differential expression

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.

Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback

The paper introduces CSDE, a method that improves differential expression analysis in spatial transcriptomics by incorporating expert feedback to mitigate preprocessing biases.

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.

Roles of Neuromedin-U and Endothelin-1 in human cardiac organoid differentiation

This study identifies Neuromedin-U (NMU) and Endothelin-1 (ET-1) as key signaling factors influencing cardiomyocyte differentiation and electrophysiology in human cardiac organoids.

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 Relaxin-Defined Late-Luteal Endocrine Transition State in the Human Menstrual Cycle

This study identifies relaxin-2 as a late-luteal hormone with a distinct peak in the menstrual cycle, showing precise timing and ovulation dependence.

Quantifying epigenetic reprogramming and cellular plasticity in preneoplastic lesions reveals dedifferentiation as a key precancer hallmark

PLASTIC quantifies cellular plasticity and epigenetic reprogramming in preneoplastic lesions, revealing dedifferentiation as a key factor in cancer risk.

Single-cell spatiotemporal transcriptomics reveals the origin, cellular heterogeneity and regulatory network of seed fiber cells in poplar

This study uses single-nucleus RNA sequencing and spatial transcriptomics to map seed fiber development in poplar, identifying their origin and regulatory network.

3D Histology Validates 2D Histology for Axon Radius Distributions and Conduction Velocities

The paper validates 2D histology for representing axon radius distributions and conduction velocities using 3D reconstructions of rat axons and applies this to human data.

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

Building virtual cell dynamics that evolve with biological measurements

CellCompass, an agentic AI system, models cell dynamics from single-cell measurements and improves predictions by integrating new biological constraints and experimental data.

Systems level phosphoproteomics reveals CAMKK2 driven kinase signaling underlying malignant phenotypes in gastric cancer

This study identifies CAMKK2 as a key driver of kinase signaling in gastric cancer through phosphoproteomic analysis, showing its role in promoting proliferation and malignant traits.

Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

The paper introduces PIPPA, a pipeline for processing large-scale ATAC-seq data, showing that peak calling performance varies by dataset and recommending parameters for high-confidence chromatin accessibility profiles.

Inferring somatic copy number aberrations from spatial transcriptomics data to study early cancer development

This study infers somatic copy number aberrations from spatial transcriptomics data to identify spatially coherent SCNA-defined populations in early cancer development.

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.

Single-Cell Atlas of Non-Functioning Gonadotroph Tumors and Anterior Pituitary Reveals Lineage Infidelity and Clinically Associated Transcriptional Programs

This study compares single-cell transcriptomes of non-functioning gonadotroph tumors and normal anterior pituitary to identify lineage infidelity and growth-associated programs.

Lineage-specific transcription factor CEBPA accelerates RNA Polymerase I dynamics

This study shows that the myeloid transcription factor CEBPA accelerates RNA Polymerase I dynamics at rDNA repeats by modulating promoter escape, Pol I accumulation, and DNA supercoiling resolution.

N-glycoproteomic profiling of the hookworm Ancylostoma ceylanicum reveals heterogeneity and phosphorylcholine-modified glycans in larval and adult parasites.

This study performs N-glycoproteomic profiling of Ancylostoma ceylanicum, identifying stage-specific glycoproteins and phosphorylcholine-modified glycans in larval and adult parasites.

Lysosomal adaptation to extracellular acidity compromises CD8+ T cell cytotoxicity

This study shows that chronic extracellular acidosis remodels lysosomes in CD8+ T cells, impairing their cytotoxicity by depleting granzyme B through vesicle release.

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.

Amino Acid Remodeling Precedes Malignant Transformation in Oral Epithelial Cells

The paper identifies distinct Raman and proteomic signatures in potentially malignant oral epithelial cells that differentiate them from healthy and malignant cells, highlighting amino acid metabolism changes as early indicators of malignancy.

Modeling of human MLH1 and MLH3 variants in mice reveals novel functions of MutLγ in meiotic DNA repair and the ovarian reserve

This study models human MLH1 and MLH3 variants in mice, revealing MutLγ's roles in meiotic DNA repair and ovarian reserve maintenance through multiple mechanisms.

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.

Comparative Multi-omics Reveals Conserved Membrane Architecture and Selective Metabolic Cargo Enrichment Across Yeast-Derived Extracellular Vesicles

This study compares multi-omics data from yeast-derived extracellular vesicles to show conserved membrane architecture and strain-specific metabolic cargo enrichment.

Genetic interaction between Adgrg6 and Sox9 reveals a feedforward mechanism for postnatal spinal stability

The paper identifies a genetic interaction between Adgrg6 and Sox9 that contributes to spinal stability and AIS-like pathology in mice.

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.

NK Cells Engineered with a Chimeric Antigen Receptor Delay HIV Rebound and Reshape HIV Reservoir Composition

This study shows that engineered NK cells with a CD4-based CAR delay HIV rebound and alter the reservoir's composition in humanized mice.