bulk RNA-seq

Inflammatory signaling drives SQSTM1-dependent suppression of interferon-γ-induced MHC class I

This study shows that IL-1β suppresses IFN-γ-induced MHC-I surface expression in NSCLC cells through SQSTM1-dependent autophagy, revealing a post-transcriptional regulatory mechanism.

Genetic drivers shape TREM2-dependent myeloid responses and glioblastoma progression

This study shows TREM2's role in glioblastoma depends on genetic context and timing, with different effects in Nf1-silenced/Ras-driven and PDGFB-driven models.

KLF17 acts as a dual reporter for tracking naive pluripotency and 8-cell-like states

The paper uses KLF17 expression levels to track transitions between primed, naive, and 8-cell-like states in human pluripotent stem cells.

Dietary fructose promotes anxiety through impairment of microglia physiology

This study shows that dietary fructose causes anxiety by impairing microglia function, with sex-specific effects on metabolism and behavior.

Global RNA-RNA interactome mapping in B. burgdorferi reveals base-pairing sRNAs that rewire gene expression across growth

The paper identifies sRNA candidates in B. burgdorferi and maps their regulatory interactions across growth phases, revealing a dynamic RNA-RNA interactome.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

Habitual sleep duration is associated with the cortical organisation of brain network controllability

The paper links habitual sleep duration to brain network controllability, finding longer workday sleep is associated with higher somatomotor controllability and lower visual cortex controllability.

Dimensionality Reduction for Cyclic Compositional Data

clrcycle is a dimensionality reduction method for cyclic data that captures phase and magnitude in biological systems, showing effectiveness in circadian and cell-cycle analysis.

Isocaloric restriction normalizes body weight but not relative adiposity, adipose inflammation, or gut microbial diversity in high-fat diet-fed mice

Pseudoarthrobacter BD237 volatile organic compounds promote Brachypodium distachyon growth

This study shows that mVOCs from Pseudoarthrobacter BD237 enhance Brachypodium distachyon growth and stress tolerance by promoting photosynthesis and abiotic stress response.

EcoHIV Treated Primary Microglia Exhibit a Highly Specialized and Sex-Dependent Transcriptional State

This study investigates how EcoHIV affects microglial proliferation and gene expression, revealing a sex-dependent transcriptional response and a significant role for the Trem2/Dap12 signaling complex.

Generation of hepatocyte-like cells from sheep embryonic stem cells

This study generates hepatocyte-like cells from sheep embryonic stem cells using a serum-free method, showing hepatic functions and gene expression patterns.

In Step, the sole Drosophila TENT5 poly(A) polymerase, is required for spermatid elongation and individualization

This study identifies the Drosophila TENT5 poly(A) polymerase, Isep, as essential for spermatid elongation and individualization, with its function independent of poly(A) polymerase activity.

CircEPSTI1 regulates miR-942-5p-SERPINE1-AKT1 signaling axis to enhance dengue infection and is suppressed by Tiplaxtinin

This study identifies circEPSTI1 as a regulator of dengue infection through a miR-942-5p-SERPINE1-AKT1 signaling axis and shows that Tiplaxtinin suppresses this pathway to inhibit DENV replication.

Early innate immune signatures correlate with Ad26.COV2.S vaccine durability and protective efficacy

This study identifies early innate immune signatures following Ad26.COV2.S vaccination that correlate with vaccine durability and protective efficacy in rhesus macaques and humans.

Comparative characterization of OncoPro™ and Wnt-Based media reveals distinct phenotypic and pharmacologic states in patient-derived tumor organoids

This paper compares OncoPro™ and Wnt-based media in patient-derived tumor organoids, finding distinct phenotypic, transcriptomic, and pharmacologic differences.

Machine learning classification of fibromyalgia from blood transcriptomes: confounder benchmarking and implications for endometriosis-associated pain

This paper evaluates machine learning models for classifying fibromyalgia from blood transcriptomes, finding that demographic and cell-composition factors explain much of the signal.

Decoding calcium oscillation frequency in transcriptional regulation

This study shows that cells decode calcium oscillation frequency through a multi-kinase network that regulates transcription via NF-κB and MYC.

Colorectal cancers with distinct metastatic potential trigger divergent early T cell responses

This study shows that colorectal cancers with different metastatic potential trigger distinct early T cell responses, with non-metastatic tumors inducing cytotoxic T cells and pro-metastatic tumors causing hypoactivated T cells.

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.

Prediction of Systemic Lupus Erythematosus from Genotype and Gene-Expression Data: Batch Correction and Leakage Free Evaluation

This paper evaluates the prediction of SLE using genotype and gene-expression data with batch correction and leakage-free cross-validation, finding that expression data perform better than SNPs but face confounding issues.

The transcription factor BCL11A restores differentiation potential to aged oligodendrocyte progenitor cells

The paper identifies BCL11A as a transcription factor that restores differentiation potential in aged oligodendrocyte progenitor cells through computational analysis and experimental validation.

The epidermal growth factor (EGF) receptor family network in cardiac hypertrophy and heart failure

EGFR-family ligand mRNAs shift in failing human hearts; NRG1 and EGF drive distinct, differently ERBB2-dependent transcriptional programmes in rat cardiomyocytes; afatinib blunts mouse angiotensin II hypertrophy but worsens fibrosis.

UV-induced translation capacity is regulated developmentally in fungi.

This study shows UV radiation increases ribosome levels and translation capacity in filamentous fungi after filament formation, enhancing UV survival and repair through mechanisms involving TOR signaling and gene expression modules.

Identification of insecticidal double-stranded RNAs targeting the proteasome pathway in the hop flea beetle Psylliodes attenuata using dsRIP

This study identifies insecticidal dsRNAs targeting the proteasome pathway in the hop flea beetle using dsRIP and demonstrates their efficacy in bioassays.

Targeting IGF2BP1 Creates a Mitotic Vulnerability in Colorectal Carcinoma

This study identifies IGF2BP1 as a regulator of mitotic integrity in CRC, showing that its inhibition creates a therapeutic vulnerability that synergizes with paclitaxel.

Transcriptome dissection of the Zeb2-associated network reveals a role for NRPS15 in zearalenone biosynthesis in Fusarium graminearum

The paper identifies NRPS15 as a key gene in zearalenone biosynthesis in Fusarium graminearum through transcriptomic analysis and functional screening.

Transcriptomic rejuvenation during intestinal and liver regeneration in mice

This study shows that tissue regeneration in mice reduces transcriptomic age temporarily, with variations depending on tissue type and repair stage.

HEPLISAV-B Breaks Immune Tolerance and Induces HBV Control via CD4 T Cell-Dependent Mechanisms in a Chronic Hepatitis B Mouse Model

HEPLISAV-B vaccine breaks HBV immune tolerance in a mouse model, inducing HBsAg clearance and anti-HBs immunity through CD4 T cell-dependent mechanisms.

Host response against SARS-CoV-2 infection is impacted by allosteric modulation of cholinergic and purinergic receptors

Ivermectin's protection in SARS-CoV-2-infected hamsters depended partly on both α7 nicotinic and P2X4 receptors; in co-cultures its effects were α7nAChR-independent, and P2X4 blockade prevented CXCL10 induction at 48 hpi.