differential expression

VIPER-seq: Protein-mediated small RNA enrichment enhances plant virus detection at low viral abundance

VIPER-seq improves virus detection in plants by enriching viral small RNAs using protein-mediated methods, showing better sensitivity in low-titre infections.

Reference normalizations of Effort-To-Compress across length, alphabet size, and composition

The paper introduces normalized versions of Effort-To-Compress (ETC) to enable fair comparisons of symbolic complexity across different sequence lengths, alphabet sizes, and compositions.

Predicting clonal mutations from tumour spatial transcriptomics data using a graph convolutional neural network

This paper introduces SPOT-Mut, a graph convolutional neural network that predicts clonal mutations from spatial transcriptomics data, achieving high precision and recall for key driver genes.

Sequence-Independent In Situ Imaging of GlycoRNA in Living Cells and Tissues based on COMPASS

The paper introduces COMPASS, a method for sequence-independent imaging of glycoRNAs in living cells and tissues, revealing their distribution in cancer and neurogenesis.

High-resolution analysis of T cell subsets, clonality, and trajectories in psoriasis

This study analyzes T cell subsets, clonality, and trajectories in psoriasis using single-cell RNA and TCR sequencing, revealing tissue-specific and shared features of the T-cell repertoire.

An aged human bone marrow mesenchymal niche causes impaired function of human hematopoietic stem cells under regeneration-induced stress

This study shows that aged human bone marrow mesenchymal stromal cells impair hematopoietic stem cell function under regeneration stress by promoting myeloid bias.

CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition

The paper identifies a mitochondrial co-expression module in microglia linked to cognition using snRNA-seq data from the SEA-AD dataset and shows that filtering by %MT may remove cognitively relevant cells.

Male youth BMI is associated with epigenetic ageing of female descendants but not blood or sperm DNA methylation

Maternal Folate Nutrition Programs Adult Hematopoietic Stem Cell Function Through Mitochondrial Remodeling

This study shows maternal folate levels influence adult hematopoietic stem cell function through mitochondrial and chromatin changes in offspring.

Stromal COL12A1 defines a pro-invasive extracellular matrix niche in appendiceal mucinous neoplasms and pseudomyxoma peritonei

This study identifies stromal COL12A1 as a key component of the extracellular matrix niche that supports invasion in appendiceal mucinous neoplasms and pseudomyxoma peritonei.

Transient Splicing-Associated Isoform Remodeling Defines Early MAPKi Resistance Adaptation in Melanoma

The paper identifies transient isoform remodeling as a key mechanism in early MAPKi resistance in melanoma, showing it is distinct from gene expression changes and linked to splicing regulators and developmental pathways.

Longitudinal single-cell RNA sequencing of a neuroendocrine transdifferentiation model reveals transcriptional reprogramming in treatment-induced neuroendocrine prostate cancer

This study uses longitudinal scRNA-seq to track neuroendocrine transdifferentiation in a prostate cancer model, identifying transcriptional changes and key regulators during treatment-induced NEPC progression.

Stress-response regulators tune enterobacterial common antigen synthesis to support acid and reactive nitrogen species stress resistance

This study identifies regulators that control ECA biosynthesis in E. coli, showing ECA's role in acid and reactive nitrogen species stress resistance.

GlioVision: A Multi-Modal MRI Framework for Non-Invasive Glioma Molecular Biomarkers Prediction

GlioVision predicts four glioma molecular biomarkers from MRI data using a multi-modal framework, achieving high AUC scores across multiple cohorts.

Visual experience-driven switch in endothelial metabolic transporters is essential for cerebrovascular maturation

The paper shows that visual experience drives metabolic changes in endothelial cells by switching lactate and glucose transporters, essential for vascular and BBB maturation.

Asymmetric regeneration dynamics in zebrafish pectoral fins

This study quantifies spatial asymmetry in zebrafish pectoral fin regeneration, revealing differential gene expression and signaling dynamics between anterior and posterior regions.

Nascent transcription profiling identifies H3K36 methylation as a custodian of the somatic transcriptome

The paper identifies H3K36 methylation as critical for maintaining transcriptome fidelity in metazoans by suppressing aberrant initiation in heterochromatin.

Therapeutic Targeting of the TGFβ Pathway Augments CAR T cell Efficacy in Glioblastoma

This study shows that targeting the TGFβ pathway improves CAR T cell efficacy in glioblastoma by enhancing antitumor activity and modulating the tumor microenvironment.

Temporal mapping of the anti-tumor effects of nanobody-based MSLN.CAR-T cell therapy in metastatic solid tumors

This study tracks the temporal changes in the tumor microenvironment after nanobody-based CAR-T therapy, revealing dynamic gene expression shifts and identifying potential therapeutic targets.

Neuronal Hyperactivity Induces Tau Phosphorylation Selectively in Excitatory Pyramidal Neurons Which Contributes to GluA2 Regulation

This study shows that neuronal hyperactivity selectively increases tau phosphorylation at S202/T205 in excitatory hippocampal neurons, which reduces GluA2 surface expression and may contribute to Alzheimer's disease pathology.

Rescued from extinction in two buckets: genomic consequences of an extreme bottleneck in the endangered Owens pupfish

The paper analyzes the genomic consequences of a severe bottleneck in Owens pupfish, finding reduced genetic diversity and a 17-fold contraction in effective population size, but low recent inbreeding due to population expansion.

Interspecific hybrids reveal a deeply conserved nuclear role of EIF1A-family proteins in zygotic genome activation

The paper uses interspecific hybrid embryos to identify EIF1A-family proteins as conserved nuclear regulators of zygotic genome activation across mammals.

Identification of an Endothelial Senotype Predicted by Ion Channel Expression in Aged Murine Perigonadal Adipose Tissue

The paper identifies age-dependent senescent endothelial cells in adipose tissue using snRNA-Seq and finds ion channel genes as predictive biomarkers.

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Promises and limitations of current ancient human epigenetic clocks

This study evaluates epigenetic clocks for age estimation in ancient human DNA, finding they are unreliable for continuous age-at-death but accurate for sex determination.

Environmental risk reshapes high-confidence schizophrenia risk genes during a developmental window of vulnerability

The paper investigates how early-life stress alters the expression of schizophrenia risk genes in mice during development, identifying region- and cell-type-specific effects.

High-throughput mapping of kinase-substrate interactions with protein language models and phospho-PCA

This paper develops a framework combining a protein language model and a screening assay to predict kinase-substrate interactions and map the human kinome.

Oncogenic PIK3CA mutations cause lineage-selective niche corruption

This study shows that PIK3CA mutations cause lineage-specific niche changes in vascular endothelium, leading to tissue malformations that can be partially prevented by PI3K inhibition.

IFNγ-CXCL9-CXCR3 axis links T cell recruitment to skeletal muscle remodelling in human physical frailty

This paper identifies an IFNγ-CXCL9-CXCR3 axis linking T cell recruitment to skeletal muscle remodelling in human physical frailty, showing its association with fibrosis and potential therapeutic targets.

Erythrocyte aging links hypocalcemia to impaired flow dynamics and oxygen transport through volume dysregulation

This study shows that aging red blood cells rely on calcium for volume stability under shear stress, and impaired calcium regulation leads to flow and oxygen transport issues.