bulk RNA-seq

Cytoplasmic genomes change allelic expression bias in plant seeds independently of parental imprinting: evidence for cytonuclear regulatory epistasis in Arabidopsis thaliana

The paper identifies cytoplasmic effects on allelic expression in Arabidopsis thaliana, showing cytoplasmic-genome interactions with nuclear genes and independence from genomic imprinting.

Intermittent exposure to high ambient heat during the second half of gestation in mice causes mild alterations of reproductive endpoints in male embryos

This study shows that intermittent heat exposure during mid-to-late gestation in mice leads to reduced anogenital distance and increased hypospadias in male embryos, without affecting gene expression in the fetal testis.

Genetic control and tissue specificity of transcriptomic rhythmicity

This study identifies genetic regulators of transcriptomic rhythmicity using GTEx data and links them to phenotypes in the Pan-UK Biobank.

The impact of patient biology on racial disparities in breast cancer outcome

This study identifies molecular differences in HR+ breast cancer between Black and White women, linking structural factors like poverty to tumor biology and immune signatures.

Functional and Structural Brain Age Gaps as Complementary Predictive Markers for Cognitive Performance

The paper predicts structural and functional brain age gaps from MRI data to assess their predictive power for cognitive performance in healthy adults.

Trichomonas vaginalis pseudocysts are a quiescent cell stage characterized by a differentially regulated transcriptome and intact membranes

This paper characterizes Trichomonas vaginalis pseudocysts as a quiescent cell stage with distinct transcriptomic features and intact membranes, suggesting a potential role in persistent infections.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

EV-Tracer enables lineage-resolved detection and molecular profiling of extracellular vesicle-associated signals in cancer-fibroblast co-culture

EV-Tracer detects and profiles lineage-specific extracellular vesicles in cancer-fibroblast co-cultures, revealing interferon-related RNA signatures associated with cell-cell contact.

Osteopontin Mediates Uterine Artery Dysfunction in Hypertensive Pregnancy

This study identifies osteopontin as a mediator of impaired uterine artery remodelling in hypertensive pregnancy, showing its deficiency improves vascular function and fetal growth.

New Insights on Bridging Integrator 1 Protein Isoforms as a Risk Increasing Gene in Alzheimer's Disease

The paper identifies BIN1 isoform expression patterns and genetic variants associated with Alzheimer's disease risk using GWAS and hiPSC differentiation data.

Aquaporin-4 Regulates Edema, Sustains Astrocyte Differentiation, and Constrains Immunosuppressive Remodeling in Glioblastoma

This study shows that AQP4 regulates edema, maintains astrocyte differentiation, and limits immunosuppressive changes in glioblastoma.

Immune-Epithelial Interactions via TGF-β Orchestrates Stem-Cell Niche Formation and Morphogenesis

This study shows immune cells influence stem-cell niche formation and organoid development through TGF-β signaling in a 3D breast organoid model.

Transient efferocytosis-induced activation of IKKβ reprograms macrophages to promote tissue resolution

This study identifies IKKβ activation as a transient upstream signal triggered by efferocytosis that promotes tissue resolution through multiple downstream pathways.

Functional impact of PCSK9 variants on LDL uptake in a knockout hepatic model

The paper assesses the functional impact of PCSK9 variants on LDL uptake using a knockout hepatic model, revealing heterogeneity in variant activities and providing insights into their mechanisms.

Anti-HIV Immunotoxin and Antibody-Drug Conjugate Display Both Common and Distinct Effects in Killing Target Cells

This study compares the cytotoxic effects of an immunotoxin and antibody-drug conjugate using the same antibody, revealing both shared and distinct molecular mechanisms of cell killing.

Limb-localized induction of regeneration reshapes brain and amputation-site transcriptional states in adult Xenopus laevis

This study examines how limb regeneration in Xenopus laevis affects brain and amputation-site gene expression, identifying changes in metabolic and immune pathways and cross-species similarities in regenerative responses.

Dynamics of cell states and alternative splicing following kidney ischemia-reperfusion injury

The paper analyzes bulk RNA-seq data from a kidney IRI mouse experiment to identify temporal phases and alternatively spliced genes, revealing potential splicing regulators involved in injury and repair.

Primary Human Macrophages Exhibit Functional CYP3A4 Activity with Marked Expression-Function Discordance and Cocaine-Induced Catalytic Activation

This study shows human macrophages have functional CYP3A4 activity, with expression and function discordance, and cocaine increases CYP3A4 activity across donors.

Mechanical history shapes phenotypic plasticity and fibroblast-autonomous 3D remodeling in iPSC-derived cardiac fibroblasts

This study shows that mechanical culture history affects iPSC-derived cardiac fibroblasts' phenotype and TGF-beta1 response, but later passages can alter these effects.

Oncogenic KRAS-MAPK signaling sustains a CD73 dependent therapeutic vulnerability in pancreatic cancer

This study shows that combining CD73 and RAS(ON) inhibition reduces tumor growth and immune suppression in pancreatic cancer by targeting KRAS-MAPK driven CD73 signaling.

Cellular and mitochondrial correlates of regional glucose metabolism in the human cortex

The paper investigates the cellular and mitochondrial factors influencing regional glucose metabolism in the human cortex using multimodal data integration.

DELLA proteins modulate responsive and buffered transcriptional programs in Arabidopsis and rice roots under water limitation

This study shows DELLA proteins in Arabidopsis and rice roots modulate transcriptional responses to water limitation, with conserved function but species-specific outcomes.

Host brain infection induces RNAi epimutation in Mucor circinelloides and enhances blood-brain barrier invasion

The paper shows brain infection induces RNAi epimutations in Mucor circinelloides that enhance blood-brain barrier invasion.

A Pan-Cancer Benchmark of Clustering Strategies for Patient-Specific Gene Regulatory Networks

The paper benchmarks clustering strategies for patient-specific gene regulatory networks across 9,778 cancer samples, finding that standard deviation-based feature selection with k-means performs best.

A synchronization modulation electric field reduces early ischemic kidney injury in pigs and suppresses a stress and inflammatory program without detectable leukocyte accumulation

Building Bridges Belowground: Pythium oligandrum En-hances Rhizosphere Network Connectivity

This study shows that Pythium oligandrum modifies microbial interactions in the potato rhizosphere without changing overall bacterial community composition, affecting network connectivity.

From Splicing to Survival: Understanding the Molecular Basis of Prognostic Differences in advanced Small Intestine Neuroendocrine Tumors

This study investigates the relationship between spliceosomic changes and patient survival in advanced SI-NETs, identifying CPSF2 as a key factor linked to poor prognosis.

Targeting cyclic-AMP/phosphodiesterase signaling to quiet nasal tuft cell calcium responses

This study investigates the role of cyclic-AMP/phosphodiesterase signaling in modulating nasal tuft cell calcium responses and IL-25 release using mouse and human models.

Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells

This paper introduces a method to measure RNA structure and protein binding in human cells, showing how RNA folding and sequence determine protein occupancy and function.

Cisplatin Exposure Alters the Effects of Honokiol on Genes Involved in Outer Hair Cell Physiological Function

The paper examines how honokiol affects gene expression in outer hair cells under cisplatin exposure, finding significant gene interactions that suggest potential protective mechanisms against cisplatin-induced hearing loss.