bulk RNA-seq

Social ties are maintained through sensory adaptations in green chromides

The paper investigates how visual gene expression changes in green chromides under different light environments and how these changes relate to stable conspecific preferences.

Gene expression in Anolis sagrei suggests conservation of patterning mechanisms drives formation of two high acuity areas

The paper identifies conserved gene expression patterns in the retina of Anolis sagrei that suggest shared developmental mechanisms for forming multiple high acuity areas.

A trustworthy semantic knowledge network linking data-driven cell phenotypes to diseases and drugs

The paper develops NLM-CKN, a semantic knowledge network linking cell phenotypes to diseases and drugs using integrated data from 88 datasets.

Biological Signaling Pathways Associated with Late Tendon Development in Chicken Embryos and Their Dependence on Mechanical Stimulation

This study identifies mechanotransduction pathways involved in chicken tendon development and shows how paralysis disrupts these processes.

Long-term dysregulation of histone acetylation, BDNF expression, and the hippocampal transcriptome in adult rats exhibiting a depressive-like phenotype following repeated chlorpyrifos exposure

This study shows that repeated chlorpyrifos exposure in rats leads to long-term epigenetic and transcriptional changes in the hippocampus, including reduced BDNF and altered neuronal plasticity pathways, associated with a depressive-like phenotype.

When perfect is a warning: explanations expose shortcuts that accuracy hides in cancer gene-expression classifiers

The paper shows cancer classifiers can achieve perfect accuracy by learning data source shortcuts rather than biological features, and introduces a method to detect and mitigate this issue.

A compact motif vocabulary is differentially interpreted across human cell types

The paper shows that a compact set of regulatory motifs can explain gene expression across diverse human cell types through context-dependent interpretation.

Distinct antischistosomal profiles of antimalarials and TRP agonists

This study compares the antischistosomal effects of antimalarials and TRP agonists using RNA-seq and efficacy tests in mice, finding distinct transcriptional responses and retained activity against praziquantel-resistant parasites.

CrJAMs are transcriptional repressors of the monoterpenoid indole alkaloid pathway in Catharanthus roseus

This study identifies CrJAM2 and CrJAM3 as transcriptional repressors of the MIA pathway in C. roseus, showing their repression is modulated by methyl JA treatment.

Apelin signaling controls neuroendocrine homeostasis via Atoh8-dependent transcriptional regulation

This study shows Apelin signaling regulates neuroendocrine homeostasis in zebrafish via Atoh8-dependent transcriptional control, affecting development, fertility, and aging.

Follow-up availability and the robustness of immune transcriptomic recovery after myocardial infarction

The paper assesses the robustness of immune transcriptomic recovery after myocardial infarction by evaluating how missing data and assay availability affect inflammatory-response scores over time.

A candidate HNRNPU-CHD2 RNA-processing axis in neurodevelopmental disease

The paper identifies a HNRNPU-CHD2 RNA-processing axis linked to neurodevelopmental disease by showing HNRNPU depletion causes splicing changes in CHD2 that may lead to nonsense-mediated decay.

Shared and divergent features of the immune response to acute and chronic Trypanosoma cruzi infection in mice revealed by cardiac transcriptomics

This study uses cardiac transcriptomics in mice to compare immune responses during acute and chronic Trypanosoma cruzi infection, identifying shared and divergent features.

Endogenous PROM1 activation redistributes liver cancer cells along a preexisting differentiation axis

The paper shows PROM1 activation in liver cancer cells shifts their state along a preexisting differentiation axis, suggesting CD133's role extends beyond being a stem-like marker.

A Reproducible Pre-Transplant γδ T-cell Effector Signature Reveals Immune-Metabolic Programs Associated with Kidney Allograft Rejection

The paper identifies a pre-transplant γδ T-cell effector signature associated with kidney allograft rejection using multi-omics data from transplant recipients.

A Deep Phylogenetic Split Between Short- and Long-Wavelength-Tuned Visual Systems in Surgeonfishes (Acanthuridae)

This study investigates visual plasticity in surgeonfishes by analyzing opsin gene expression across 22 species, revealing a deep phylogenetic split in visual systems that predates ecological diversification.

Anti-TGFβ peptide P144 augments CAR-T cell efficacy through neutrophil recruitment and TME remodeling in malignant mesothelioma

This paper shows that delivering the anti-TGFβ peptide P144 via CAR-T cells enhances their efficacy in mesothelioma by recruiting neutrophils and remodeling the tumor microenvironment.

Antibiotics drive immunometabolic rewiring of human immune responses

This study examines how antibiotics affect immune cell function by altering mitochondrial activity, showing antibiotic-specific immunomodulatory effects in humans and mice.

ANABOLIC FAILURE, NOT CATABOLIC ACTIVATION, UNDERLIES GLYCOGEN DEPLETION IN CERVICAL CARCINOGENESIS: A MULTI-COHORT TRANSCRIPTOMIC ANALYSIS

LplA-mediated rescue of lethal myopathy and cardiomyopathy in mitochondrial lipoylation-deficient mammalian caused by Lipt1

This study uses AAV-delivered LplA to rescue lethal mitochondrial lipoylation defects in Lipt1-deficient mice, improving survival, motor function, and cardiac health.

Synthetic lethality of p97 inhibition and PSMC2-overexpressionovercomes bortezomib resistance in multiple myeloma

This study identifies PSMC2 overexpression as a driver of bortezomib resistance in multiple myeloma and shows that combining p97 inhibition with bortezomib overcomes this resistance.

Herboxidiene and EGFR expression in A172 glioblastoma cells

This study investigates how herboxidiene affects EGFR expression and proliferation in A172 glioblastoma cells, finding that it inhibits growth without causing intron 2 retention seen in lung adenocarcinoma cells.

An LRH-1 agonist reverses hepatic metabolic dysfunction in obesity

This study develops an LRH-1 agonist that improves insulin sensitivity and reduces liver fat in obese mice, revealing peroxisomal lipid metabolism as a key pathway.

Extracellular DDR1 targeting remodels collagen-rich tumor stroma and local immunity

This study develops DDR1-targeting nanobodies that remodel collagen-rich tumor stroma and immune compartments, enhancing tumor control without direct tumor-cell inhibition.

Metabolic complexity in the human brain supports metastable network dynamics and declines in normative ageing

This study investigates metabolic complexity in the human brain using PET and fMRI, finding that metabolic entropy correlates with network metastability and declines with age.

Prokaryotic Community Structures in the Bering and Chukchi Seas

The paper characterizes bacterial communities in the Bering and Chukchi Seas using 16S rRNA gene sequencing, finding that water mass, salinity, and bloom stage shape community structure.

Knockdown of fibrillarin reveals cell- and virus- dependent restriction of henipavirus replication and enhanced antiviral immune signalling

This study shows that fibrillarin depletion affects henipavirus replication differently across cell types and viruses, and enhances antiviral immune signaling.

Donor Aware Reanalysis of Neuronal Nuclei Supports STMN2 Depletion Associated with Nuclear TDP 43 loss in FTD and ALS

The paper reanalyzes RNA-seq data from neuronal nuclei to identify gene expression changes associated with nuclear TDP-43 loss in FTD and ALS, finding STMN2 depletion and other transcriptomic variations.

Characterizing nascent readthrough transcripts in human cells

The paper identifies widespread readthrough transcription in human cells and shows that depletion of specific factors increases its extent.

RELAY: Relational In-Context Learning for Cellular Perturbation Prediction

RELAY predicts cellular responses to perturbations by learning relational patterns from measured data, outperforming existing methods on unseen variable values and combinations.