bulk RNA-seq

Anti-Nucleolin Aptamer iSN04 Inhibits Alveolar Rhabdomyosarcoma Cell Growth by Inducing Myogenic Differentiation

This study shows that the anti-nucleolin aptamer iSN04 inhibits alveolar rhabdomyosarcoma cell growth by promoting myogenic differentiation and enhancing the efficacy of vincristine.

Timed binary WNT activity is sufficient to model the early human neural axis

This paper shows that timed WNT pulses can specify distinct neural domains in human pluripotent stem cells, enabling the generation of specific neuron and progenitor types.

Functional genomics identifies therapeutic options, biomarkers, and resistance mechanisms for high-grade gliomas

This study identifies therapeutic options, biomarkers, and resistance mechanisms for high-grade gliomas using genomic, transcriptomic profiling, and drug testing in patient-derived models.

mRNA deep sequencing profiling and integrative miRNA-mRNA network analysis in pediatric Burkitt leukemia and lymphoma

This study profiles mRNA and miRNA expression in pediatric Burkitt leukemia and lymphoma, identifying dysregulated miRNA-mRNA networks and key pathways involved in proliferation and immune signaling.

Interactome-based deep learning and path-level decomposition reveal TGFβ-IFNα competition in MASH

The paper uses a deep learning framework to analyze drug-induced transcriptomics and identifies a four-node module involved in TGFβ-IFNα competition in MASH.

The BAF chromatin remodeling subunit ARID1B coordinates cell-cycle exit and motor neuron differentiation

This study shows ARID1B is essential for transitioning from cell-cycle progression to motor neuron differentiation in mouse embryonic stem cells.

Topological dependent modifications of gene expression in the preeclamptic placenta under aspirin treatment.

This study identifies aspirin's molecular effects on preeclamptic placenta by analyzing gene expression in different placental regions, showing downregulation of inflammatory and metabolic pathways.

CBX3 Deletion Overcomes Ferroptosis Resistance in Colorectal Cancer by Targeting IFNγ/SLC7A11/SLC3A2 Axis

This study shows that CBX3 deletion increases ROS and lipid ROS levels in CRC cells, sensitizing them to ferroptosis by disrupting the IFNγ/SLC7A11/SLC3A2 axis.

The Cardiovascular Benefit of Menopause Hormone Treatment is Age-Dependent in Ldlr-/- Mice

This study shows that menopause hormone treatment (E2) reduces atherosclerosis in young mice but not older mice, due to age-related changes in inflammation and estrogen receptor signaling.

Foxp1 Coordinates Early Temporal Identity and Neurogenic Progression in Retinal Progenitors

This study identifies Foxp1 as a transcriptional regulator that coordinates early progenitor identity with neurogenic progression in the developing retina by activating early-stage genes and proneural factors while repressing late temporal factors.

Light-entrained chromatin priming poises rapid metamorphosis in a marine sponge

The paper shows that light cues prepare the genome for rapid metamorphosis in marine sponges by priming chromatin structure before environmental induction.

Tetrahydrobiopterin restores oligodendrocyte maturation after hypoxic white matter injury by reprogramming translational output

The paper investigates how BH4 restores oligodendrocyte maturation after hypoxia by analyzing translational changes using TRAP-seq and other methods.

SAHA increases chaperone expression and reduces Z-alpha-1-antitrypsin polymers in a patient specific iPSC-based liver model for alpha-1-antitrypsin deficiency

The paper uses iPSC-derived liver cells to show SAHA reduces Z-alpha-1-antitrypsin polymers by increasing chaperone expression in AATD models.

Genedex: Contextualizing gene signatures across Alzheimer's disease pathology, cell types, and brain regions

Genedex integrates gene signatures from Alzheimer's disease studies to contextualize gene expression across pathology, cell types, and brain regions, revealing new insights into disease mechanisms.

The human-specific lncRNA HD-LINC drives lipid droplet-associated neurodegeneration in Huntington's disease

This study identifies HD-LINC, a human-specific lncRNA, as a driver of lipid droplet-associated neurodegeneration in Huntington's disease, showing its role in lipid metabolism and neuronal death.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

Development of gemcitabine-modified miR-15a as a novel, multimodal treatment strategy to overcome 5-FU and oxaliplatin resistance in colorectal cancer

This paper develops Gem-miR-15a, a gemcitabine-modified microRNA, which overcomes 5-FU and oxaliplatin resistance in colorectal cancer with high potency and low toxicity.

Unconventional Small Molecule MNP-021 Protects Neuronal and Glial Function from Diabetes-Associated Glucotoxicity and Neuroinflammation

This paper tests the neuroprotective effects of MNP-021 against diabetes-induced glucotoxicity and neuroinflammation in neurons and glial cells, finding it restores glucose handling, mitochondrial function, and pro-resolving signaling.

Early tuberculosis treatment remodels blood mRNA and small RNA, and a baseline host signature is associated with early culture conversion

This study identifies blood-based biomarkers that predict early tuberculosis culture conversion by analyzing mRNA and small RNA changes during treatment.

Brain Age Gap Associations with Externalising Behaviours in Youth: A Longitudinal Investigation in the Adolescent Brain Cognitive Development (ABCD) Cohort

This study investigates the association between brain age gap and externalising behaviours in youth, finding a cross-sectional link that weakens over time.

The broccoli derivative sulforaphane extends lifespan by slowing the transcriptional aging clock

This study shows sulforaphane extends C. elegans lifespan by over 50% when administered early and reduces transcriptional age by 20%.

Genome-Wide Transcriptomics Uncovers a Lung-to-Aorta Inflammatory Program Driving Influenza-Induced Atherosclerosis Exacerbation

This study identifies a lung-to-aorta inflammatory program driven by influenza that exacerbates atherosclerosis through shared circadian and Hippo/YAP pathway suppression.

Shared Genetics of Hypertension and Preeclampsia Converges on Immune Regulation

The paper identifies shared genetic variants between hypertension and preeclampsia that regulate immune-related genes, linking gene expression to blood pressure traits and clinical phenotypes.

Natural killer cell TGF- signaling regulates senolytic activity and vascular patterning in the postnatal lung

This study shows that NK cell TGF-β signaling regulates postnatal lung development and BPD by affecting vascular patterning and senolytic activity.

Integration of ATAC and RNA-sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

Cellular context defines brain-specific functions of genes associated with neurodevelopmental disorders

The paper identifies brain-specific functions of NDD-associated genes by analyzing gene expression and regulatory mechanisms across tissues.

Experimentally Defined Tm-Guided Exon Exon Junction Primer Design Enables Specific Discrimination of Highly Similar RNA Variants

The paper introduces a Tm-guided exon-exon junction RT-PCR method to specifically detect RNA variants with similar exonic regions, showing improved discrimination and clarity.

Linking cross-species hemodynamics with neuronal activity in prefrontal cortex during abstract sequence viewing

This study links hemodynamic responses and neuronal activity in prefrontal cortex across humans and macaques during abstract sequence viewing, showing functional homology and distinct spiking dynamics.

A molecular circuit integrates environmental cues to coordinate the exit from developmental dormancy

The paper identifies molecular mechanisms that integrate environmental cues to trigger diapause exit in killifish embryos using transcriptomics and chemical screening.

A rare pre-existing progenitor-like Primed SMC compartment is the dominant inferred source of SMC-derived cellularity in vascular injury and atherosclerosis