differential expression

Dysplastic Alveolar Basaloid Cells Provide a Protective Barrier via KRT17-Stratifin Complex during Chronic Fibrosis

The paper identifies KRT17-Stratifin complex as a protective barrier in dysplastic alveolar basaloid cells during chronic fibrosis, revealing mechanisms of alveolar metaplasia and its functional relevance.

Conserved cell state dynamics reveal targetable resistance patterns in ovarian high-grade serous carcinoma

The paper identifies conserved cell states in ovarian high-grade serous carcinoma that correlate with poor prognosis and presents actionable targets for improving platinum response.

Stream and lake network position structures freshwater microbial communities across multiple catchments

The paper shows bacterial community composition changes consistently across hydrological network positions in freshwater systems.

Transformer Language Models Reveal Distinct Patterns in Aphasia Subtypes and Recovery Trajectories

This paper uses GPT-2 to analyze aphasia subtypes and recovery by examining activation patterns in narrative speech over time, finding distinct differences across subtypes and changes during recovery.

Aneuploidy profiling among different types of brain metastases reveals a colon cancer-specific chromosomal signature

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

A convergent proline biosynthetic step couples cell wall integrity to virulence in Cryptococcus neoformans

This study identifies Pro3 as a key enzyme linking proline biosynthesis to cell wall integrity in Cryptococcus neoformans, showing its critical role in virulence and growth.

Sugar-induced cell death in exponentially growing yeast depends on the functionality of the nonoxidative branch of the pentose phosphate pathway.

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

The paper introduces ATLAS, a method to map transcriptional differences across genetic backgrounds in mouse brains, revealing significant cell type distribution changes between sexes and genetic models.

Paternal epigenetic inheritance encoded by sperm histones shapes offspring prenatal development and viability

This study shows that paternal sperm histone H3K27me3 marks influence offspring development and viability by affecting organ and tissue formation.

Tamoxifen Targets Wisp2 to Impair Subcutaneous Adipocyte Progenitor Self-Renewal and Adipogenic Differentiation

This study shows tamoxifen reduces subcutaneous adipocyte progenitor self-renewal and adipogenesis by suppressing Wisp2, linking endocrine therapy to metabolic risks like T2D.

SRSF1 coordinates transcription and alternative splicing to modulate p53 and apoptosis

This study identifies SRSF1's role in coordinating transcription and alternative splicing, showing its impact on p53 regulation and apoptosis across multiple cell lines and cancer cohorts.

Single-nucleus transcriptomics links telencephalic cell signatures to ocean acidification effects on social behaviour in a coral reef fish

The paper uses single-nucleus transcriptomics to identify neural cell type responses to elevated CO2 in cleaner wrasse, revealing disruptions in myelination, glutamatergic signalling, and cell-cell communication.

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

A Blast Fungus Effector Targets a Tubby-like F-box Protein to Suppress Plant Immunity

This study identifies Tie1, a fungal effector that targets OsTLP7 to suppress plant immunity by altering its localization and transcriptional activity.

CD4 T cell surface architecture is associated with response to anti-PD-1 therapy in non-small cell lung cancer

The paper shows that CD4 T cell surface protein organization predicts response to anti-PD-1 therapy in NSCLC, outperforming protein abundance alone.

Dietary fibre responses emerge through host-dietary regime interplay: Apple pectin modulates immune reactivity in adult zebrafish

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.

Imbalance between RNA-binding proteins and the WAVE regulatory complex underlies the toxic gain-of-function effects of the CYFIP2 Arg87Cys variant in neurodevelopmental disorders

Differential endothelial cell remodeling in Down syndrome and APP duplication drives distinct blood brain barrier dysfunction

Combinatorial logic of Nav channels in nociceptor excitability: Different degrees of synergy define distinct neuronal groups

The paper investigates how combinations of Nav1.7 and Nav1.8 channels affect nociceptor excitability, showing that their synergistic effects vary across neuronal subtypes.

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

Vascular normalization in breast cancer confers an endothelial immune suppressive gene expression profile

The paper examines immune suppressive gene expression in normalized breast cancer endothelial cells and finds similarities with healthy human endothelial cells.

Integrative multi-omics decoding of the host response to Klebsiella pneumoniae infection reveals an itaconate-centred metabolic-immune axis and a spatially organised inflammatory programme

This study integrates multi-omics data from Kp infection to identify an itaconate-centred metabolic-immune axis and a host-response signature with high diagnostic accuracy.

Comparative transcriptomic analysis of intestinal Tuft cells reveals species selectivity of DCLK1 expression

This study compares transcriptomic data across species to assess DCLK1 expression in intestinal tuft cells, highlighting species-specific differences in its expression.

Dietary tryptophan rescues growth impairment during giardiasis independently of parasite burden

This study shows dietary tryptophan improves growth in Giardia-infected mice without reducing parasite load, suggesting a role for AHR signaling in epithelial barrier function.

Alignment-Free k-mer Analysis Reveals Age-Associated k-mer Signals in Canine Buccal DNA and Cell-Free DNA

This study identifies age-associated k-mer signals in canine buccal and cell-free DNA using alignment-free k-mer analysis and ridge regression models.

Neuro-mimetic reprogramming and epigenetic unlocking drive lung cancer stem cell adaptation to the brain microenvironment

This study shows lung cancer stem cells adapt to the brain microenvironment through neuro-mimetic reprogramming and epigenetic changes, enabling metastasis.

mTOR signalling, not clock gene rhythms, organises daily physiology

This study shows that mTOR signalling, not clock gene rhythms, drives daily physiological variations in mammals and plants.

Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Decoder-FFPE-seq improves sensitivity and resolution for spatial transcriptomics in FFPE tissues, enabling analysis of rare genes and tumor microenvironments.

Concurrent cognitive, behavioral and systemic physiological features mark preclinical Alzheimer's disease

The paper identifies subtle cognitive, behavioral, and physiological features in preclinical Alzheimer's disease using a risk factor-controlled cohort and an AI classifier.

Ume6 Coordinates Lysosomal Remodeling and Autophagy Through Transcriptional Repression in S. cerevisiae

This study identifies Ume6 as a transcriptional repressor that regulates vacuolar protein composition and autophagy in yeast by interacting with Rph1 and being modulated by protein kinases.