bulk RNA-seq

PARP1/2-linked ADP-ribosylation impairs trophoblast mitochondrial respiration in a TNF-α model of inflammation-mediated preeclampsia.

This study shows PARP1/2-linked ADP-ribosylation impairs trophoblast mitochondrial respiration in inflammation-mediated preeclampsia, with olaparib improving respiration.

Combining RNA-seq and proteomics boosts sensitivity to detect differentially expressed genes by rpMeta

rpMeta integrates RNA-seq and proteomics data to improve sensitivity in detecting differentially expressed genes, identifying new genes and processes in lung cancer subtypes.

When do hybrid models help? Combining mechanistic modelling and machine learning to predict gene regulatory network dynamics

This study investigates when combining mechanistic and machine learning models improves predictions of gene regulatory network dynamics using synthetic data.

Epstein-Barr Virus in HIV-Associated Conjunctival Squamous Cell Carcinoma and Transcriptional Reprogramming of Conjunctival Epithelial Cells

This study identifies Epstein-Barr virus (EBV) in a subset of HIV-associated conjunctival squamous cell carcinomas and establishes an epithelial model to study host responses to EBV infection.

Snail restricts SARS-CoV-2 entry by limiting ACE2 expression as part of broader remodelling of epithelial determinants of viral tropism

This study identifies Snail as a host restriction factor that limits SARS-CoV-2 entry by reducing ACE2 expression through transcriptional regulation and translational suppression.

T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

A CAR T cell-amplified suppressive B cell circuit in AML

The paper identifies suppressive atypical memory B cells in AML that are amplified by CAR T cell interactions and shows that targeting both B cells and AML blasts can overcome this suppression.

GEO-BERT: A Retrieval augmented LLM Framework for Intelligent Dataset Retrieval from the Gene Expression Omnibus

GEO-BERT improves dataset retrieval from GEO by using a retrieval-augmented LLM framework with a hierarchical hybrid field-aware system, enhancing semantic search and traditional search performance.

Severity-stratified, longitudinal cis-eQTL mapping enables high-sensitivity detection of candidate causal genes for critical COVID-19

This paper identifies 23 candidate causal genes for critical COVID-19 by integrating severity-stratified, longitudinal cis-eQTL mapping with GWAS signals from 1,031 patients.

Habituation drives elevated antimicrobial resistance, functional, and compositional shifts in the black bear gut microbiome

This study shows that habituation in black bears alters their gut microbiome composition and function, leading to increased antimicrobial resistance and other health-related changes.

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.