bulk RNA-seq

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.

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.

Root gene regulatory network analysis reveals roles for defense hormones and secondary metabolites in establishment of disease-suppressive soil

The paper analyzes root gene regulatory networks in Arabidopsis thaliana to identify roles of defense hormones and secondary metabolites in disease-suppressive soil establishment.

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.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

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.

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

Generation of an induced pluripotent stem cell line, LCSBi021-A, from a Parkinson's disease patient harboring the missense mutation c.213C>G (p.Ser71Arg) in the RAB32 gene

The paper generates iPSCs from a Parkinson's patient with a RAB32 mutation and confirms their pluripotency and differentiation potential.

Expanding Therapeutic Target Space from Genes to Disease-Relevant Molecular Forms with Agent3Diso

Agent3Diso identifies disease-relevant molecular forms by integrating molecular data with agentic reasoning to guide therapeutic discovery beyond gene-level targets.

Persistently activated virus-specific CD8 T cells indicate antigen-driven immune aberrations in long COVID

The paper identifies persistently activated virus-specific CD8 T cells in long COVID patients, suggesting chronic antigen stimulation by SARS-CoV-2 or herpesvirus.

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.

The E525K β-Myosin Mutation Causes Hypocontractility in Cardiomyocytes Without Altering Crossbridge Cycling

This study shows that the E525K β-myosin mutation reduces cardiomyocyte contraction without altering crossbridge cycling, through structural and computational analysis.

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.

Renal adaptation to primary aldosteronism requires GDF15 to control plasma potassium level in mice and human.

This study shows GDF15 helps mice and humans maintain potassium levels by promoting intercalated cell proliferation in response to aldosterone excess.

N-Acetylglucosamine ameliorates knee osteoarthritis by enhancing UDP-GlcNAc conversion and chondrocyte DNA repair capacity

This study compares N-acetylglucosamine (GlcNAc) and glucosamine hydrochloride (GlcN·HCl) in a rat model of knee osteoarthritis, finding GlcNAc more effective in reducing inflammation, cartilage degradation, and promoting DNA repair.

LMNA Haploinsufficiency in Human iPSC-Derived Cardiac Organoids Reveals Early Fibrotic Signaling as a Therapeutically Targetable Process

This study uses cardiac organoids derived from patient iPSCs to show that LMNA haploinsufficiency causes early fibrotic signaling, which can be targeted by antifibrotic drugs.

ResponseVerdict overturns computationally validated immunotherapy signatures, recovers their missed responders and outperforms every published response predictor

ResponseVerdict improves immune checkpoint blockade response prediction by outperforming existing signatures and predictors using data from prior studies.

Extracellular Vesicles Derived from L-MYC Neural Stem Cells Mediate Neuroprotection in 3D Models of Chemotherapy- and Radiation-Induced Neurotoxicity

This study uses a 3D neural tissue model to show that extracellular vesicles from L-Myc neural stem cells promote recovery from chemotherapy- and radiation-induced neurotoxicity by modulating inflammatory and stress pathways.

Genetic Determinants of Cell-Type-Specific Responses to Cardiotoxic Chemotherapeutic Agents

The paper identifies genetic variants associated with cardiotoxic responses to chemotherapeutic drugs using single-cell RNA-seq and eQTL analysis.

The PGC-1α Gly482Ser rs8192678 SNP reprograms oxidative metabolism to favor energy storage in females

This study shows that the PGC-1α Gly482Ser SNP reprograms oxidative metabolism to favor energy storage, especially in females, through reduced respiratory capacity and altered metabolic responses.

Common and Sex-Biased Muscle Transcriptomic Aging Signatures Across Diverse Species

The paper identifies common and sex-biased aging biomarkers in skeletal muscle transcriptomes across six species, revealing shared and divergent molecular mechanisms of aging.

SMAD3-driven cell state transitions underpin immunoresistance in bladder cancer

The paper identifies SMAD3-driven cell state transitions as a mechanism of immunoresistance in bladder cancer and shows that SMAD3 inhibition sensitizes tumors to T cell-mediated cytotoxicity.

A scalable in vitro cell competition model identifies preleukemic super competitor clones

This study develops an in vitro clonal competition model to identify preleukemic TET2-mutant clones that suppress wild-type cells through RAC1-GEF signalling inhibition.

Evidence for a central ecological function of predatory Myxococcota in soil ecosystems

This study examines the ecological role of Myxococcota in soil habitats, finding they are more abundant and diverse in field soil than in sand biofilters, with distinct interaction patterns.

Metabolic vulnerabilities in Down syndrome B-cell acute lymphoblastic leukemia can be targeted using Venetoclax

This study identifies metabolic vulnerabilities in Down syndrome B-cell acute lymphoblastic leukemia and shows that Venetoclax effectively targets these vulnerabilities.

Circulating extracellular vesicles display immunotherapeutic targets and complement circulating tumor DNA in high-risk neuroblastoma

The paper identifies tumor-associated surface markers on circulating extracellular vesicles as complementary biomarkers to circulating tumor DNA in high-risk neuroblastoma.

An Interpretable Machine Learning Framework for Early- versus Late-Stage Classification of Breast Cancer from Gene Expression, with Co-expression Network Analysis

This paper evaluates machine learning models to classify breast cancer stages using gene expression data and identifies co-expressed genes associated with stage, though results are limited by small sample size and lack of external validation.

Small molecules targeting BRCA1-deficient cancer cells

The paper identifies small molecules that induce apoptosis in BRCA1-deficient cancer cells and links PPAR beta/delta inhibition to poor survival in breast cancer patients.

Host response and cell fates of human U937 monocytes upon infection with vancomycin-resistant E. faecium

This study examines how vancomycin-resistant E. faecium interacts with human U937 monocytes, showing early pro-inflammatory responses and isolate-specific cell death at later stages.