bulk RNA-seq

KH1 Domain of Poly C Binding Protein 1 (PCBP1) Interacts with Utrophin-A mRNA and Modulates Utrophin-A Expression in Mouse Myoblasts

This paper shows PCBP1 interacts with utrophin-A mRNA, represses its expression by promoting nuclear retention, and identifies the KH1 domain as critical for this interaction in mouse myoblasts.

Sex differences in fear extinction are conditional, not categorical

This study shows that sex differences in fear extinction depend on experimental conditions, not being uniformly present across all contexts.

Ontogenetic and time-course transcriptomic analyses of maize leaf primordia reveal regulators of transverse vein development

This study identifies regulators of transverse vein development in maize through transcriptomic and anatomical analyses, revealing EREB41 and EREB114 as essential genes.

SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication

SEngEAR is a web platform for annotating senescent cells, visualizing communication networks, and comparing senescence signatures across datasets and contexts.

Transcriptome analysis provides insights into candidate genetic regulators of birch response to salt stress

The paper compares gene expression in salt-tolerant and salt-sensitive birch species under salt stress to identify genetic regulators of their response.

Uncovering the Multifaceted Role of the Kinetochore Scaffold 1 (KNL1) in Hepatocellular Carcinoma: Integrative Bioinformatics Analysis and CRISPR-Cas9 Experimental Study

This study identifies KNL1 as a key driver of chromosomal instability and immune evasion in HCC through integrative bioinformatics and CRISPR-Cas9 experiments.

Mechanotransduction tuned by intermediate filaments promotes DNA repair in stiff environments

The paper shows that rigid tissue environments enhance DNA repair efficiency and may contribute to cancer risk by promoting survival of damaged cells.

Ambivalent roles of nonsense-mediated mRNA decay in heat stress tolerance

This study shows that NMD deficiency in Arabidopsis leads to biphasic heat tolerance, with initial tolerance due to transcriptome priming and later sensitivity linked to reduced HsfA2 function and altered gene expression.

A multi-tissue RNA-seq atlas of adult medaka (Oryzias latipes) under salinity and winter-summer sampling contrasts

The paper generates a multi-tissue RNA-seq atlas of adult medaka under salinity and seasonal contrasts to study gene-expression plasticity and comparative biology.

Prefrontal cortex transcriptomes distinguish Alzheimers disease from asymptomatic amyloid pathology, neuropeptide loss, immune-complement activation and glial remodelling

This study identifies distinct transcriptional signatures in the prefrontal cortex of Alzheimer's disease patients compared to asymptomatic amyloid pathology and controls, highlighting neuropeptide loss, immune activation, and glial remodeling.

Spatiotemporal mapping of endothelial proliferative response in acute chemical liver injury

This study characterizes the spatiotemporal proliferative response of endothelial cells in acute liver injury and introduces a novel pipeline for analyzing hepatic cell states.

DECAPPING PROTEIN 5 regulates the circadian clock in Arabidopsis

This study identifies DCP5 as a key regulator of circadian RNA stability in Arabidopsis by modulating the decay of high-amplitude clock-controlled genes.

CMVAE: Contrastive Supervision Improves Single-Omic Latent Manifold for Breast Cancer Survival Prognosis

GraphExperiment: infrastructure for high-dimensional quantitative data and associated networks in R/Bioconductor

GraphExperiment provides an R/Bioconductor package to store and manipulate high-dimensional quantitative data alongside associated networks in a unified framework.

Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions

The paper benchmarks sparse-to-transcriptome reconstruction models using high-expression profiles from mouse adrenal cells under sex and sex-steroid conditions, finding that gene-wise metrics and strong baselines are critical for evaluation.

Fentanyl and fentanyl-xylazine co-exposure influence mitochondrial transcriptional programs in human trophoblasts

This study examines how fentanyl and fentanyl-xylazine co-exposure affect mitochondrial transcription in human trophoblasts, showing suppression in syncytiotrophoblasts and discordant regulation with FMX.

A new tool for quantifying mitochondrial RNA processing intermediates reveals increased levels of immature mRNA species under oxidative stress

LAMA2-related muscular dystrophy alters Schwann cell calcium homeostasis and increases peripheral nerve inflammation

This study examines LAMA2 deficiency in mice, showing altered Schwann cell calcium homeostasis and increased nerve inflammation into adulthood.

Multi-modal in situ profiling of human cells using the AVITI24 platform characterizes single-cell responses to acute stress

The paper uses a multi-modal platform to profile single-cell stress responses in human cell lines, finding a shared stress response program with cell-specific magnitude variations.

CD19-CAR T-cell therapy resets the EBV+ autoreactive B cell repertoire in autoimmune disease

This study shows CD19-CAR T-cell therapy depletes EBV+ autoreactive B cells and resets their repertoire, leading to sustained remission, while rituximab does not.

Revamped transposon-induced hepatocellular carcinoma model reveals deep similarities of cancer-driver landscapes across mice and humans

The paper develops a new transposon-induced model to identify cancer drivers in mice and shows similarities in driver landscapes between mice and humans.

GDF15 modifies NAD+ salvage pathway and dampens immune response in mitochondrial disease

This study shows GDF15 enhances NAD+ salvage and reduces immune response in mitochondrial disease by upregulating NMRK2 and modulating redox homeostasis.

A minimal two-residue C-terminal truncation of AID in adult-onset hyper-IgM syndrome type 2 (HIGM2)

This study identifies a two-residue C-terminal truncation variant in AID causing adult-onset HIGM2 and shows it disrupts CSR and SHM.

Transcriptomic Signatures Suggest Epigenetic Programming of Molecular Defense in Biochar-Exposed Formica japonica

The paper reanalyzes transcriptomic data to show that biochar exposure primes Formica japonica ants epigenetically, enhancing their resilience to environmental stressors.

Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions

This paper introduces a method to improve RNA-seq transcript quantification by reducing mapping ambiguity through minimal-shared region analysis, showing improved accuracy in isoform detection and abundance estimation.

Peripheral Exercise Transcriptomes Do Not Converge on Glutamatergic or Neuroinflammatory Signatures: A Cross-Platform Meta-Analysis

This study analyzes peripheral transcriptomic responses to exercise and finds no convergence on glutamatergic or neuroinflammatory signatures across tissues.

Incorporating tandem repeats improves gene expression prediction models

This study improves gene expression prediction models by incorporating tandem repeats, showing significant performance gains and identifying nonlinear effects on gene expression.

Prolactin Receptor Long Isoform ΔS1 Expression is Reduced in the Dorsal Root Ganglia of Humans with Chronic Pain

The paper examines PRLR isoform expression in human dorsal root ganglia, finding higher PRLR-L (ΔS1) expression in females and reduced expression in females with chronic pain.

An Isogenic iPSC Model of LMNA p.R482W Recapitulates Adipocyte Dysfunction in Familial Partial Lipodystrophy Type 2

This paper develops an isogenic iPSC model of FPLD2 carrying the LMNA p.R482W variant, showing adipocyte dysfunction including insulin resistance and metabolic impairment.

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

The paper presents the Almond Expression Atlas, a comprehensive transcriptomic resource integrating RNA-seq data to identify tissue-specific genes and improve gene expression analysis in almond.