differential expression

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

Personalized Prediction of Differences in fMRI Connectivity Estimates Across Preprocessing Pipelines

The paper predicts how preprocessing affects fMRI connectivity estimates using prior scans, showing personalized models outperform average predictions.

Systematic comparison of gliflozins identifies a selective anti-calcifying effect of canagliflozin beyond canonical SGLT2 inhibition

This study compares gliflozins and finds canagliflozin uniquely reduces vascular calcification through mechanisms beyond SGLT2 inhibition, affecting VSMC metabolism and calcification.

Mathematical model of phenotypic plasticity predicts interconversion is a drug target for neuroblastoma.

The paper develops a mathematical model to show that targeting interconversion patterns in neuroblastoma can improve treatment outcomes by stabilizing tumor dynamics.

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

Optogenetic induction of TAD boundary pairing promotes gene activity

This study uses OptoTet to manipulate TAD boundaries and shows that boundary pairing enhances gene activity for ERRFI1 but not MYC.

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

Ribosomal Remodeling and Translational Suppression in the Post-Arrest Heart

This study investigates how cardiac arrest affects myocardial ribosome biology and protein synthesis in pigs and mice, finding increased ribosomal transcripts with ischemic burden and suppressed ribosome activity post-arrest.

Application of metagenomic sequencing to improve sessile serrated lesion detection using the faecal immunochemical test

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

Breaking the bottleneck: semi-automated quantification of actin filament dynamics

The paper introduces SMAUG, a semi-automated tool for analyzing actin filament dynamics from TIRF microscopy images, reducing analysis time while maintaining accuracy.

Preferential Isoform Usage and Isoform Switching in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Profile

The paper identifies subgroup-specific isoform usage and switching in SLE patients with distinct autoantibody profiles, highlighting their functional relevance in autoimmune pathogenesis.

Early AAV9-mediated SLC9A6 gene replacement preserves cerebellar structure and motor function in the shaker rat model of Christianson syndrome

This study evaluates AAV9-mediated SLC9A6 gene replacement in shaker rats, showing early treatment preserves cerebellar structure and motor function, while later treatment has diminishing effects.

Establishing an ex vivo platform for molecular profiling of skin structural cells using frozen human skin biopsies

This study establishes a scalable ex vivo platform using frozen human skin biopsies to study inflammatory responses in skin structural cells.

Arrest-associated transcriptional programmes outweigh apoptosis-associated programmes in treatment-naive pancreatic ductal adenocarcinoma

The paper examines the balance between apoptosis and arrest-associated transcriptional programs in untreated PDAC, finding a consistent bias toward arrest programs.

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

No Evidence of an Effect of a Single Mirror Visual Feedback Session on Subsequent Motor Imagery

This study finds that a single session of mirror visual feedback does not significantly alter subsequent motor imagery-related neural activity.

Sex differences in agonistic social behavior: Effects of exercise and ovariectomy

This study examines how sex, exercise, and ovariectomy affect offensive and defensive aggression in rats, finding sex-specific behavioral differences and no effect of exercise.

Temporal Structure in Resting-State fMRI under Marginal and Cross-Spectral Surrogate Controls

The paper evaluates temporal complexity measures in resting-state fMRI to identify disease-related changes, finding that real data show greater outliers than randomized controls.

Deducing splicing events from transcript sets with splicelogic

splicelogic converts transcript-set comparisons into interpretable splicing events, enabling downstream analysis of isoform changes in RNA-seq data.

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.

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.