differential expression

Uncovering the Multifaceted Role of the Kinetochore Scaffold 1 (KNL1) in Hepatocellular Carcinoma: Integrative Bioinformatics Analysis and CRISPR-Cas9 Experimental Study

This study identifies KNL1 as a key driver of chromosomal instability and immune evasion in HCC through integrative bioinformatics and CRISPR-Cas9 experiments.

Mechanotransduction tuned by intermediate filaments promotes DNA repair in stiff environments

The paper shows that rigid tissue environments enhance DNA repair efficiency and may contribute to cancer risk by promoting survival of damaged cells.

Ambivalent roles of nonsense-mediated mRNA decay in heat stress tolerance

This study shows that NMD deficiency in Arabidopsis leads to biphasic heat tolerance, with initial tolerance due to transcriptome priming and later sensitivity linked to reduced HsfA2 function and altered gene expression.

A multi-tissue RNA-seq atlas of adult medaka (Oryzias latipes) under salinity and winter-summer sampling contrasts

The paper generates a multi-tissue RNA-seq atlas of adult medaka under salinity and seasonal contrasts to study gene-expression plasticity and comparative biology.

Prefrontal cortex transcriptomes distinguish Alzheimers disease from asymptomatic amyloid pathology, neuropeptide loss, immune-complement activation and glial remodelling

This study identifies distinct transcriptional signatures in the prefrontal cortex of Alzheimer's disease patients compared to asymptomatic amyloid pathology and controls, highlighting neuropeptide loss, immune activation, and glial remodeling.

DECAPPING PROTEIN 5 regulates the circadian clock in Arabidopsis

This study identifies DCP5 as a key regulator of circadian RNA stability in Arabidopsis by modulating the decay of high-amplitude clock-controlled genes.

Quantitative imaging of native tissue architecture combined with deep multi-omics reveals the spatial biology of kidney aging

This paper introduces NORIGAMI, a multi-omics pipeline that combines imaging and deep learning to analyze kidney aging, revealing age-related structural and molecular changes.

NEPTUNE: a neuronal cell death pathway prediction tool used to decipher neurodegeneration using single cell RNA-seq datasets

NEPTUNE identifies neuronal cell death markers from single-cell RNA-seq data, revealing non-apoptotic mechanisms in photoreceptor degeneration in rd1 mice.

Local fractal dimension as an indicator of functional reorganization in molecular interaction networks

The paper introduces DIFFRACT, a framework that uses local fractal dimension changes in protein interaction networks to detect functional reorganization, showing its utility in identifying novel biological roles in RAVER1-deficient cells.

Generation of functional adipoids from human induced pluripotent stem cells

This study develops a scalable method to generate functional adipoids from hiPSCs, which mimic human adipose tissue and can be used for metabolic disease research and drug screening.

SpaceBlocks: an expert-supervised workflow for cohort-level spatial transcriptomics analysis

SpaceBlocks is a workflow for reproducible, expert-supervised spatial transcriptomics analysis across platforms, identifying new cell types and differentially expressed genes in multiple datasets.

Lymphangiogenesis is Critical for Healing and Survival in a Murine Model of Laryngotracheal Injury

This study shows that lymphangiogenesis is essential for healing and survival after laryngotracheal injury in mice, as blocking it leads to worse outcomes.

Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions

The paper benchmarks sparse-to-transcriptome reconstruction models using high-expression profiles from mouse adrenal cells under sex and sex-steroid conditions, finding that gene-wise metrics and strong baselines are critical for evaluation.

Fentanyl and fentanyl-xylazine co-exposure influence mitochondrial transcriptional programs in human trophoblasts

This study examines how fentanyl and fentanyl-xylazine co-exposure affect mitochondrial transcription in human trophoblasts, showing suppression in syncytiotrophoblasts and discordant regulation with FMX.

A new tool for quantifying mitochondrial RNA processing intermediates reveals increased levels of immature mRNA species under oxidative stress

LAMA2-related muscular dystrophy alters Schwann cell calcium homeostasis and increases peripheral nerve inflammation

This study examines LAMA2 deficiency in mice, showing altered Schwann cell calcium homeostasis and increased nerve inflammation into adulthood.

Tropical Peatlands as Hotspots of Hidden Arcellinida Diversity: Insights from Maludam National Park, Borneo (Sarawak, Malaysia)

This study investigates Arcellinida diversity in tropical peatlands, finding higher species richness in zones with developed understory vegetation and distinct community composition compared to extratropical ecosystems.

Multi-modal in situ profiling of human cells using the AVITI24 platform characterizes single-cell responses to acute stress

The paper uses a multi-modal platform to profile single-cell stress responses in human cell lines, finding a shared stress response program with cell-specific magnitude variations.

CD19-CAR T-cell therapy resets the EBV+ autoreactive B cell repertoire in autoimmune disease

This study shows CD19-CAR T-cell therapy depletes EBV+ autoreactive B cells and resets their repertoire, leading to sustained remission, while rituximab does not.

GDF15 modifies NAD+ salvage pathway and dampens immune response in mitochondrial disease

This study shows GDF15 enhances NAD+ salvage and reduces immune response in mitochondrial disease by upregulating NMRK2 and modulating redox homeostasis.

A minimal two-residue C-terminal truncation of AID in adult-onset hyper-IgM syndrome type 2 (HIGM2)

This study identifies a two-residue C-terminal truncation variant in AID causing adult-onset HIGM2 and shows it disrupts CSR and SHM.

Transcriptomic Signatures Suggest Epigenetic Programming of Molecular Defense in Biochar-Exposed Formica japonica

The paper reanalyzes transcriptomic data to show that biochar exposure primes Formica japonica ants epigenetically, enhancing their resilience to environmental stressors.

Refining RNA-Seq Transcriptome Profiles with Transcript-Specific Minimal-Shared Regions

This paper introduces a method to improve RNA-seq transcript quantification by reducing mapping ambiguity through minimal-shared region analysis, showing improved accuracy in isoform detection and abundance estimation.

Peripheral Exercise Transcriptomes Do Not Converge on Glutamatergic or Neuroinflammatory Signatures: A Cross-Platform Meta-Analysis

This study analyzes peripheral transcriptomic responses to exercise and finds no convergence on glutamatergic or neuroinflammatory signatures across tissues.

Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns

This paper detects neuronal DNA in cfDNA using non-CpG methylation patterns, finding elevated levels in neurological conditions and brain-dead donors.

Pathological levels of α-synuclein increase basal mitophagy in Parkinson's dopamine neurons

This study shows that elevated α-synuclein increases basal mitophagy in Parkinson's dopamine neurons, leading to mitochondrial dysfunction and neuronal activity deficits, which can be reversed by DRP1 inhibition.

Incorporating tandem repeats improves gene expression prediction models

This study improves gene expression prediction models by incorporating tandem repeats, showing significant performance gains and identifying nonlinear effects on gene expression.

Mitotic centromeres organize in repeat-subunits with specialized histone landscape and multi-domain architecture as revealed by expansion microscopy

The paper uses expansion microscopy to reveal the repeat-subunit organization and multi-domain architecture of human mitotic centromeres, including specialized histone modifications.

A Unique Promoter Architecture Defines Menin-KMT2A Complex Selectivity

The paper identifies a unique promoter architecture that defines Menin-KMT2A complex selectivity and its association with gene regulation and leukemia.

Cellular context shapes the transcriptomic impact of somatic variants

The paper shows that somatic variants' transcriptomic impact depends on cellular context, not just sequence, using single-cell transcriptomics and new tools.