differential expression

Single-nucleus transcriptomics and phosphoproteomics identify misregulated sperm components in mice carrying a selfish supergene

The paper identifies misregulated sperm components in mice with a selfish supergene using single-nucleus transcriptomics and phosphoproteomics, revealing dysregulated phosphorylation and gene expression related to sperm motility.

Transcriptomic and lipidomic profiles reveal higher thermal adaptability in a tropical versus a temperate isolate of Chromera velia

This study compares transcriptomic and lipidomic responses of two Chromera velia isolates from different thermal environments to elevated temperatures, finding that the tropical isolate shows greater thermal adaptability.

Pediatric brain charts reveal ADHD biotypes with distinct developmental, molecular, and therapeutic profiles

The paper identifies two distinct ADHD biotypes using brain imaging and transcriptomic data, showing different developmental, molecular, and treatment responses.

A coordinated and reproducible multicellular response to AD pathology

The paper identifies robust multicellular axes associated with Alzheimer's disease pathology and sex using single-cell data from 427 donors, validated in an independent dataset.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

Human lymph node CD8+ T cell memory is nested within drainage regions

The paper shows that human CD8+ T cell memory is nested within drainage regions, with shared repertoires among nodes within a region regardless of virus specificity.

NAD metabolism mediates a sex-specific protection against early life infections

This study identifies NAD metabolism as a sex-dependent factor influencing early-life infection outcomes, showing sex-specific effects of NAD precursor supplementation in mice and humans.

Shared and distinct immunometabolic states link to divergent pathology in cutaneous mycobacterial infections

This study identifies shared and distinct innate immune programs in cutaneous mycobacterial infections and links them to divergent pathological outcomes through metabolic interactions.

Information contracts determine what inverse perturbation benchmarks measure

The paper introduces InverseBench and FSTN to evaluate inverse perturbation benchmarks, showing varying accuracy across tasks and highlighting the importance of endpoint construction.

EpiSignaLR: an open resource for genome-wide episignature analysis from methylation-aware short- and long-read sequencing

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

Cytoplasmic localization of 5hmC reveals RNA hydroxymethylation in breast cancer

The paper identifies cytoplasmic 5hmC in breast cancer tissues and cell lines, linking it to TET3 expression and RNA processing, with implications for triple-negative breast cancer.

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

The paper maps subgingival microbiome states in 1,355 adults, identifying divergent dysbiosis trajectories linked to periodontitis and host factors.

Inference and validation of causal genetic interactions in aging human fibroblasts

This paper uses convergent cross mapping to infer causal genetic interactions from cross-sectional transcriptomic data of aging human fibroblasts and validates these interactions experimentally.

Sex Differences in DNA Methylation and Gene Expression Reveal Distinct Molecular Programs in Muscle-Invasive Bladder Cancer

This study identifies sex-associated epigenetic and transcriptional programs in muscle-invasive bladder cancer, showing distinct DNA methylation and gene expression patterns between males and females, with conservation in a mouse model.

Nonsense-mediated decay constrains transposable element-driven evolutionary innovation

This study shows NMD limits TE-driven transcriptomic innovation by degrading TE-derived transcripts, affecting evolutionary novelty and cancer outcomes.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Pat1 globally activates deadenylation-dependent decapping to clear inefficiently translated oligo(A)-tailed transcripts

Human and Mouse Models of the Bipolar Disorder-Associated ANK3 p.W1989R Variant Display Altered Somatostatin Interneuron Connectivity and Function

This study investigates the effects of the ANK3 p.W1989R variant in human and mouse models, showing altered somatostatin interneuron connectivity and function linked to bipolar disorder.

Ancient genomes chronicle the history of adaptive evolution in East Asia

This study uses ancient genomes to analyze adaptive evolution in East Asia, finding pre-Neolithic selection at key loci and a link between ADH1B*48His and wheat farming.

Exome-based Preconception Carrier Screening for the Mexican Jewish Community; Yields and Implications

This study uses exome sequencing to identify genetic variants in the Mexican Jewish Community, finding higher rates of carrier status and novel alleles compared to standard panels.

Elucidating changes in gene expression driving nuclear dynamics across a foraminiferal life cycle with Pheno2Seq

The paper develops Pheno2Seq to study gene expression changes in foraminifera life cycle transitions, identifying genes involved in nuclear dynamics and genome stability.

CCTP-Atlas: Compartment-Resolved Ciliary Transcriptional Dysregulation in Tetralogy of Fallot, A Six-Dataset Integrative Meta-Analysis

The paper performs a meta-analysis of six TOF snRNA-seq datasets to identify compartment-resolved ciliary transcriptional dysregulation, finding module-specific gene expression patterns in TOF endothelium.

Multiple bottlenecks constrain presentation of Mycobacterium tuberculosis antigens on MHC class I

The paper identifies bottlenecks in MHC-I antigen presentation by Mtb, showing that only a small fraction of predicted binders are actually presented, and develops computational models to improve prediction.

Sexually dimorphic alternative splicing and its erosion following the loss of sex in stick insects

The paper examines sex differences in gene expression and alternative splicing in stick insects, finding that splicing variation declines more rapidly than gene expression after the transition to asexuality.

Spatial profiling of Kawasaki disease cardiac inflammation identifies STING as a therapeutic target

This study identifies STING as a therapeutic target for Kawasaki disease by analyzing spatial immune architecture in cardiac inflammation.

Dietary fiber-type-specific gut microbiome preconditioning drives differential susceptibility to sporadic colon cancer development

The paper shows that inulin supplementation increases colon tumor incidence in mice by altering gut microbiome and metabolome, creating a tumor-promoting environment when exposed to carcinogens.

MYC Suppresses Mitochondrial Function in Hepatocellular Carcinoma through NRF1-Driven Receptor-Mediated Mitophagy

This study shows MYC suppresses mitochondrial function in HCC by promoting mitophagy via NRF1, and inhibiting this pathway reduces tumor growth.

Directional information flow as a tool for analyzing protein allostery

The paper develops a method using transfer entropy to analyze directional information flow in proteins, identifying key residues involved in allosteric communication and demonstrating its utility in capturing dynamic changes.

Genetic and environmental factors associated with DNA methylation across childhood and adolescence in individuals with and without attention-deficit/hyperactivity disorder

The paper identifies genetic and environmental factors influencing DNA methylation in ADHD and controls across childhood, showing income and school quality affect methylation changes differently by ADHD trajectory.

Reduced baseline male fertility and increased sensitivity to hypoxic stress in high-elevation deer mice

This study finds that high-elevation deer mice have reduced baseline fertility and greater sensitivity to hypoxia compared to low-elevation mice, with gene expression changes suggesting adaptive testicular regression.