bulk RNA-seq

Sister species, shared and divergent responses: early transcriptomic profiling of Bursaphelenchus xylophilus exposed to Esteya spp.

This study compares the early transcriptomic responses of Bursaphelenchus xylophilus to two closely related nematophagous fungi, finding divergent and shared transcriptional patterns.

Efficient approximate Bayesian inference for large, heterogeneous biological datasets

The paper introduces an adaptive minibatch approach for approximate Bayesian inference, improving speed-precision tradeoffs for large, heterogeneous biological datasets.

T cell engagers convert acute tumor killing into endogenous vaccination

This study shows that T cell engagers induce endogenous vaccination by triggering a cytotoxic wave and cross-priming of CD8 T cells via dendritic cells.

A Multi-Omic Phenobank Reveals Axes of Glioblastoma Growth, Invasion, and Therapeutic Vulnerability

The paper establishes a multi-omic PDX resource linking GBM invasion phenotypes to molecular programs and therapeutic responses, identifying two invasion modes and a neurodevelopmental factor associated with tumor growth and survival.

phyloDS: phylogeny-aware differential splicing across species, beyond reference annotations

phyloDS identifies differentially used orthologous splice junctions across species by improving orthology definition, statistical testing, and sequence-level validation.

Astrocyte-Specific dsRNA-ADAR1 Signalling Links Innate Immunity to Complement Activation in Parkinson Disease

The paper identifies astrocytes as a key site of dsRNA accumulation and ADAR1 p150 induction in Parkinson's disease, linking dsRNA sensing to complement activation in a cell-type-specific manner.

Arsenic Impairs Critical Cellular Events of Human Cardiac Development Across Differentiation and Metabolic Maturation

This study shows arsenic impairs human cardiac development by inhibiting cardiomyocyte differentiation and maturation, as demonstrated through stem cell and zebrafish models.

A claim-centred atlas distinguishes biological corroboration from analytical depth in plant stress transcriptomes

The paper reanalyzes plant stress transcriptomes to distinguish biological corroboration from analytical depth using a claim-centred atlas called PLEASE.

Cytokinin regulates the gravitropic setpoint angle of seminal roots in barley and wheat

This study identifies cytokinin as a regulator of gravitropic setpoint angles in seminal roots of barley and wheat through transcriptomic and functional analyses.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

Radiotherapy Reshapes the 3D Genome in Medulloblastoma Cells

This study examines how radiotherapy affects the 3D genome of medulloblastoma cells, identifying molecular and structural changes associated with radiation response.

SP2 impedes the pluripotent-to-totipotent state transition in an RA-dependent manner

This study identifies SP2 as a barrier to the pluripotency-to-totipotency transition in mouse embryonic stem cells, showing its role in promoting alternative developmental programs.

Application of Bayesian-Derived Gene Interaction Network and Subnetwork for Classification of Idiopathic Parkinson Disease with Biomarkers

The paper develops a Bayesian gene interaction network to identify 13 genes for PD classification, achieving high AUC in a blood-based transcriptomic analysis of the PPMI cohort.

Mesodermal-niche interactions direct specification and differentiation of pancreatic endocrine cells in human multilineage organoids

The paper demonstrates that mesoderm-derived cells in organoids promote endocrine commitment and β-cell differentiation in human pancreatic development.

Surfactant-Enhanced Hybridization Capture for Direct Sequence-Specific RNA Extraction from Plasma and Whole Blood

This paper introduces a surfactant-based method for direct RNA extraction from plasma and whole blood, achieving high recovery of low-abundance RNA and outperforming existing silica-based kits.

A rapid, genetically-tractable human iPSC-derived model for studying tissue-resident macrophage biology in Alzheimer's and other diseases

This paper develops a simplified protocol to generate human iPSC-derived macrophage-like cells (iMacs) that exhibit enhanced phagocytic and TREM2-related functions, making them a useful model for studying macrophage biology in Alzheimer's and other diseases.

Svep1 orchestrates distal airway patterning and alveolar differentiation in murine lung development

This study shows that Svep1 is essential for proper lung development by regulating airway branching and alveolar differentiation in mice.

Intranasal L-MYC Neural Stem Cells Restore Neurovascular and Neuroimmune Homeostasis After TBI via CX3CL1 Upregulation and ICAM-1 Downregulation

This study shows that intranasal LMNSC01 treatment reduces neuroimmune and neurovascular dysfunction after TBI by modulating ICAM-1 and CX3CL1 expression in both male and female rats.

Context-dependent regulation of RpoS-dependent and RpoS-independent gene transcription by Crl during exponential growth in Escherichia coli

This study investigates how Crl regulates gene transcription in E. coli during exponential growth, both independently and in conjunction with RpoS, under varying environmental conditions.

Single-cell-resolved natural giant virus infections reveal conserved protist immunity

The paper identifies active giant-virus infections in protists and shows conserved antiviral defenses and potential viral counter-defense mechanisms.

Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula

This study characterizes the circadian transcriptome of Rubroshorea leprosula, revealing conserved but less robust circadian rhythms compared to Arabidopsis.

Developmental prefrontal myelination shapes inhibitory interneuron function and adult social behavior

This study shows that disrupting developmental myelination in the medial prefrontal cortex impairs adult social behavior and PV interneuron function in mice, with parallels in human schizophrenia.

Transcriptional perturbation effects remain structured beyond the leading global trend

The paper shows that transcriptional perturbations have structured effects beyond a global trend, with specific patterns transferable across datasets.

A human CHRNA6 3' UTR variant alters the molecular environment and microRNA engagement of the adolescent VTA without changing Chrna6 transcript abundance

This study identifies a non-coding variant in CHRNA6 that affects miRNA engagement and transcriptional networks in the adolescent VTA without altering transcript abundance.

CXCR3 on transferred T cells enables vaccine-boosted adoptive T-cell therapy in solid tumors

This study shows that CXCR3 on transferred T cells enhances the effectiveness of combining adoptive T-cell therapy with viral-vector vaccines in solid tumors.

Microglia transcriptomic response to doxorubicin-induced genotoxic stress

This study investigates the transcriptomic response of human microglia to doxorubicin, identifying gene expression changes and pathways involved in neurotoxicity.

Autonomic neurons are intrinsically hyperexcitable in a Friedreich ataxia iPSC model

This paper establishes that FRDA autonomic neurons are hyperexcitable and exhibit mitochondrial dysfunction using iPSC-derived models.

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

This paper introduces Droplet-MT, a method for joint methylome and transcriptome profiling, enabling clonal organization analysis in human hematopoiesis with high scalability and resolution.

Impacts of different SETD1A mutations and genetic backgrounds on human induced pluripotent stem cell-derived hippocampal neurons

This study examines how different SETD1A mutations and genetic backgrounds affect human hippocampal neurons derived from hiPSCs, revealing divergent molecular and cellular phenotypes and contrasting mutation impacts.

Transcriptomic reconstruction of an interregional molecular connectome in schizophrenia

The paper constructs an interregional molecular connectome in schizophrenia using transcriptomic data and identifies candidate dysregulations in neural circuits.