, a phosphatidic acid phosphatase, as a key factor in Toxoplasma gondii adaptation to lipid-rich conditions via keeping lipid balance, sustaining growth, ultimately ensuring survival.

By learning a semantics of gene function based on genomic context, the genomic language model Evo autocompletes DNA prompts to generate novel genes encoding protein and RNA molecules with defined activities, whose sequences generalize beyond those found in nature.

A mathematical framework to estimate the fitness of cancer driver mutations by integrating mutational bias, oncogenicity and immunogenicity finds fundamental trade-offs in cancer evolution.

Riparian vegetation reduced gulf turbidity up to 800 meters offshore, overlapping coral reefs and seagrasses, while pasture and gravel roads increased turbidity, according to a scalable framework using remote sensing and causal inference methods.

Approximately 17% of meningiomas remain genomically uncharacterized. Here, the authors analyze 105 meningiomas without known driver mutations or significant copy number alterations and identify a subgroup of meningiomas, defined by FOS/FOSB gene fusions with distinctive transcriptomic and histopathological features.

The INTIMET study is a randomized 26-week double-blind clinical trial to assess whether metformin can reduce insulin resistance in adults with type 1 diabetes. Metformin did not reduce insulin resistance in type 1 diabetes, but lowered insulin dose versus placebo – a secondary outcome.

Head motion is an artifact in structural and functional MRI signals, and some traits or groups are more strongly correlated with motion than others. Here the authors describe a method to attribute a motion impact score to specific trait-functional connectivity relationships.

After spinal cord injury (SCI), cyclic adenosine monophosphate (cAMP) levels drop in the central nervous system. Here, authors show that boosting cAMP and subsequently activating corticospinal neurons led to improved neuronal function and motor recovery in female rats after SCI, highlighting a brainstem rerouting pathway for restoring movement after injury.

Here the authors show inducible genes and enhancers are regulated mainly by transcriptional burst frequency and that this is coordinated in single cells and individual alleles. Cohesin, which is important for inducible gene expression, is largely dispensable for regulating enhancer burst frequencies; however, it is required for coupling burst frequencies of inducible enhancers and promoters.

Autoimmune encephalitis (AIE) may involve neuron-specific cytotoxic T cells, but evidence is still lacking. Here the authors use induced pluripotent stem cells from patients with AIE and single cell RNA-sequencing of ex vivo CD8 T cells to find neuron-specific, KIR⁺CD8⁺ T cells with altered transcriptome that potentially contribute to AIE etiology.

MAP-X is used to map protein complexes in P. falciparum, identifying previously undescribed interactions, revealing stage-specific dynamics and predicting moonlighting behaviour of subunits.

Integrated multi-omic analyses using samples from the TRACERx study highlight cross-talk between DNA hypermethylation and genomic lesions in non-small cell lung cancer.

Efforts to apply targeted protein degradation for antibiotic development are limited by our understanding of prokaryotic protein degradation. Here, the authors establish a chemical-genetic platform and predictive model to determine the degradation potential of essential mycobacterial proteins.

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.

Single-cell analysis of lung cancer progression uncovers developmental and regenerative programs co-opted by cancer cells and immune-mediated pruning during metastatic outbreak

Shotgun metagenomic sequencing (using the MinION platform) of mock microbial communities and faecal samples from healthy and ill preterm infants can be used to identify pathogens and their antimicrobial resistance gene profiles in real time, indicating the potential for translation into clinical settings.

Perceiving the size of objects is subjective. Here the authors show that these subjective differences in size perception can be explained by the individual variance in spatial tuning of neuronal populations in the primary visual cortex.

The genomic profiling of tumours has not been widely adopted in the clinic due to technical and practical hurdles. Here, the authors develop PGDx elio tissue complete, a scalable, standardised and FDA-cleared test comprising a targeted gene panel and automated machine-learning analysis, which detects clinically relevant sequence biomarkers in cancer samples.

Here the authors develop a probabilistic model for single-cell DNA sequencing of aneuploid tumors that infers clone-specific replication timing and S-phase fractions, unveiling their relationships with copy number evolution and clonal fitness.

In people with severe brain injuries, stimulation restored consciousness by engaging a deep brain circuit for wakefulness—revealing a target that may also guide treatment in stroke and epilepsy.

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.

Genomic analyses applied to 14 childhood- and adult-onset psychiatric disorders identifies five underlying genomic factors that explain the majority of the genetic variance of the individual disorders.

Bacteriophage diversity in cell-free DNA within human plasma can help to specify pathogenic Escherichia coli and Staphylococcus aureus during sepsis.