differential expression

Digital twins forecast individual immune trajectories

The paper introduces ImmuneTwins, a digital twin framework that personalizes immune response models for individuals, improving prediction accuracy of immune trajectory changes.

Multivariate Mutual Information based Feature Selection for Predicting Histone Post-Translational Modifications in Epigenetic Datasets

This paper introduces multivariate mutual information (MMI) for selecting histone PTM features to predict epigenetic data, showing improved accuracy over traditional methods.

Neuroinflammation is an early pathological process in a mouse model of prodromal Parkinsons disease

This study shows that neuroinflammation occurs early in a mouse model of prodromal Parkinson's disease before neuronal loss, linking Syn pathology to olfactory dysfunction.

Influenza H1N1 Imprinting Uncouples Serological and B-Cell Responses in Mice

This study shows that immunological imprinting in mice uncouples serological and B-cell responses, with B-cell repertoires updating independently of serum antibody specificity.

The Alzheimer's disease-associated rs28834970 variant in PTK2B impairs electrical activity and regulates Tau phosphorylation and APP processing in human neuronal cultures

This study identifies the rs28834970 variant in PTK2B as a risk factor for Alzheimer's disease, showing it impairs PYK2 function, increases Tau phosphorylation, and alters APP processing in human neuronal cultures.

Brain representations of visual short-term memories during healthy human aging: occipital decline and frontoparietal compensation

This study investigates age-related changes in visual short-term memory using fMRI decoding, finding that visual cortex representations weaken with age and load, while frontoparietal regions compensate by strengthening during memory maintenance.

Interpretable Deep Learning of Endogenous Fluorophore Concentration and Entropy for Lung Tissue Classification

The paper uses an interpretable deep learning model to classify lung tissue as normal or cancerous by combining fluorophore concentration and entropy features, achieving high accuracy.

Evolutionary conservation and divergence of regional fructose-responsive gene regulation in the intestine

This study examines how fructose-responsive gene regulation varies across intestinal regions in mice and fruit flies, finding conserved pathways and divergent metabolic responses.

A novel function of neuroligin 3: Beyond sociality, Regulating lifespan in Drosophila

This study shows that reducing neuroligin 3 in Drosophila extends lifespan and alters social behavior, linking synaptic function to longevity.

Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy

The paper uses scRNA-seq to compare IL-13-treated esophageal organoids with EoE biopsies, revealing shared cell state heterogeneity and differentiation hierarchy dysregulation.

Amino Acid Metabolic Signature Links Pediatric Environmental Enteric Dysfunction to Maternal-Fetal Growth Restriction Across Two Independent Cohorts

Tau-CTFP: A connectome-informed continuous-time first-passage model for forecasting the onset of regional tau PET abnormality

This paper introduces Tau-CTFP, a model for forecasting regional tau PET abnormality onset in Alzheimer's disease using connectome-informed continuous-time first-passage modeling, achieving high precision and recall in predicting abnormality onset.

YBX3 overexpression in mesothelioma drives aberrant cell proliferation

This study identifies YBX3 as an oncoprotein in mesothelioma that drives cell proliferation through SLC7A5/LAT1-mediated amino acid uptake and shows JPH203 as a potential therapeutic agent.

Accumulation of FAM98B and tRNA-Splicing Ligase Complex Proteins in Neuronal Intranuclear Inclusions in Spinocerebellar ataxia type 4.

The paper examines the localization of tRNA-splicing ligase complex proteins in SCA4 pontine neurons, finding their accumulation in neuronal intranuclear inclusions.

Transient Partial Inhibition of DNA Polymerase α Promotes Chromatin Plasticity and Enhances Human Cell Reprogramming

Transient low-dose inhibition of DNA polymerase α enhances human cell reprogramming by promoting chromatin plasticity while maintaining genomic stability.

An invariant network architecture with broadly expressed regulators distinguishes cell-type from cell-state identity in situ

The paper constructs state-level regulatory networks in mouse liver hepatocytes, revealing an invariant sub-network of broadly expressed TFs that defines cell-type identity, distinct from state-specific variations.

Temporal Dynamics Outweigh Fungicide Treatment in Shaping the Turfgrass Phyllosphere Resistome

This study shows that temporal changes in the phyllosphere microbiome have a greater impact on antibiotic resistance gene abundance than fungicide treatment.

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

Sex- and Age-Specific Development of ssRNA Virus Receptor Expression in the Human Brain

This study identifies sex- and age-specific developmental patterns of ssRNA virus receptor expression in the human brain using postmortem transcriptomic data.

A CTCF-LDHB axis converts nuclear lactate availability into an H3K18 acylation switch that directs alternative splicing in hypoxic breast cancer

Development of auxin reporters in oilseed rape (Brassica napus)

This study develops auxin reporters for oilseed rape to visualize and quantify auxin distribution and signaling during development and stress.

IFNγ and proinflammatory cytokines cooperatively license astrocytes to support antigen-dependent CD4+ T cell restimulation

The paper shows that IFNγ and proinflammatory cytokines activate astrocytes to express antigen-presenting machinery, supporting CD4+ T cell restimulation in vitro and in vivo.

Vaccination of pregnant mares with mRNA encoding a GPI-anchored form of the virulence-associated protein A of Rhodococcus equi induces strong IgG responses that are transferred to their foals

This study shows that vaccinating pregnant mares with mRNA encoding GPI-anchored VapA of R. equi leads to transfer of VapA-specific IgG to foals, providing passive immunity.

Spatial Landscape of Pregnancy-Associated Triple Negative Breast Cancer and Mammary Gland Involution

This study compares transcriptional differences between pre- and post-involution PA-TNBC tissues using spatial transcriptomics, identifying distinct inflammatory and chromatin remodeling patterns in post-involution tumors.

Sex and autism share cell type-specific effects on cortical gene expression

The paper examines cell type-specific sex effects on gene expression in autism and finds a stronger overlap with autism than schizophrenia.

Integrated tissue proteomics and lipidomics from ovine organs suggests novel functional implications for fatty acids and lipid mediators.

The paper integrates proteomics and lipidomics data from sheep organs to functionally annotate lipid mediators and identify novel roles for fatty acids in protein synthesis and inflammation resolution.

Lineage-mixed neurodevelopmental programs in pediatric sarcomas nominate tumor-selective surface antigen pairs.

This paper develops an AI framework to interpret single-cell RNA-seq data from pediatric solid tumors, identifying tumor-specific surface antigen pairs for targeted therapies.

IG-28 enables identification and quantification of high-confidence isoforms from large bulk and single-cell full-length cDNA datasets

IG-28 identifies and quantifies high-confidence isoforms from large bulk and single-cell full-length cDNA datasets more effectively than existing tools.

Keratin 17 Defines an Epithelial-Mesenchymal Transition-Associated Migratory Cell State in Pancreatic Ductal Adenocarcinoma

This study identifies K17 as a marker of an EMT-associated migratory cell state in PDAC, showing its role in promoting tumor-cell migration and poor prognosis.

Macaque Area LIP Reflects Confidence-Dependent Changes in Decision Policy

This study shows that neural activity in macaque lateral intraparietal area (LIP) reflects confidence-dependent changes in decision policy, linking confidence to subsequent decision-making.