differential expression

KIF1A-driven entry of degradative lysosomes into the axon is developmentally regulated by the microtubule environment at the axon initial segment

This study shows that KIF1A-mediated lysosomal transport into axons is regulated by the axon initial segment microtubule environment, and its disruption leads to axonal degeneration.

Predicting Differential Protein-Protein Interactions

The paper develops a random forest model to predict differential protein-protein interactions between experimental conditions using MINT embeddings and mass spectrometry data.

Blue light compromises cellular fate of intrinsically photosensitive Müller glial cells in the developing chicken retina.

This study shows blue light exposure reduces pluripotency and increases neuronal differentiation in Müller glial cells from chicken retinas.

Host transcriptional programs underlying lesion development in contagious bovine pleuropneumonia

This study identifies host transcriptional changes during different stages of Mmm infection in cattle, revealing immune and tissue remodeling pathways involved in lesion progression.

Item-specific clustering of high gamma-band activity on theta phase during speech categorization

The paper investigates phase-dependent perceptual biases during speech categorization and finds item-specific theta-gamma phase-amplitude coupling linked to neural and perceptual responses.

A composited genome approach to analyse cistrome diversity in barley

The paper develops a composite genome approach to analyze TF occupancy diversity in barley using short-read data, showing improved accuracy over SNP-replacement strategies for MOA-seq analyses.

An endothelial-specific TIE2-L914F mouse model reveals cellular mechanisms of venous malformation progression and recapitulates the patient's response to targeted therapy

This study creates a TIE2-L914F mouse model to study venous malformation progression and shows it responds to rapamycin treatment.

A droplet-to-data workflow for antimicrobial screening of complex matrices

The paper presents a droplet-based workflow for antimicrobial screening in complex matrices, showing it can detect MICs at lower concentrations and reveal extract-specific aggregation effects.

Brain and kidney Extracellular Vesicle Morphology and Complementary Brain proteomics after Inflammatory Challenge

The paper compares brain and kidney extracellular vesicle morphology and proteomics after inflammatory challenge, identifying significant protein changes but noting limitations in causal conclusions.

Genome-wide fluctuating selection under demographic cycling in Icelandic rock ptarmigan

The paper identifies genomic signatures of fluctuating selection in rock ptarmigan populations over an 11-year period, showing allele frequency changes correlated with demographic cycles.

Cognitive Control in Pediatric Cancer Survivors: A task-fMRI study

This study uses fMRI to compare brain activation during a cognitive task between pediatric cancer survivors exposed to chemotherapy and healthy controls, finding altered neural activation and cognitive control deficits in the chemo-exposed group.

A comprehensive map of the sequence basis of transcription initiation in humans

The paper develops deep learning models to predict transcription initiation patterns from DNA sequences across human tissues and cancers.

iPSC modeling of pulmonary arterial hypertension to uncover pathomechanisms and unrecognized modes of action of sotatercept

This study uses patient-derived iSMCs to uncover new mechanisms of PAH and sotatercept's effects beyond its known anti-proliferative actions.

Serum nutritional-metabolic recovery during tuberculosis treatment across BMI-defined undernutrition strata: A longitudinal proteomic reanalysis

This study reanalyzes longitudinal serum proteomics data from tuberculosis patients to assess how nutritional-metabolic recovery during treatment varies by baseline BMI, finding no significant BMI-dependent trajectories but an overall increase in a 36-protein summary axis.

High spatial resolution 23Na-MRI for ischemic brain injury detection

This study develops a high-resolution 23Na-MRI platform using implanted RF coils to detect ischemic brain injury with improved contrast-to-noise ratio.

Knockdown of the long non-coding RNA DNAAF3-AS1 activates the p53 pathway and remodels the H3K36me3 landscape

This study shows that knocking down DNAAF3-AS1 reduces gene-body H3K36me3, activates the p53 pathway, and alters promoter usage in apoptosis-related genes.

GaussF: An Unbiased Gaussian Framework for High-Precision Transcript Quantification with a Programmable Self-Benchmark Model

GaussF improves isoform quantification by using a theoretical Gaussian model to correct sequencing biases without empirical data, outperforming existing tools.

Tissue-specific transcriptomic responses to early Toxoplasma gondii infection in sheep during congenital toxoplasmosis

This study examines early transcriptomic responses to Toxoplasma gondii infection in pregnant sheep, identifying tissue-specific immune and stress pathways linked to fetal loss.

Inflammation reshapes epidermal and leukocyte differentiation resulting in altered glucocorticoid responsiveness

The paper investigates how inflammation alters cell type-specific glucocorticoid responsiveness through single-cell RNA sequencing in zebrafish.

Anatomically matched spatial comparisons identify Trps1 as a regulator of knee interzone formation

The paper identifies Trps1 as a regulator of knee interzone formation through spatial comparisons and perturbation experiments in mice, showing its role in chondrogenic differentiation.

Behavioral Markers of Essential Tremor Correlate with Distributed Alteration of Brain Functional Connectivity

The paper investigates how behavioral markers of essential tremor correlate with changes in brain functional connectivity using resting-state fMRI and kinematic data.

Defining cell type-specific diurnal gene expression in the mouse retina

The paper identifies cell-type-specific diurnal gene expression patterns in the mouse retina using single-nucleus RNA sequencing.

Sex-based differences in fibrosis markers in human abdominal aortic aneurysms

The paper identifies sex-based differences in fibrosis markers in human abdominal aortic aneurysms, showing elevated FAP and collagen in females.

Elephant seal cells export iron and form lipid droplets to evade lipid peroxidation

This study identifies a unique mechanism in elephant seal cells that prevents lipid peroxidation through lipid droplet formation and iron export, rather than traditional antioxidant pathways.

Live-cell, single-molecule imaging resolves the dual nature of mRNA silencing by SARS-CoV-2 Nsp1

This study uses live-cell imaging to show SARS-CoV-2 Nsp1 silences mRNAs by reducing their numbers through two cap-dependent mechanisms, while viral UTRs enhance translation but do not protect from Nsp1.

Complex I is essential for embryonic stem cell proliferation through NADH-mediated redox signaling

This study shows that Complex I is essential for ESC proliferation via NADH-mediated redox signaling, independent of energy or ROS levels.

Single-nucleus multiome profiling reveals osteocyte-centered remodeling of human subchondral bone across osteoarthritis severity

The paper uses single-nucleus multiome sequencing to analyze subchondral bone in OA, finding increased osteocyte SMAD2/3 activity and chondrocyte-derived FN1 signaling with disease severity.

Ex vivo autologous immune cell assay to study modulation of type 2 Inflammation by processed- or novel food extracts in peanut allergy

This paper introduces an ex vivo assay to study how peanut extracts and novel foods modulate type 2 inflammation in peanut-allergic patients.

Fatty acid synthase coordinates mTOR signaling and histone crotonylation during cardiomyocyte hypertrophy

This study identifies FASN as a regulator of mTOR signaling and histone crotonylation during cardiomyocyte hypertrophy, linking lipid metabolism to epigenetic changes and cardiac disease.

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.