differential expression

The Compositional Encoding of Hand-Eye Coordinated Movements for Single Neurons in the Posterior Parietal Cortex

The paper shows that PPC neurons encode hand-eye movements additively, allowing modular decoding of coordinated movements.

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.

ESX-1 substrates ESAT-6 and CFP-10 limit cGAS-STING activation via DNA and Zn2+ restriction

The paper shows ESAT-6 and CFP-10 limit cGAS-STING activation by degrading DNA and restricting Zn2+ availability during mycobacterial infection.

Dynamic Changes in the Urinary Proteome of Normal Pregnant Mice Carrying Phenylketonuria-Affected Fetuses

This study identifies candidate urinary proteomic biomarkers in pregnant mice carrying PKU-affected fetuses, showing temporal dynamics and non-invasive potential for early screening.

KMT2C and KMT2D regulate skeletal development through stage-specific epigenetic control of chondrogenesis

This study shows that KMT2C and KMT2D regulate skeletal development through epigenetic control of chondrogenesis, with redundancy in their function during bone formation.

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.

Functional analysis of PRPS1 disease alleles reveals altered polymerization and cytoskeletal organization

The paper investigates how PRPS1 disease alleles affect polymerization and cytoskeletal organization in yeast and human cells, linking these changes to metabolic state and phenotypic overlap.

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.

Movements for Grooming in Rhesus Macaques Co-opted from Feeding Movements

This study shows that grooming movements in rhesus macaques are adapted from feeding movements, with similar hand motions used for both tasks.

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.

Integrative Single-Cell Transcriptomics and Explainable AI for Disease Mechanism and Biomarker Discovery in Triple-Negative Breast Cancer

The paper uses single-cell RNA-seq and explainable AI to identify transcriptional features distinguishing invasive from non-invasive TNBC cells in a cell line, finding EMT-related and inflammatory genes as key predictors.

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.

Vascular specification from diversified mesoderm culminates in endothelial convergence

This study reconstructs mouse vasculogenesis using single-cell and spatial analyses, revealing a transient vascular-primed state and the role of VEGF in endothelial specification.

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.

DNA damage at Lamina-Associated Domains triggers nuclear envelope reorganization and chromatin detachment to prevent nuclear envelope blebbing and genome instability.

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.

Tumor SETDB1 expression predicts worse overall survival for bladder cancer patients

This study shows that high SETDB1 protein expression in bladder cancer is linked to shorter overall survival and specific tumor features.

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.

Locus-specific spatial and transcriptional dynamics direct T cell lineage choice in the thymus

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

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.