bulk RNA-seq

LLM-assisted analytical review catches statistical errors that human researchers miss: documented evidence from two computational biology case studies

Chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana

The paper presents a chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana using PacBio and Hi-C data.

Sodium nitrophenolates as a potential tool for the management of grapevine trunk diseases

This study evaluates the antifungal and defence-modulating effects of sodium nitrophenolate product Atonik against fungal trunk diseases in grapevines, showing reduced lesion length and increased defence gene expression.

Function-oriented microglial transcriptional scores in Alz-heimer's disease: resolving terminal functions beyond activa-tion states

The paper develops function-oriented microglial transcriptional scores to capture post-activation functions in Alzheimer's disease, validated across multiple endpoints and datasets.

Phenotype-cloud reorganization shapes cancer progression and therapeutic adaptation

This study identifies phenotype-cloud transitions as an organizational feature of cancer progression and therapeutic adaptation, showing how tumours reorganize phenotypic states during progression and treatment.

A brain immune phenotype independent of Alzheimer's Disease associates with amyloid susceptibility and systemic inflammation

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Reforestation without Belowground Recovery: Sediment Microbiomes and Organic Carbon in Caribbean Mangroves

This study shows that mangrove reforestation in the Caribbean does not restore sediment organic carbon or microbial communities to reference levels within a few years.

Temporal Dynamics of SMARCA4 Loss Define Its Role in Myogenic Differentiation of Alveolar Rhabdomyosarcoma

This study shows that acute SMARCA4 loss in ARMS cells does not induce differentiation or alter proliferation, contrasting with long-term knockdown effects.

CnidoSite: A Multi-Omics Database for Cnidarians

CnidoSite provides a centralized multi-omics database for cnidarians, integrating genomic, transcriptomic, proteomic, and phenotypic data to study thermal tolerance and environmental adaptation.

Photoperiodic Plasticity of Transcriptomic and Photosynthetic Rhythms in the Liverwort Marchantia polymorpha

This study investigates how photoperiod affects transcriptomic and photosynthetic rhythms in the liverwort Marchantia polymorpha, finding that short photoperiods increase rhythmic gene expression and alter circadian patterns.

Diaphorin induces extensive transcriptional remodeling of translation, transport, metabolism, and stress responses in Escherichia coli

This study examines how diaphorin affects E. coli transcription, revealing widespread changes in translation, metabolism, transport, and stress responses.

STAT3 dual role in sex-biased and differentiation-gated interferon gamma memory

The paper investigates the role of STAT3 in IFN-gamma memory in human macrophages, revealing its dual function in repression and recall, and identifies sex-biased and differentiation-dependent mechanisms.

MiR-208b-3p is an upstream regulator of redox-associated cardiomyocyte survival

This study identifies miR-208b-3p as a regulator linking cardiac stress adaptation with redox and survival responses through its effects on Myh7 and ATM.

The increased production of monocytes with immunosuppressive transcriptional profiles predicts the development of SIV encephalitis

The study identifies immunosuppressive monocytes predicting SIV encephalitis by analyzing their transcriptional changes during infection.

Abnormal nuclear organization impairs adipogenic lineage commitment and terminal maturation in Hutchinson-Gilford progeria syndrome (HGPS)

This study shows that HGPS disrupts adipogenic lineage maturation through chromatin reorganization defects, despite normal lineage commitment rates.

Hypoxia reduces induced LRIG1 protein despite sustained mRNA induction in colorectal cancer organoids

This study shows hypoxia reduces LRIG1 protein levels in colorectal cancer organoids despite increased mRNA, suggesting limitations in LRIG1-based cancer therapies under hypoxic conditions.

Early-life PFAS exposure induces systemic metabolic alterations in plasma and brain in mice

This study shows that early-life PFAS exposure causes sex-dependent metabolic changes in plasma and brain of mice, with females showing more extensive alterations.

SlMYB21 and SlMYB24 cooperatively regulate petal coloration and movement in Solanum lycopersicum

This study identifies SlMYB21 and SlMYB24 as cooperative regulators of petal coloration and movement in tomato by modulating carotenoid biosynthesis, ABA levels, and water transport.

Epithelial function of the circadian clock gene, Bmal1, in regulating the mucosa.

This study shows that Bmal1 in colon epithelial cells promotes mucus production and is essential for sex-specific tissue regeneration after injury.

HaloPROTAC-mediated degradation reveals SOX10-dependent gene expression changes in melanoma cells

This study uses HaloPROTAC-mediated SOX10 degradation in melanoma cells to identify novel target genes and reveal SOX10's role in drug resistance and metastasis.

Tetraspanin changes in septic blood are organized by cell type, with monocyte CD82 induction and leukocyte CD37 loss associated with mortality

The paper identifies cell-type-specific tetraspanin changes in sepsis, finding CD37 loss and monocyte CD82 induction linked to mortality.

Expanding Hippocampal Ensembles through LINE-1 RNA Downregulation Enhances Cognition

This study shows that reducing LINE-1 RNA in hippocampal neurons increases their firing capacity and expands neuronal ensembles, improving spatial memory but reducing pattern separation.

Advancing CD38 from a marker of disease activity to an active regulator of interferon responses in juvenile dermatomyositis

This study identifies CD38 as a regulator of interferon responses in juvenile dermatomyositis and suggests its inhibition as a potential therapeutic strategy.

The RES complex core subunits Snu17 and Bud13 buffer the spliceosome against intrinsically weak splicing signals in budding yeast

The paper investigates the role of RES complex subunits Snu17p and Bud13p in splicing efficiency in budding yeast, finding they buffer against weak splicing signals and are critical for inefficient intron splicing.

PDGFRα-directed fibroblast-homing peptides for targeted delivery of nucleic acid therapeutics

The paper identifies fibroblast-homing peptides targeting PDGFR for targeted delivery of nucleic acid therapeutics, showing enhanced efficacy in a collagen VI-related muscular dystrophy model.

Estradiol Modulates Cytotoxic Responses to Topoisomerase II Targeting Agents in Estrogen Receptor Positive Breast Cancer Cells

This study shows estradiol enhances the cytotoxicity of topoisomerase II poisons in ER+ breast cancer cells, suggesting E2-induced cell death relies on TOP2-mediated DNA breaks.

MINT Block: multivariate integration across independent studies to identify multi-omics signatures

MINT Block integrates multi-omics data across studies to identify generalisable signatures while accounting for study-specific variation, improving prediction accuracy.

Coffee induces chromatin structural changes associated with histone H4K16 hypoacetylation

This study shows coffee reduces H4K16ac levels and alters chromatin structure, with transcriptional changes in K562 cells.

Pharmacologic inhibition of OLIG2 by CT-179 disrupts mitotic progression and enhances standard-of-care chemoradiotherapy in glioblastoma

This study shows that CT-179, an OLIG2 inhibitor, reduces glioblastoma growth and enhances chemoradiotherapy efficacy in preclinical models.