differential expression

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.

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.