differential expression

Gene context shapes spatial organization and transcriptional heterogeneity of extrachromosomal DNA in cancer cells

This study investigates how gene context influences the spatial organization and transcriptional behavior of extrachromosomal DNA in cancer cells using a new imaging method called FLAGx.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

The paper maps m6A modifications and polyadenylation events in Plasmodium falciparum mRNAs, identifying stage-specific m6A sites and their potential role in 3' end processing.

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

Response to SMAC mimetics in patient-derived models of triple-negative breast cancer relies on RIPK1 activation

This study identifies RIPK1 activation as a key determinant of response to SMAC mimetics in TNBC, showing that resistance is linked to impaired RIPK1 autophosphorylation and HOIP overexpression.

Transcriptomic and metabolomic profiling reveals early responses of tomato plants elicited by compost-derived bacteria

This study examines the early molecular and metabolic responses of tomato plants to compost-derived bacteria, identifying common and strain-specific physiological signatures.

An information-theoretic analysis of the tsetse fly (Glossina morsitans) antenna reveals trichoid sensilla as the main carriers of odor identity

This paper uses information-theoretic methods to analyze tsetse fly antenna responses to odors, finding that trichoid sensilla carry more odor identity information than basiconic sensilla.

Circulating hematopoietic stem and progenitor cells in myeloproliferative neoplasms

This study profiles circulating hematopoietic stem and progenitor cells in MPN patients, identifying transcriptional signatures and quantitative readouts to distinguish MF from other MPNs and predict progression.

Targeting MK2-Driven Stromal Senescence Sensitizes Breast Cancer Bone Metastasis to Immunotherapy

This study identifies senescent cancer-associated fibroblasts (senCAFs) driven by MK2 that promote immunosuppression in bone metastases and shows that combining MK2 inhibition with OX40 agonists enhances immunotherapy efficacy.

Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

This study uses single-nucleus RNA-sequencing and multiome data to identify neuronal mitochondrial gene suppression as a driver of Alzheimer's dementia, revealing genetic and epigenetic mechanisms underlying cognitive resilience.

3D-genome impacts of TAD-boundary-disrupting ultra-rare structural variants identified in schizophrenia

The paper identifies and functionally characterizes TAD-boundary-disrupting ultra-rare structural variants in schizophrenia using CRISPR/Cas9 in iPSCs, showing cell-type-specific effects on 3D-genome organization and gene expression.

Network Analysis of Rare Single-Nucleotide Polymorphisms Suggests a Central Role for Type 17 Immune Responses in Trauma-induced, Genotypically Associated Hypo-Inflammation and Critical Illness

The paper identifies rare SNPs associated with hypo-inflammation and adverse outcomes in trauma patients, highlighting type 17 immune responses as central to critical illness.

Genetics and genomics of enteroarthroconidial development in Coccidioides

This study uses single-cell RNA-seq and genetic approaches to identify a role for pyropoptosis-like cell death in enteroarthroconidial development in Coccidioides.

Inhibition of CDK7, CDK9 or CDK12 affects phosphorylation of human SPT5.

The paper shows that CDK7, CDK9, and CDK12 phosphorylate SPT5, with CDK9 having the strongest effect on SPT5 phosphorylation and PAF1C interaction.

TEDEdb: a large-scale resource and multi-cohort analysis of transposable element differential expression in cancer

The paper re-analyzes over 7,000 RNA-seq samples to study transposable element differential expression in cancer and finds TE expression is more prone to batch effects and can be induced by various compounds.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

An auto-generated ADP-ribosyl-cysteine degron drives DTX2-dependent turnover of PARP7

This study identifies an ADP-ribosyl-cysteine degron in PARP7 that is recognized by DTX2, leading to PARP7 degradation and affecting AR signaling in prostate cancer.

Multiplex-GCN Predicts Clinically Actionable Tumor Microenvironment Subtypes in Pancreatic Cancer

The paper develops a multi-layered GCN to identify TME-guided PDAC subtypes, revealing seven subtypes with distinct molecular and prognostic features.

Transcriptome profiling reveals differential expression of virulence genes in Xylella fastidiosa under nutrient-rich and xylem-like conditions

This study compares transcriptomes of Xylella fastidiosa under nutrient-rich and xylem-like conditions, identifying differential gene expression and regulatory divergence between strains.

Systematic analysis of genetic vulnerabilities caused by chromosome loss events in cancer

This study identifies genetic vulnerabilities from chromosome loss events in cancer by analyzing CRISPR screening data and copy number profiles, revealing paralogous gene dependencies as therapeutic targets.

Hybrid Drosophila cell lines show selective genome instabilities

The paper establishes hybrid Drosophila cell lines to study genome instabilities and identifies incompatibility genes and chromosomal regions prone to loss in hybrids.

Cancer cells hijack mitochondria from Bhlhe40+ T cells for immune evasion

The paper identifies the Bhlhe40-S100a4 cascade as a key regulator of cancer cell mitochondrial transfer from T cells, offering a target for immunotherapy.

Single-cell profiling quantifies the dose gap between population-average and complete pY-STAT1/3 suppression by JAK inhibitors

The paper quantifies the discrepancy between population-average and single-cell suppression of pY-STAT1/3 by JAK inhibitors, showing that strong average suppression leaves many cells with elevated responses.

Genetic axes of hand and shoulder soft-tissue disease and their divergent responses to adiposity and incretin therapy: a cross-biobank genomic and randomised trial study

This study identifies two genetically distinct axes of hand and shoulder soft-tissue disorders and shows divergent responses to adiposity and incretin therapy.

Neutrophil Extracellular Trap Deposition Establishes an Immunosuppressive Environment in Non-metastatic Lymph Nodes and Facilitates Heterologous Metastatic Outgrowth

This study shows that neutrophil extracellular traps (NETs) in lymph nodes create an immunosuppressive environment that promotes metastasis by altering Treg and CD8 T cell function and organization.

IL-27 Reduces Cell-Surface LDLR in Human Macrophages and Restricts VSV-G-Pseudotyped HIV infection

This study shows IL-27 reduces cell-surface LDLR in macrophages and limits VSV-G-pseudotyped HIV infection through receptor downregulation and post-entry mechanisms.

Nuclear NPR1 Modulates Salicylic Acid/Jasmonic Acid Crosstalk via Transcriptional Control of WRKY Transcription Factors

This study identifies WRKY transcription factors as mediators of NPR1-regulated SA/JA crosstalk in Arabidopsis, showing nuclear NPR1 controls JA repression through these factors.

Functional characterization of the strawberry calcium-dependent protein kinase FvCPK28

This study identifies and characterizes FvCPK28, a strawberry ortholog of Arabidopsis CPK28, showing it retains similar biochemical and biological functions.

T lymphocyte regulatory cytokines predict frailty in older adults

This study identifies T lymphocyte regulatory cytokines as predictors of frailty in older adults using machine learning and serum cytokine analysis.

The Aging Brain Matrix: Cross-Species Evidence Linking FREM3 to Brain and Cognitive Aging

This study links the FREM3 gene to brain and cognitive aging using cross-species evidence from mice and humans, showing reduced brain volume and cognitive performance in Frem3 knockout mice and lower FREM3-GReX associated with reduced brain surface area and cognitive performance in humans.