differential expression

Distinct transcriptional remodeling of immune and metabolic pathways in severe undernutrition during latent tuberculosis infection does not consistently predict tuberculosis progression across independent cohorts

The paper examines transcriptional changes in severe undernutrition during latent TB infection and finds inconsistent associations with TB progression across cohorts.

Pan-gastrointestinal prioritization links LINC01094 to a colorectal cancer transcriptional state and replication-associated checkpoint activation

This study identifies LINC01094 as a key lncRNA in colorectal cancer, showing its role in transcriptional states and replication-associated checkpoint activation through functional analysis.

Stimulus-specific recruitment of human amygdala neurons predicts episodic memory encoding success

The paper shows that specific amygdala neurons in humans fire more during encoding of items later remembered, predicting episodic memory success, particularly in the right amygdala.

CDH1 loss remodels gene expression and lineage identity in human mammary epithelial cells

This study shows that CDH1 loss in human mammary epithelial cells remodels gene expression and lineage identity toward a luminal progenitor-like state, contributing to ILC oncogenesis.

Identification of gene kinetics patterns improves RNA velocity and cell fate prediction using JuloVelo

JuloVelo improves RNA velocity and cell fate prediction by incorporating gene kinetics patterns, outperforming existing methods across multiple differentiation programs.

Stochasticity in Metabolism: Oxidative Stress Response Phenotypes As Emergent Consequences of Network Topology

The paper models oxidative stress response in E. coli using a genome-scale metabolic model to show that bimodal killing under H2O2 stress emerges from network topology and stochastic sampling.

The sex determination gene fruitless is essential for male Aedes aegypti mosquito swarming and attraction to female flight sounds

This study shows that the fruitless gene in male Aedes aegypti mosquitoes is essential for swarming and attraction to female flight sounds, with its disruption causing loss of these behaviors.

Transcriptome-wide Differential Expression and Splicing in Inflammatory Bowel Disease Patients

The paper identifies differential expression and splicing in IBD patients, showing distinct molecular mechanisms in CD and UC.

Comparing the Phenotypic and Genetic Differences Between Autistic Regression and Autism Without Regression Using the SPARK Cohort

The paper compares phenotypic and genetic differences between autistic regression and autism without regression using the SPARK cohort, finding increased neurodevelopmental morbidity and minimal genetic explanation.

STRADA Deficiency Impairs Cortical Interneuron Development in Humans and Mice

This study shows STRADA deficiency reduces cortical inhibitory interneurons and increases striatal interneurons in mice and a human PMSE brain, suggesting impaired interneuron migration contributes to the disorder.

Stimulation strategy matters: A B-cell focused single-cell transcriptomic study on in vitro stimulated immune cells

This study compares B-cell stimulation strategies using single-cell transcriptomics, finding distinct transcriptional responses and cell-cell interactions depending on the stimulation method and time.

Intermediate, rather than Isohydric or Anisohydric, Species were More Resilient to an Extreme Heatwave in a Common Garden in Sydney

The study evaluates resilience of urban tree and shrub species to an extreme heatwave using functional traits, finding that crown dieback better predicts thermal stress than survival.

Regularized logistic regression-based gene selection for functional analysis of heterogeneous scRNA-seq macrophage populations in muscle aging and regeneration.

The paper introduces DisTwiner, a method for subgroup-aware gene selection in scRNA-seq data, showing it captures biologically relevant aging pathways in macrophages.

Kcs1-dependent inositol pyrophosphates promote DNA double-strand break repair via Pho80-Pho85 in budding yeast

This study identifies Kcs1-dependent inositol pyrophosphates as regulators of DNA repair via Pho80-Pho85 in budding yeast, independent of homologous recombination.

High-content imaging of live microglia-containing Alzheimer's disease brain organoids

This study uses microglia-containing Alzheimer's disease brain organoids to monitor Aβ aggregation and cellular viability, identifying age-dependent disease-associated phenotypes.

Intraoperative glucocorticoids confound surgical biopsy transcriptomics

This study shows that intraoperative dexamethasone significantly alters hepatic gene expression in biopsy samples, confounding transcriptomic analyses of liver tissue.

Disease-associated NK-cell state remodeling reveals transcriptional profiles predictive of clinical phenotypes

The paper establishes the Human NK-cell Atlas and identifies disease-specific NK-cell state remodeling, developing a model to predict clinical phenotypes.

Genetic control couples TGFβ-independent pluripotent stem cell renewal to deterministic forward programming across germ layers

This paper introduces GERALT, a genetic circuit that enables TGFβ-independent hiPSC renewal and inducible lineage programming, improving differentiation efficiency and reducing medium complexity.

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

ctDNA-BERT scores individual bisulfite reads for cell-free DNA methylation analysis, achieving high accuracy in cancer staging without cohort-specific retraining.

Lymphoma response to chimeric antigen receptor T cell therapy is driven by endogenous tumor-reactive CD8⁺ T cells

This study shows that durable CAR-T therapy in lymphoma requires cooperation with endogenous CD8 T cells, and tumors lacking MHC class I or CD58 resist treatment.

Direct effects on gene transcription revealed by global and CRISPR-targeted oxidative DNA damage

The paper shows oxidative DNA damage directly affects gene transcription through repair-dependent mechanisms using RNA-Seq, ChIP-seq, and chemogenetic approaches.

Perturbation-based propagation of bacterial composition uncertainty improves robustness and reproducibility of microbiome differential abundance analysis.

PARALLAX improves microbiome differential abundance analysis by addressing compositional data, uncertainty, and experimental design through a unified framework with stability-based metrics.

The RNA m6A reader YTHDF2 depletion phenocopies high glucose induced-cellular stress response in diabetic kidney disease

This study shows that YTHDF2 depletion mimics high glucose-induced stress in diabetic kidney disease by altering RNA processing and increasing oxidative stress.

Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes

This study tracks intestinal CD4+ T cells from suckling to adulthood, showing they adopt a transient cytotoxic-regulatory state at weaning, influenced by microbiota and early-life commensals.

CREBBP variants underlying Menke-Hennekam syndrome exhibit histone acetyltransferase hyperactivity with divergent phase behaviors

This study identifies two CREBBP variants causing Menke-Hennekam syndrome that increase HAT activity but disrupt phase separation differently, with HAT inhibition restoring condensate dynamics in one variant.

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer

This study shows that matrix stiffness in gastric cancer affects immunometabolic states and response to PD-1 blockade, with softer matrices improving treatment efficacy.

Anti-Nucleolin Aptamer iSN04 Inhibits Alveolar Rhabdomyosarcoma Cell Growth by Inducing Myogenic Differentiation

This study shows that the anti-nucleolin aptamer iSN04 inhibits alveolar rhabdomyosarcoma cell growth by promoting myogenic differentiation and enhancing the efficacy of vincristine.

Ambient light color does not detectably change the transient, flight-specific DEET response of Aedes aegypti

The study reanalyzes mosquito flight data to show DEET's transient repellent effect is not influenced by ambient light color.

Mitochondrial and bioenergetic processes are enriched in large-but are reciprocally depleted in small extracellular vesicles

The paper shows that mitochondrial and bioenergetic processes are enriched in large EVs but depleted in small EVs using proteomics and gene-set enrichment analysis.

A Cell-Autonomous Cold Sensor Promotes Lipolysis Through Phase Separation

The paper identifies a cell-intrinsic cold-sensing mechanism that enhances lipolysis through phase separation of perilipin 1 in adipose tissue.