bulk RNA-seq

Human-targeted drugs impact antibiotic sensitivity and growth of Campylobacter jejuni

This study shows that human-targeted drugs can both enhance antibiotic resistance and inhibit Campylobacter jejuni growth through efflux pump activation and direct toxicity.

Recapitulating the notochord to nucleus pulposus transition from human mesendoderm progenitors in 3D

This study develops a 3D model to recapitulate the transition from human mesendoderm progenitors to nucleus pulposus-like cells using single-cell transcriptomics and spatial profiling.

lisaR: An LLM-Inferred Semantic Annotation of biological categories for gene set enrichment analysis

lisaR organizes gene set enrichment analysis results into semantic categories using LLM-inferred dictionaries, improving interpretability of biological findings.

Genomic SEM reveals shared genetic architecture and expands locus discovery for locomotor activity in heterogeneous stock rats

The paper uses Genomic SEM to identify loci underlying locomotor activity in rats, finding 31 loci compared to fewer from other methods.

SroA links SigS-dependent stress signaling to metabolic remodeling in Staphylococcus aureus

This study identifies SroA as a regulator linking SigS-dependent stress signaling to metabolic remodeling in S. aureus by altering gene expression related to nitrate respiration and nucleotide biosynthesis.

CRISPR-Cas9 Editing of Myeloid Lectins Reveals Target-Dependent Transcriptional Remodeling in Tumor-Associated Macrophages

This study uses CRISPR-Cas9 to perturb myeloid lectins in macrophages, revealing target-specific transcriptional changes and immunometabolic reprogramming in tumor-associated macrophages.

Hydrodynamics structure the physiological trajectory and bloom dynamics of a harmful diatom species across neighboring coastal ecosystems

This study shows that hydrodynamics, specifically dilution and advection, significantly influence the physiological trajectory and bloom dynamics of the harmful diatom Pseudo-nitzschia australis across coastal ecosystems.

Initiation codon context governs translation-coupled mRNA decay and coordinated expression in the human parasite Leishmania

This study shows that the Kozak sequence context influences mRNA stability and protein expression in Leishmania by modulating translation-coupled decay and polysome recruitment.

Integrin α3β1 is required for alveolar-capillary barrier formation through regulation of epithelial differentiation

This study shows that integrin α3β1 is essential for alveolar-capillary barrier formation by regulating epithelial differentiation during lung development.

Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss

This study identifies SRSF2 and U2AF1 mutations as biomarkers of sensitivity to ATR-CHK1 pathway inhibitors and RUNX1 mutations as a mechanism of resistance in MDS/AML.

KRAS-driven metabolic reprogramming of enhanced MFSD2A-mediated lysophosphatidylcholine scavenging promotes survival and progression of pancreatic ductal adenocarcinoma

This study identifies KRAS-driven metabolic reprogramming through MFSD2A-mediated lysophosphatidylcholine scavenging as a driver of PDAC progression and shows that targeting this pathway with edelfosine has anti-cancer effects.

Autonomic and neurotrophic signaling in alcohol-associated liver disease

This study identifies stage-dependent changes in autonomic and neurotrophic signaling in alcohol-associated liver disease using bulk and single-cell transcriptomics.

Discovery of a hydrolysis operon in Lachnospiraceae provides a genetic basis to understanding castalagin metabolism by the human microbiome in a clinical study.

The paper identifies a hydrolysis operon in Lachnospiraceae that enables castalagin metabolism to urolithins and flavogallonic acid in the human gut microbiome using multi-omics analysis of fecal samples from a clinical trial.

Establishment and characterization of LNCaP-TR-BoM, a bone metastasis-derived prostate cancer cell line with an intermediate AR-attenuated phenotype

This paper establishes and characterizes LNCaP-TR-BoM, a bone metastasis-derived prostate cancer cell line with an intermediate AR-attenuated phenotype, showing transcriptomic and functional similarities to metastatic castration-resistant prostate cancer.

Integrating single-cell and bulk transcriptomes identifies neuronal heat-stress-associated candidate genes in a reef-building coral

Integrative genetic and transcriptomic analysis identifies candidate genes and compounds for Fragile X syndrome and autism spectrum disorder

Evolution of compound eye cell types shapes visual behaviors across Heliconius butterflies

This study identifies genetic and cellular mechanisms underlying visual system evolution in Heliconius butterflies by analyzing compound eye cell types across species.

Sex-Dependent Microbiome-Metabolome Remodeling Associated with Bacteroides acidifaciens Modulation of Acute Respiratory Distress Syndrome

This study investigates sex-dependent microbiome and metabolome changes in mice with ARDS induced by Bacteroides acidifaciens, finding distinct metabolic and microbial responses in males and females.

Lactate epigenetically shapes tumor cell states in H3K27M diffuse midline gliomas

This study shows lactate epigenetically regulates cell states in H3K27M diffuse midline gliomas by modifying histones, and targeting CBP/p300 reduces tumor heterogeneity and improves preclinical outcomes.

A phage-encoded host transcription modulator, Htm, reprograms the transcriptome of ESBL Escherichia coli

This study identifies Htm, a phage-encoded protein that reprograms the transcriptome of ESBL-E. coli to support phage replication by altering gene expression and metabolic pathways.

Jasmonate restrains the enhanced growth response of lateral roots induced systemically by a local water deficit

The paper shows that jasmonate inhibits lateral root growth in response to local water deficit, counteracting systemic growth promotion and fine-tuning root architecture.

PLANT WATER-CARBON RELATIONS IN HUANGLONGBING-AFFECTED CITRUS TREES AND THE IMPACT OF HLB EXPOSURE DURATION, FRUIT DEVELOPMENTAL STAGE, AND SOURCE-SINK MANIPULATION ON THESE RELATIONS

This study examines how Huanglongbing (HLB) affects water-carbon relations in citrus trees, showing that long-term HLB exposure alters leaf water status and fruit shrinkage responses to source-sink manipulation.

Mechanophenotype of synovial fibroblasts correlates with patients' pathotypes and treatment response in Rheumatoid Arthritis

The paper identifies 'soft' and 'stiff' fibroblast states in rheumatoid arthritis using mechanophenotyping and transcriptomics, linking them to patient pathotypes and treatment response.

Exitron-type splicing of intrinsically disordered regions recurs across jawed vertebrates despite sequence divergence: donor-proximal cis control in TARDBP

The paper identifies exitron-type splicing events in IDR-coding sequences across jawed vertebrates, showing donor-proximal cis control in TARDBP despite sequence divergence.

A reversible GNAS-PKA-RUNX2 checkpoint governs skeletal stem cell fate in fibrous dysplasia

This study identifies a reversible GNAS-PKA-RUNX2 checkpoint that governs skeletal stem cell fate in fibrous dysplasia and shows PKA inhibition can reverse disease features.

Macrophages from Holstein and Normande cows respond differently to Escherichia coli and Streptococcus uberis

The paper compares immune responses of Holstein and Normande cattle macrophages to E. coli and S. uberis, finding breed-specific gene expression differences and differential bacterial survival.

Cholera toxin remodels intestinal immunity and suppresses systemic metabolism

This study shows that cholera toxin alone rapidly reorganizes intestinal immunity, epithelial, metabolic, and microbial environments while suppressing whole-body metabolism in mice.

A long-term organotypic slice culture model of patient high-grade glioma preserving tumor heterogeneity and architecture, and specificity of CAR T cell targeting

Synergistic effects of hypergravity and immune challenge on the zebrafish larval transcriptome

This study examines how hypergravity and immune challenge interact in zebrafish larvae, finding that hypergravity alone has minimal transcriptomic impact but combined with LPS causes significant gene expression changes.

Wildfire emitted particulate matter induces ovarian hyperandrogenism through aryl hydrocarbon receptor activation

This study shows wildfire particulate matter induces hyperandrogenism in mice by activating the aryl hydrocarbon receptor, affecting ovarian function.