ATAC-seq

Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers

This paper introduces EpiOut, a tool to detect chromatin accessibility outliers in ALS, showing they correlate with gene expression and protein level aberrations.

Leveraging single cell multiomic analyses to identify factors that drive human chondrocyte cell fate

This study uses single-cell multiomic data to identify transcription factors and regulatory networks driving human chondrocyte differentiation and cartilage development.

Comprehensive profiling of transcriptional regulation in cartilage reveals pathogenesis of osteoarthritis

The paper identifies eQTLs and regulatory mechanisms in cartilage to uncover potential mechanisms of osteoarthritis pathogenesis.

Hippo-YAP1/TAZ-TEAD signaling coordinates myoblast fusion and sarcomere assembly in skeletal muscle development

This study shows Hippo-YAP1/TAZ-TEAD signaling coordinates myoblast fusion and sarcomere assembly in skeletal muscle development through transcriptional regulation.

Skeletal Muscle Mitochondrial Dysfunction Mediated by Pseudomonas aeruginosa Quorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds

This study investigates how Pseudomonas aeruginosa's MvfR quorum sensing transcription factor disrupts mitochondrial function in skeletal muscle and shows that inhibiting MvfR or using mitochondrial-targeted compounds can reverse these effects.

Network-based prioritisation and validation of novel regulators of vascular smooth muscle cell proliferation in disease

The paper identifies and validates novel regulators of vascular smooth muscle cell proliferation using network analysis and experimental validation, highlighting RUNX1 and the TIMP1-CD74 axis as potential therapeutic targets.

Mechanical Rejuvenation of Mesenchymal Stem Cells from Aged Patients

This study shows that mechanical conditioning improves the regenerative potential of aged mesenchymal stem cells by reducing senescence and altering their genetic landscape.

Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development

The paper maps chondrogenic enhancers in limb and axial skeleton development and shows their role in explaining human height heritability.

Circadian Control of Histone Turnover During Cardiac Development and Growth

This study shows Bmal1 is essential for neonatal myocyte growth, histone turnover, and chromatin organization, with Sik1 as a novel clock-controlled gene linking myocyte growth to gene transcription.

Defining the cellular origin of seminoma by transcriptional and epigenetic mapping to the normal human germline

This study maps seminoma transcriptomes and epigenetic features to the normal human germline trajectory, revealing similarities to primordial germ cells and identifying gene dosage effects in a patient-derived model.

Figeno: multi-region genomic figures with long-read support

Figeno generates publication-quality genomic figures with support for multi-region views, long reads, and epigenomic data.

Integrated genomic analysis of AgRP neurons reveals that IRF3 regulates leptin's hunger-suppressing effects

The paper identifies IRF3 as a key transcriptional regulator of leptin's hunger-suppressing effects in AgRP neurons through integrated genomic analysis.

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

This study identifies heightened TNF pathway activity and chromatin remodeling in pancreatic lymph node CD4+ T cells from T1D patients, supporting the use of TNF inhibitors in clinical trials.

Dynamic Single Cell Transcriptomics Defines Kidney FGF23/KL Bioactivity and Novel Segment-Specific Inflammatory Targets

This study uses single-cell transcriptomics to analyze FGF23 bioactivity and identify novel inflammatory targets in the kidney, revealing interactions between FGF23 and TNF/NF-κB pathways.

Multi-omics analysis of longitudinal patient samples reveals the molecular mechanism of AML progression

This study uses multi-omics analysis to identify genetic and epigenetic changes in AML progression and relapse.

Clock-dependent chromatin accessibility rhythms regulate circadian transcription

This study shows that chromatin accessibility oscillates with the circadian cycle in Drosophila clock neurons, with distinct motifs associated with dusk and dawn accessibility, and that Period protein is essential for these rhythms.

Chromatin remodeling protein BPTF regulates transcriptional stability in planarian stem cells

This study investigates the role of BPTF in regulating chromatin accessibility and transcription in planarian stem cells, showing its importance in gene expression and stem cell function.

Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity

The paper identifies joint-specific regulatory patterns in rheumatoid arthritis fibroblast-like synoviocytes by integrating chromatin accessibility and transcriptional data, revealing differences in proliferation, migration, and inflammation between hand and non-hand joints.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Single-cell genomics and regulatory networks for 388 human brains

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

Genetic regulation of cell-type specific chromatin accessibility shapes the etiology of brain diseases

The paper identifies cell-type specific chromatin accessibility QTLs and their functional impact on brain disease risk.

Molecular cascades and cell-type specific signatures in ASD revealed by single cell genomics

The paper uses single nuclear RNAseq and epigenetic profiling to identify molecular changes and cell-type specific signatures in ASD, linking them to genetic risk factors.

Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues

The paper introduces BALI, a method for spatially tuneable multi-omic profiling using light-driven combinatorial barcoding, demonstrating its application on mouse brain tissue.

Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome

This study uses single-cell multi-omics to map genotype-to-phenotype relationships in VEXAS syndrome, identifying PERK pathway activation as a therapeutic target.

Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics

The paper uses single-cell multi-omics to study early cardiac lineage specification in mouse embryos, identifying key transcription factors and regulatory networks.

TRAPT: A multi-stage fused deep learning framework for transcriptional regulators prediction via integrating large-scale epigenomic data

TRAPT predicts transcriptional regulators by integrating multi-omics epigenomic data, outperforming existing methods in identifying co-factors and chromatin regulators.

CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations

CellWalker2 improves cell type annotation and mapping by integrating multi-omic data and hierarchical relationships, outperforming existing methods in simulations and demonstrating applications in brain and immune system data.

Identification of the molecular components of enhancer-mediated gene expression variation in multiple tissues regulating blood pressure

The paper identifies genes regulating blood pressure by analyzing enhancer variants and integrating epigenomic data with genotype-phenotype associations across multiple tissues.

Genetic implication of prenatal GABAergic and cholinergic neuron development in susceptibility to schizophrenia

The paper investigates genetic risk for schizophrenia by analyzing gene expression and regulatory elements in developing ganglionic eminence neurons.

Cactus: a user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis