bulk RNA-seq

Systematic evaluation of incomplete penetrance in 4,325 rare disease families reveals divergent transcriptional networks in CHD8 pathology

The paper evaluates incomplete penetrance in 4,325 rare disease families, finding 1.6% of diagnosed cases involve inherited variants from unaffected parents and showing divergent transcriptional effects in CHD8-related cases.

PKA disrupts adult ovarian identity circuits through direct inhibition of TRIM28-chromatin binding

This study shows PKA inhibits TRIM28-chromatin binding in ovarian granulosa cells, disrupting ovarian identity through SUMOylation dysregulation.

Integrated in vivo and transcriptomic analyses of lethal Oropouche virus infection reveal suppression of pathogenic host responses by antiviral therapy

This study shows favipiravir suppresses OROV replication and disease in hamsters, preventing neuroinvasion and pathogenic host responses through transcriptomic analysis.

Placental cis-eQTL analysis identifies preeclampsia-dependent genetic regulation at promoters

The paper identifies PE-dependent genetic regulation at promoters using cis-eQTL analysis of placental RNA sequencing data from the FINNPEC cohort.

Distinct Progression Paths Underlie the Diversity of Pancreatic Papillary Cystic Neoplasms

The paper identifies distinct progression paths in pancreatic papillary cystic neoplasms using integrated transcriptomics and histology, enabling phenotype-specific prediction of high-grade dysplasia.

Degraded myelin is associated with cold hypersensitivity in paclitaxel-induced peripheral neuropathy

In paclitaxel-treated mice, cold hypersensitivity outlasts mechanical hypersensitivity and coincides with reduced myelin gene expression, lower chromatin accessibility at Egr2/Yy1 motifs, and fragmented sciatic nerve myelin.

Persistent CCL3 expression sustains neutrophil recruitment and contributes to delayed wound healing in advanced age

This study shows that persistent CCL3 expression in aged wounds sustains neutrophil recruitment and delays healing by impairing inflammatory resolution.

Host Metabolic Reprogramming Defines Macrophage Antifungal Activity Against Cryptococcus neoformans

The paper investigates how metabolic reprogramming in macrophages affects antifungal activity against Cryptococcus neoformans, finding that glycolytic metabolism is enhanced in antifungal cells while mitochondrial and anabolic pathways are reduced.

DNA replication stress redistributes the histone methyltransferase G9a and activates lineage-specific gene expression

The paper shows DNA replication stress redistributes G9a to stalled forks, activates gamma-globin genes, and explains how hydroxyurea increases fetal hemoglobin in sickle cell anemia.

Herpes simplex virus pUL56 abolishes neuronal activity by removing voltage-gated ion channels from the plasma membrane

This study identifies HSV-1 protein pUL56 as responsible for removing voltage-gated ion channels from neuronal plasma membranes, disrupting calcium signaling and neuronal activity.

Triple-Omics Analysis Unveiled the Neuroprotective Mechanisms of Akkermansia muciniphila in an Environmental Exposure-Linked Mouse Model of Alzheimer's Disease

This study identifies A. muciniphila's neuroprotective effects against Cd-induced hippocampal dysfunction through restoration of post-transcriptional RNA regulation and splicing patterns.

Prenatal Alcohol Exposure Downregulates Focal Adhesion Molecules Tensin 1 and Tensin 2 Contributing to Cerebrovascular Dysfunction

This study shows prenatal alcohol exposure reduces Tns1 and Tns2 in brain microvascular endothelial cells, impairing angiogenesis, and that miR-150-5p mediates this effect.

Computational identification of candidate human long noncoding RNAs associated with PBMC responses to Candida auris and its cell wall components

The paper identifies 4 candidate lncRNAs associated with human PBMC responses to C. auris and its cell wall components through RNA-seq analysis and coexpression patterns.

A Ribosomal RNA modification regulates translation of PI3K/AKT activators in high-grade serous ovarian carcinoma

This study identifies a ribosomal RNA modification regulated by SNORA81 that affects translation of PI3K/AKT activators in high-grade serous ovarian carcinoma.

PPARα-dependent effects in the liver and jejunum of mice in response to pemafibrate

This study examines pemafibrate's tissue-specific transcriptional effects in PPAR-dependent mice, showing strong responses in liver and jejunum but not in other tissues.

GALC variants affect Glucocerebrosidase to Galactosylceramidase activity ratio

The paper examines how genetic variants in GALC affect the ratio of glucocerebrosidase to galactosylceramidase activity and its association with Parkinson's disease risk.

Cell jamming transition is regulated by mitochondrial pyruvate transport and endocytosis

The paper shows that mitochondrial pyruvate transport and endocytosis regulate the cell jamming transition in epithelial tissues.

Sphingolipid-Driven Lipotoxicity Promotes Calcific Aortic Valve Disease Through ER-Stress-NF-κB-EndMT Signaling and Is Therapeutically Targetable Through Serine Palmitoyltransferase Inhibition

This study identifies ceramide-driven lipotoxicity as a driver of calcific aortic valve disease and shows that SPT inhibition can reverse disease progression in vivo.

iPSC-Derived Myotubes from ME/CFS Patients Reveal Signature Genes, Isoforms and Pathways with Drug Repurposing Potential

The paper uses iPSC-derived myotubes from ME/CFS patients and controls to identify differentially expressed genes, isoforms, and pathways, and prioritizes compounds for drug repurposing.

The neuronal plasticity gene CRTC1 links survival with mitochondrial programs and tumor microenvironment features in Group 3 β medulloblastoma

This study identifies CRTC1 as a marker of transcriptional heterogeneity in Group 3 β medulloblastoma, linking its expression to survival and tumor microenvironment features.

Adenosylhomocysteinase drives epigenetic and metabolic reprogramming in ZFTA-RELA ependymoma

This study identifies AHCY as a key driver of epigenetic and metabolic reprogramming in ZFTA-RELA ependymomas, revealing its role in promoting tumor growth through pyrimidine synthesis and asparagine dependency.

The Spliceosome Scaffold Component BCAS2 Promotes Pancreatic Cancer Progression through Weak 5 Splice Site Dependent Splicing Regulation

This study identifies BCAS2 as a critical regulator of PDAC progression by promoting alternative splicing of weak 5' splice sites, specifically enhancing SOS1 exon 21 inclusion and RAC-signaling activation.

Pulsed Field Ablation Enables Stromal Manipulation and Tumor Reduction in Pancreatic Ductal Adenocarcinoma

This study shows pulsed field ablation (PFA) reduces tumor growth in a mouse model of pancreatic ductal adenocarcinoma by altering the tumor microenvironment and stromal cells.

Maternal repression of imprinted genes in endosperm by gene body demethylation

The paper shows that maternal removal of gene body methylation drives imprinting of PEGs in maize, with implications for gene regulation in rice but not Arabidopsis.

Molecular characterization of a cytochrome P450 involved in the skeletal diversification of tricyclic coumarins in Angelica keiskei.

This study identifies a cytochrome P450 enzyme in Angelica keiskei that determines the skeletal structure of tricyclic coumarins by preferentially forming dihydrofuranocoumarins over unsaturated furanocoumarins.

Hormonal factors are poor indicators of endometriosis pain

This study examines the relationship between sex hormone levels and endometriosis-related pain in women, finding weak associations between specific receptor transcript levels and pain intensity.

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

Enrich.AI: An Agentic AI Platform for Interactive GeneSet Enrichment Analysis and Biological Interpretation

Enrich.AI provides an AI-driven platform for gene set enrichment analysis and biological interpretation, offering interactive visualizations and literature-based insights.

A tonic PDGFA-dependent niche organizer maintains alveolar homeostasis

This study identifies PDGFA-expressing alveolar type 1 cells as a tonic niche organizer that maintains alveolar homeostasis by restraining fibroblast activation and promoting tissue repair.

Genetic dissection of grafting traits reveals regulators of graft union formation in grapevine

The paper identifies QTLs for grafting-related traits in grapevine and shows conservation of regulatory mechanisms across species.