differential expression

Citrobacter rodentium infection disrupts colonic mucus barrier function via ablation of intercrypt goblet cells

This study shows that Citrobacter rodentium infection disrupts the colonic mucus barrier by ablating intercrypt goblet cells, leading to impaired barrier integrity and enhanced pathogen colonization.

Dual kinase inhibition provides early clues to restoration of neuroimmune homeostasis in an AAV-haSyn model of Parkinsons disease

This study shows that dual inhibition of MLK3 and LRRK2 with URMC-099 reduces PD pathology and motor deficits in an AAV-haSyn rat model.

Identification of Kinome Biomarkers and Therapeutic Rescue in cGMP-Linked Retinal Degeneration

This study identifies kinome biomarkers and shows therapeutic rescue in cGMP-linked retinal degeneration using LP-CN03 in mouse models.

Identification and characterization of new P. aeruginosa phages using a surface receptor platform

The paper introduces a SURFAR platform to identify and characterize new P. aeruginosa phages by targeting specific receptors, isolating two novel phages with distinct host ranges.

Fatty Acid Synthase Binds Cellular mRNAs and its Depletion Reduces Translational Efficiency

This study identifies FASN's RNA binding sites and shows its depletion reduces translational efficiency of associated mRNAs.

Epidermal Langerhans Cells Act as Neuroimmune Regulators of Pain and Itch

This study identifies Langerhans cells as immune-derived amplifiers of cutaneous sensory signaling and identifies semaphorin 7A as a mediator of LC-induced itch potentiation.

Label-free flow operators and stability operators from single-cell time courses: what local dynamical operators can and cannot identify

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

DisCell: Separating Spillover from Niche Response in Spatial Transcriptomics

DisCell identifies and separates spillover from niche responses in spatial transcriptomics data, confirming a previously reported finding about esophageal cancer cells.

Network analysis of mouse brain proteomes resolves molecular and cellular endophenotypes of aging and Aβ pathology

This study uses proteomics to identify aging and Aβ-related molecular changes in mouse brains and finds they are conserved in human AD proteomes.

From Fill to Freeze: Redesigning homeRNA to Enable Robust Sampling and Scalable Downstream Processing Workflows for Remote Blood Transcriptomics

This paper validates the redesigned homeRNA platform's robustness to remote study stresses, showing it maintains RNA quality under varied conditions and storage times.

ER stress-associated IRE1α signalling links impaired QPRT-dependent NAD⁺ biosynthesis to reduced oocyte competence

This study links ER stress and impaired NAD biosynthesis via QPRT to reduced oocyte quality and shows that NMN supplementation improves oocyte function and early embryonic development.

Mutant Isocitrate Dehydrogenase 1 Alters Extracellular Vesicle Secretion and Cargo Composition in Cellular Models

This study shows mutant IDH1 increases sEV secretion and alters their cargo composition in glioma and chondrosarcoma cells, with D2HG packaged into sEVs and cell-type-specific cargo remodeling.

Learning interpretable compositional features associated with continuous covariates

This paper introduces IsoVita, a framework for learning interpretable compositional features from continuous covariates, showing improved detection of temporal isoform variation in human brain RNA-seq data.

Human organoid screen links transient translational modulation to progenitor progression in corticogenesis

The paper screens human cortical organoids with small molecules to identify translational modulators affecting progenitor progression in corticogenesis, finding Emetine promotes neuronal differentiation.

CD300f is required for efficient lipid handling during cuprizone-induced demyelination

This study shows CD300f is essential for microglial lipid handling and remyelination during demyelination, with deficits in lipid metabolism and motor coordination in its absence.

TailEnrich enables discovery of dysregulated genes through disease sample enrichment testing

TailEnrich identifies dysregulated genes in patient subsets by testing expression distribution tails, outperforming DESeq2 and edgeR in simulated data and uncovering novel genes in Alzheimer's disease.

Satellite cell glucocorticoid receptor restrains myogenic commitment without mediating the effects of therapeutic glucocorticoids on muscle repair

This study shows that satellite cell glucocorticoid receptor (GR) maintains quiescence but does not mediate therapeutic GC effects on muscle repair, highlighting the importance of treatment timing and context.

Secondary growth in the tomato stem is suppressed by the flowering regulators FUL2 and STM3

This study identifies FUL2 and STM3 as repressors of secondary growth in tomato stems, showing their role in limiting xylem accumulation during stem development.

Quantum Entanglement as a Physical Determinant of Genomic Instability in TP53

The paper explores whether quantum entanglement, measured via von Neumann Entropy, influences TP53 mutation patterns, finding elevated entropy at known mutational hotspots but cautioning about limited validation.

Druggable CSNK2A1-MeCP2 regulatory axis links Okur-Chung neurodevelopmental syndrome with MECP2-related disorders

The paper identifies a druggable CSNK2A1-MeCP2 regulatory axis linking Okur-Chung neurodevelopmental syndrome with MECP2-related disorders through CRISPR screens and mouse models.

Integrative Multiomics Analysis of the Angiogenesis-EMT Interface in Head and Neck Squamous Cell Carcinoma

This study identifies coordinated angiogenesis-EMT gene programs in OSCC using multi-omic analysis and validates candidate genes through external datasets and protein-level confirmation.

Material context and TGF-β blockade timing determine retained matrix in patient-derived bioprinted keratoconus stroma

This study shows that timing of TGF-β blockade and material context affect matrix retention in bioprinted keratoconus stroma, with optimal regimens improving collagen retention and reducing contractile gene expression.

LinearRaccess: linear-time approximation of RNA accessibility without base-pair span limits

LinearRaccess computes RNA accessibility for long windows in linear time without base-pair span limits, achieving high accuracy and efficiency.

Elevated precontractile calcium set point is sustained by limited PMCA1 export in dystrophic muscle

The paper shows that dystrophic muscle has an elevated precontractile calcium set point sustained by limited PMCA1 export in C. elegans and human myoblasts.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

Hyperactivity preferentially disrupts scotopic retinal circuits in the early stages of diabetic retinopathy

This study identifies scotopic retinal circuit dysfunction in early diabetic retinopathy, linking hyperactivity to rod bipolar cell abnormalities and visual impairment under low-light conditions.

MOCHI enables systematic identification of candidate independent intronic transcriptional signals from short-read RNA-seq data

MOCHI identifies candidate independent intronic transcripts from short-read RNA-seq data, revealing novel transcripts associated with cancer survival.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

MitoDecode: quantitative phenotypic decoding of mitochondrial stress states from fluorescence images

MitoDecode assesses mitochondrial stress types and severity from fluorescence images without segmentation, showing adaptability across cell types and stress conditions.

Evaluating non-oxidative glycolysis using 13C metabolic flux analysis

This study evaluates the precision of 13C metabolic flux analysis using different glucose tracers to estimate non-oxidative glycolysis fluxes in E. coli.