bulk RNA-seq

Inbred and outcrossed Drosophila embryos diverge in stress defense and developmental maintenance during heat stress

This study compares stress responses in inbred and outcrossed Drosophila embryos under heat stress, finding that inbred embryos show greater stress response activation and reduced developmental survival.

RBFOX2 restrains oncogenic cell plasticity in Group 3 medulloblastoma

This study identifies RBFOX2 as a suppressor of oncogenic cell plasticity in Group 3 medulloblastoma by regulating alternative splicing and cytoskeletal dynamics.

Structural basis of eIF4E recognition of synthetic mRNA 5' cap analogues links cap architecture to affinity and biological activity

This study investigates how synthetic 5' cap analogues interact with eIF4E, revealing structural features that influence mRNA translation efficiency and biological activity.

Conserved transcriptional plasticity, not local adaptation, dominates early climate responses across wild and cultivated apples

This study shows that conserved transcriptional plasticity, not local adaptation, is the main molecular response to climate variation in apples.

The Gαi/o GPCR LPAR2 Acts as a Non-Classical Factor for Aldosterone Induced Injury in a Cardiomyocyte Model

The paper identifies LPAR2 as a non-classical GPCR mediating aldosterone-induced cardiomyocyte injury, showing its requirement alongside MR for collagen expression and cell death.

In situ identification of pre-hematopoietic stem cells and their niche

The paper identifies pre-hematopoietic stem cells and their niche using spatial transcriptomics in the AGM region, revealing spatial signaling patterns and cellular interactions that support HSC development.

Neutrophil-Derived Oncostatin M Contributes to Endothelial Cell Dysfunction During Treponema denticola interaction

This study shows that neutrophil-derived oncostatin M (OSM) contributes to endothelial dysfunction during Treponema denticola infection, linking periodontitis to cardiovascular disease.

PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets

Predicting differentially expressed genes and expression shifts per condition from database embeddings plus per-gene evidence, PIE reaches 1.2–3.2 times the best baseline's AUPRC on unseen contexts, perturbations and datasets.

Cajal bodies shape the nuclear transcriptome, intron retention and transcripts redistribution in Arabidopsis roots under hypoxia

This study shows that Cajal bodies in Arabidopsis roots regulate transcript retention and processing during hypoxia, affecting gene expression and stress tolerance.

Integrating dorsolateral prefrontal cortex multi-omics and GWAS summary data enhances gene-mapping of Parkinson's disease

This study integrates multi-omics data from DLPFC with GWAS summary data to identify PD risk genes, finding significant overlaps between bulk and cell-type-aware TWAS and PWAS results.

nHOTAIRM1 scaffolds ANXA11-dependent assemblies to drive axonal mRNA localization in human motor neurons

This study identifies nHOTAIRM1's role in axonal mRNA localization by scaffolding ANXA11-dependent transport assemblies in human motor neurons.

Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators

The paper introduces SNACKKSS, a tool that integrates RNA-Seq data and biomedical literature to predict protein-inhibiting drugs, showing improved performance when combined with existing predictors.

Streptomyces induces unisexual reproduction of a major human fungal pathogen

This study shows that tunicamycin from Streptomyces induces unisexual reproduction in Cryptococcus species through meiotic processes and developmental reprogramming.

LGR5-high colorectal cancer defines a Wnt-active stem-like state with multimodal therapeutic vulnerabilities

The paper identifies LGR5-high colorectal cancer as a Wnt-active stem-like state with therapeutic vulnerabilities across multiple modalities.

Senotherapeutic potential against xeroderma pigmentosum

This study identifies senomorphic and senolytic agents that counteract UV-induced senescence in XP-derived melanocytes, reducing SASP gene expression and related pathway activation.

Identification of senescence-associated drivers of tumour growth and progression using a novel microarray platform

This study identifies SASP factors that drive tumorigenesis in breast and lung cancer cells using a microarray platform and validates their role in growth and survival.

Pancreatic progenitor cells respond to laminar shear stress with transcriptomic changes, accompanied by reduced YAP1 activity

This study investigates how pancreatic progenitor cells respond to fluid shear stress, finding transcriptomic changes and reduced YAP1 activity.

EndoMT: An R Package Resource for Endothelial-Mesenchymal Transition Gene Set Enrichment Analysis

The paper introduces an R package for EndoMT gene set enrichment analysis, showing its utility in detecting EndoMT-associated transcriptional changes across different experimental conditions.

Lipocalin-2-expressing red pulp macrophages link ischemic stroke to systemic immune reprogramming in mice and humans

Splenic Lcn2 is induced biphasically after mouse stroke and localizes to red pulp macrophages; recombinant LCN2 induces T cell and monocyte hyporesponsiveness and monocyte phagocytosis-ROS uncoupling, with human spleen support.

Intra-uterine position modulates lifelong hippocampal neurogenesis and anxiety-related behavior

This study shows that intra-uterine position affects lifelong hippocampal neurogenesis and anxiety-related behavior in mice by altering prenatal steroid exposure and neural development.

Scalable and semi-automated Boolean network inference from multi-condition single-cell transcriptomes with scBOLT

The paper introduces scBOLT, a framework for inferring Boolean networks from multi-condition single-cell transcriptomes, improving computational tractability for large-scale models.

Metabolic rewiring induces a viral mimicry-mediated quiescence in glioblastoma

This study identifies SAT1 as a key driver of quiescence in glioblastoma stem cells through metabolic rewiring and viral mimicry, showing it can induce reversible growth arrest.

High-throughput functional genomics and transcriptomics reveal molecular mechanisms regulating the synergistic fungicidal activity of copper and zinc

The paper identifies genes involved in the fungal response to a copper-zinc fungicide using high-throughput screens and transcriptomics, showing limited overlap between the two methods.

The Two-Component System CrdRS Mediates Sub-inhibitory Antibiotic-Induced Biofilm Formation in Helicobacter pylori via Bidirectional Regulation of Transporters PlpA and GlnP

This study identifies the CrdRS two-component system as a key regulator of antibiotic-induced biofilm formation in H. pylori through bidirectional control of transporters PlpA and GlnP.

Genetic control of leaf carbon- and water-related traits in grapevine under greenhouse and field conditions

The paper identifies genetic regions associated with leaf ecophysiological traits in grapevine under greenhouse and field conditions, showing that multi-environment analysis improves the detection of stable QTLs.

Paired sequencing of IgA-bound bacteria reveals widespread associations between adaptive immunity and gut microbiome gene expression.

The paper introduces PIg-seq to study IgA-bound bacteria and finds widespread transcriptional responses, including changes in conjugation genes and prophages, linking IgA to horizontal gene transfer.

DLGAP5 promotes vascular cell proliferation and remodeling in pulmonary arterial hypertension

This study identifies DLGAP5 as a driver of pulmonary vascular remodeling in PAH by promoting cell proliferation and survival through cyclin A2 and DEPDC1 upregulation and BIM suppression.

Transient 5-azacytidine exposure elicits persistent myogenic-like transcriptional remodeling in zebrafish fibroblasts: implications for cultivated seafood

The paper shows that zebrafish fibroblasts can undergo persistent myogenic-like transcriptional changes after transient 5-azacytidine exposure, suggesting potential for cultivated seafood applications.

Endothelial gain of PIEZO/TRPV mechanosensors drives cavernous malformations

This study identifies PIEZO1, TRPV2, and TRPV4 as mechanosensors overexpressed in CCM lesions, showing their role in driving disease through altered adhesion and matrix degradation.

Ref(2)P/p62 protein pleomorphism confers tissue-specific function

One Drosophila Ref(2)P polypeptide takes different structures in midgut and muscle, driving autophagy or mitochondria-associated degradation; deleting disordered region IDR2 switches muscle Ref(2)P to midgut state.