bulk RNA-seq

The cyclin-G associated kinase (GAK) is a novel mitotic kinase and therapeutic target in diffuse large B-cell lymphoma

This paper identifies GAK as a novel mitotic kinase and therapeutic target in DLBCL, showing that GAK inhibition causes mitotic defects and that existing drugs can be repurposed for its targeting.

Repurposing Regulatory Toxicology Safety Data to Identify Potential Pro-Longevity Substances

This paper uses pesticide toxicity data to identify substances that improve survival and healthspan by affecting mitochondrial bioenergetics.

Farm exposure is associated with human breast milk immune profile and microbiome

The paper compares immune profiles and microbiomes of breast milk from mothers with different farm exposures to identify associations with immune development and atopic disease.

The epidermal stem cell-supporting matricellular protein fibulin 7 modulates skin inflammatory response in a psoriasis model

This study shows fibulin 7 protects against skin inflammation by modulating IL-17A signaling in a psoriasis model.

Systematic assessment of transcriptomic and phenotypic biological profiling for mechanism-based hazard assessment using target-annotated reference chemicals in renal proximal tubular epithelial cells

This study evaluates transcriptomic and morphological profiling methods for hazard assessment using reference chemicals in renal cells, finding HTTr provides higher mechanistic resolution than CPP.

Distal super-enhancer drives aberrant CXCL13 expression in Cancer cells driving growth and p53 dysregulation via CXCR5-CXCL13 axis

This study identifies a distal super-enhancer near CCNG2 that drives aberrant CXCL13 expression in cancer cells, leading to growth promotion and p53 dysregulation via the CXCR5-CXCL13 axis.

Tamoxifen Targets Wisp2 to Impair Subcutaneous Adipocyte Progenitor Self-Renewal and Adipogenic Differentiation

This study shows tamoxifen reduces subcutaneous adipocyte progenitor self-renewal and adipogenesis by suppressing Wisp2, linking endocrine therapy to metabolic risks like T2D.

Vascular normalization in breast cancer confers an endothelial immune suppressive gene expression profile

The paper examines immune suppressive gene expression in normalized breast cancer endothelial cells and finds similarities with healthy human endothelial cells.

RNA binding by ADARs prevents RNA interference from attacking self-produced dsRNA

This study shows ADARs prevent RNAi from targeting self-produced dsRNA by reducing siRNA production and interfering with RNAi processing in C. elegans.

Host transcriptional programs underlying lesion development in contagious bovine pleuropneumonia

This study identifies host transcriptional changes during different stages of Mmm infection in cattle, revealing immune and tissue remodeling pathways involved in lesion progression.

YBX3 overexpression in mesothelioma drives aberrant cell proliferation

This study identifies YBX3 as an oncoprotein in mesothelioma that drives cell proliferation through SLC7A5/LAT1-mediated amino acid uptake and shows JPH203 as a potential therapeutic agent.

Sex- and Age-Specific Development of ssRNA Virus Receptor Expression in the Human Brain

This study identifies sex- and age-specific developmental patterns of ssRNA virus receptor expression in the human brain using postmortem transcriptomic data.

Fetal sex is associated with the maternal gut microbiota composition and its metabolic function

This study finds that fetal sex influences maternal gut microbiota composition and metabolic function, with female pregnancies showing higher diversity and increased beta-glucuronidase activity.

An infusible decellularized extracellular matrix material binds to vasculature in infarcted myocardium and induces pro-reparative gene expression following acute myocardial infarction through inherent avidity and bioactive signaling

This study investigates the effects of different molecular weight components of an intravascularly infusible decellularized extracellular matrix (iECM) on vascular binding and pro-reparative gene expression after myocardial infarction.

Citizen science gamers enable automated flow cytometry gating through machine learning

The paper develops flowMagic, a machine learning tool for automated flow cytometry gating trained on expert data and citizen science gaming annotations, achieving high accuracy in cell population identification.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

Conserved Axonal Transcriptome Dynamics Underlie PGE2-Induced Sensitisation and Identify Tnfrsf12a/Fn14 as a Regulator of Neuronal Excitability in DRG Neurons

The paper identifies a conserved axonal transcriptome involved in PGE2-induced sensitisation and shows Tnfrsf12a regulates neuronal excitability in DRG neurons.

Neuronal late endosomes serve as selective RNA hubs disrupted by ALS-linked FUS mutation

The paper identifies late endosomes as selective RNA carriers in motor neurons and shows that ALS-linked FUS mutations disrupt this process.

Endothelin 2-Mediated Neuroinflammation Drives Hypertension-Associated Retinal Dysfunction

This study shows that endothelin-2 drives hypertension-related retinal dysfunction through neuroinflammation, independent of intraocular pressure, and identifies EDNRA as a therapeutic target.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

The paper maps m6A modifications and polyadenylation events in Plasmodium falciparum mRNAs, identifying stage-specific m6A sites and their potential role in 3' end processing.

Environmental RNA improves detection and surveillance of schistosomiasis transmission

This study develops and validates an environmental RNA (eRNA) method to detect and quantify specific life stages of Schistosoma mansoni in water samples, outperforming environmental DNA (eDNA) in sensitivity and stage discrimination.

TEDEdb: a large-scale resource and multi-cohort analysis of transposable element differential expression in cancer

The paper re-analyzes over 7,000 RNA-seq samples to study transposable element differential expression in cancer and finds TE expression is more prone to batch effects and can be induced by various compounds.

Transcriptome profiling reveals differential expression of virulence genes in Xylella fastidiosa under nutrient-rich and xylem-like conditions

This study compares transcriptomes of Xylella fastidiosa under nutrient-rich and xylem-like conditions, identifying differential gene expression and regulatory divergence between strains.

The RNA virome of intertidal kelp in New Zealand reveals novel viral lineages associated with unhealthy kelp

The study identifies novel viruses in New Zealand kelp, finding higher viral diversity in unhealthy kelp at a polluted site.

Lysine Crotonylation Acts as an Epigenetic Switch for Glutamate Neurotransmission and Spatial Memory

This study identifies lysine crotonylation (Kcr) as an epigenetic regulator of long-term memory and glutamatergic neurotransmission, showing its role in gene expression and synaptic function.

T lymphocyte regulatory cytokines predict frailty in older adults

This study identifies T lymphocyte regulatory cytokines as predictors of frailty in older adults using machine learning and serum cytokine analysis.

Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome

This study shows that RBFOX2 autoregulation is critical for cardiomyocyte differentiation by maturing the transcriptome, and its disruption leads to congenital heart disease.

B-cell follicles of lymphatic tissues act as a critical microanatomical niche for sustained viral replication, virus-host interaction and damage during chronic SIV infection

The paper shows that in chronic SIV infection, viral RNA is mainly found in B-cell follicles of lymphatic tissues, leading to structural damage and sustained virus-host interactions.

Out-of-balance Growth Enables Cost-free Synthesis of the Flagellum and Other Proteins in a Single Bacterium

The paper shows that single-cell growth rates increase with flagellar gene activity, contradicting bulk measurements, and attributes this to inherited growth factors.

Reconstruction of the human nigrostriatal pathway in vitro reveals target-dependent dopamine neuron maturation

The paper introduces a human stem cell-based model of the nigrostriatal pathway that mimics in vivo connectivity and reveals target-dependent dopamine neuron maturation.