differential expression

Rapid, accurate, and memory-frugal sub-gene-level quantification of probe-based, multiplexed single-cell data

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

siRNA/mRNA payload of lipid nanoparticles quantified using fluorescence microscopy and correlation spectroscopy

The paper quantifies mRNA and siRNA payload in lipid nanoparticles using fluorescence microscopy and FCS, showing size-dependent payload and coencapsulation dynamics.

Onsite fixation preserves phosphoprotein profile in human whole blood

This study shows that fixing whole blood at collection preserves phosphoprotein profiles, particularly in neutrophils and monocytes, better than cryopreserved PBMCs.

Single-Cell Transcriptomics Reveals Tumorigenic Lineages and Interactions Persisting and Evolving From Premalignancy to Cancer in the Stomach

The paper uses single-cell transcriptomics to track molecular changes from premalignancy to cancer in gastric tissue, identifying persistent and evolving tumorigenic lineages and markers like EMB.

The mycotoxin zearalenone couples secondary metabolism to N-acetylglucosamine catabolism

This study shows that zearalenone production in Fusarium graminearum is linked to N-acetylglucosamine catabolism, with NAG playing a critical role in both GlcNAc utilization and ZEA tolerance.

Clinical relevance of diffusion tensor imaging-based parameters estimated with deep learning: the effect of model retraining

This study evaluates how retraining deep learning models affects the statistical consistency of diffusion tensor imaging parameters in bipolar disorder, showing significant variability across models.

RadMultiBench: A Reproducible Dual-Task Benchmark Exposing the Limits of Pre-Trained Vision-Language Models Across Thoracic and Breast Imaging

RadMultiBench evaluates pre-trained vision-language models on medical imaging tasks, showing performance gaps in report generation and classification across thoracic and breast imaging.

Unraveling Systemic Responses to NQO1-Activated IB-DNQand Rucaparib Single and Dual Agent Therapy in Triple-Negative Breast Cancers

This study evaluates the effects of IB-DNQ and Rucaparib on TNBC cells, revealing synergistic effects and novel protein biophysical changes via thermal proteome profiling.

A mammalian fibroblast zoo reveals barriers to cross-species virus replication and differential regulation of antiviral immunity

The paper uses fibroblasts from 86 mammalian species to study virus-host susceptibility and innate immune responses across diverse mammals.

Prenatal THC exposure alters metabolic gene expression and KEAP1 regulation in the mouse placental labyrinth

This study shows prenatal THC exposure reduces metabolic gene expression and KEAP1 in mouse placental labyrinth, while CBD has no significant effect.

Extended Pavlovian conditioned approach training and devaluation in Long-Evans rats using time-restricted feeding

This study develops an extended Pavlovian conditioned approach paradigm in Long-Evans rats under time-restricted feeding to better identify phenotypes linked to compulsive behaviors and stress-related dysregulation.

Endothelial Cell Specific Thioredoxin 1-Dependent Signaling in Oxygen-1 Induced Retinopathy

This study shows that endothelial cell-specific TXN1 protects against oxygen-induced retinopathy by regulating proliferation and redox signaling.

Microglial AhR Drives Sex-Biased Amyloid Pathology

This study identifies microglial AhR as a regulator of sex-biased amyloid pathology, showing that AhR activation exacerbates amyloid deposition and that AhR deficiency reduces amyloid burden.

Evaluating State-Transition Models in Short Resting-State fMRI with Continuous-Dynamics Controls

This study compares hidden Markov models (HMMs) and vector autoregressive (VAR) models in resting-state fMRI to determine if apparent state transitions reflect discrete dynamics or continuous activity, finding that VAR often outperforms HMMs in continuous cases.

Early Increases in Hippocampal Synchrony Predict Chronic Epileptiform Burden in a Temporal Lobe Epilepsy Model

Acute nicotine exposure produces a spatially organized transcriptional response in mouse olfactory cortex

This study shows that acute nicotine exposure induces a spatially organized transcriptional response in mouse olfactory cortex, affecting specific neurons and their surrounding astrocytes.

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

Variation in the embryonic cell lineages of Caenorhabditis elegans natural populations

The paper quantifies developmental variation in C. elegans natural populations using embGAN, finding genotype-specific differences in cell-cycle timing that exceed within-strain variation.

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

Failed allogeneic corneal lenticules show fibrosis and identity loss without dominant T cell rejection

The paper examines failed allogeneic corneal lenticules, finding fibrosis and loss of corneal identity without dominant T cell rejection, and explores treatment strategies.

LCN2+ Astrocytes Mark a Pro-inflammatory Astrocyte State Associated with Secondary Brain Injury After Cerebral Venous Thrombosis

Live attenuated YFV-17D vaccine induces robust B and T cell immunity in vaccine-draining lymph nodes

This study examines immune dynamics in lymph nodes after YFV-17D vaccination, identifying robust B and T cell responses and a conserved germinal center program across different vaccines.

Cytomegalovirus Infection in Human Cortical Organoids Induces Unique Developmental and Viral Substates

This study uses single-cell RNA sequencing to analyze HCMV infection in cortical organoids, identifying viral sub-states and cell type changes.

Response to azacitidine and the TIM-3 inhibitor, sabatolimab, in MDS and CMML is associated with distinct immune and antigen-presentation states

This study identifies immune and antigen-presentation states associated with response to azacitidine and sabatolimab in MDS and CMML using single-cell RNA sequencing.

Single-Cell Transcriptome-Wide Mendelian Randomization and Colocalization Analysis Reveals Immune Cell-Specific Mechanisms in Alzheimer's Disease

This paper uses single-cell eQTL-MR and colocalization analysis to identify immune cell-specific genetic mechanisms associated with Alzheimer's disease risk.

Simple, static, spiking nonlinearities can account for seemingly complex interactions between visual, motor and cognitive variables in the visual cortex.

The paper shows that simple nonlinearities in the visual cortex can explain complex interactions between visual, motor, and cognitive variables through additive input modulation.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

memVar: an integrated resource for interpreting human membrane protein variation in molecular and disease contexts

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

Sex-specific gene and isoform expression characterizes hippocampal aging in rhesus macaques

This study identifies sex-specific gene and isoform expression changes in hippocampal aging of rhesus macaques and finds shared transcriptional signatures with Alzheimer's disease.

T cell transcriptomes in simulated microgravity in vivo

This study examines how simulated microgravity affects T cell transcriptomes in humans, finding altered gene expression and inter-individual variability in response.