ATAC-seq

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq

This paper introduces TraceBIND, a method to correct Tn5 bias in ATAC-seq data, improving TF footprint detection and revealing age-related regulatory changes in scATAC-seq.

Cell-specific regulatory circuits connect genetic variation to disease susceptibility

The paper identifies dual-acting regulatory QTLs and gene regulatory networks in immune cells to better understand how genetic variation influences disease susceptibility.

Butyrate preserves cardiac health during aging

This study shows that long-term butyrate supplementation in aged mice reduces left ventricular mass and improves diastolic function by altering proteomic and multiome profiles in the heart.

MLL3 adaptor function, not methyltransferase catalytic activity, is essential for breast tumor suppression

This study shows that MLL3's tumor suppressor role in breast cancer depends on its adaptor function, not its catalytic activity.

Metadata Collector: An Open-Source Platform for Standardized Metadata Management in Multi Centre Sequencing Projects

Metadata Collector is an open-source platform designed to standardize metadata management in multi-centre sequencing projects, ensuring FAIR-aligned and reproducible metadata across distributed research groups.

Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning

The paper develops a machine learning framework to assess quality of chromatin accessibility bigWig tracks using biologically relevant features and internal controls.

Enhanced γ-globin reactivation and sickle cell correction through a repressor-to- activator motif switch in the HBG1/2 promoters

This paper demonstrates that replacing the BCL11A repressor binding site with a TAL1:GATA1 activator motif in HBG1/2 promoters enhances γ-globin reactivation and corrects sickle cell disease in hematopoietic stem/progenitor cells.

Hyperactive BMP and Mechanosignaling Remodel Chromatin to Drive Aberrant Osteogenesis in FOP

This study shows that the Acvr1R206H mutation in FOP remodels chromatin through BMP-SMAD and Rho/ROCK signaling, driving aberrant osteogenesis, and identifies reversible chromatin changes as a therapeutic target.

The molecular asynchrony of single cells

The paper introduces SeqTag, a single-cell multiomics method, to analyze molecular asynchrony in regulatory layers and model cellular kinetics during aging.

The HuBMAP Framework for Advancing Data FAIRness

The paper describes the HuBMAP framework for creating FAIR data through standardized metadata reporting across diverse assays and institutions.

Dysregulated flow responses drive pathogenesis in a cellular model of Sturge-Weber syndrome

This study investigates how dysregulated flow responses in endothelial cells contribute to Sturge-Weber syndrome pathogenesis using cellular models and omics analyses.

Aberrant chromatin remodeling influences human neural cell fate change in Trisomy 21

This study identifies aberrant chromatin remodeling in Trisomy 21 NPCs that impairs neurogenesis and shows that PRC2 inhibition can partially restore neurogenic potential.

Lamin A/C coordinates nuclear mechanics, chromatin architecture, and transcriptional homeostasis in skeletal muscle in vivo

This study investigates how Lamin A/C disruption affects nuclear mechanics, chromatin architecture, and transcription in skeletal muscle in vivo, finding that it alters chromatin organization and gene expression in mechanically stiff tissues.

Characterization of Human Ectocentromeric Sites.

The paper characterizes human ectocentromeric sites as evolutionarily constrained and functionally heterogeneous elements along chromosome arms with context-dependent roles in chromatin state and transcription regulation.

Single-cell mapping of regulatory DNA:Protein interactions

This paper introduces D&D-seq, a single-cell method to map DNA:Protein interactions with high specificity and resolution, and applies it to study TF binding in human cells.

Chronic Mild Stress Impairs Hippocampal Myelination through SOX6-Dependent Dysfunction of Oligodendrocyte Lineage Cells

This study identifies SOX6 as a key regulator of oligodendrocyte dysfunction under chronic stress, linking stress to myelination deficits through molecular mechanisms.

Epigenetic Profiling of Human Insulinomas Reveals AP-1 Family as Critical Regulators of Beta Cell Maturation

The paper identifies AP-1 family transcription factors as critical regulators of beta cell maturation by analyzing epigenomic and transcriptomic profiles of human insulinomas.

Mapping genetic risk mechanisms for immune-mediated diseases across human dendritic cell differentiation

This study maps genetic risk mechanisms for immune-mediated diseases by integrating single-cell multi-omic data with fine-mapped variants from genome-wide association studies.

Molecular grammar of RNA m6A modification in ribonucleoprotein granules

The paper uses SMART-epi to study how m6A modification affects RNP granule assembly and RNA interactions, revealing functional divergence among YTHDF proteins.

Leveraging epigenetic vulnerabilities of the stem cell-related HOX-signature in glioblastoma

This study identifies epigenetic vulnerabilities in high-HOX glioblastoma by showing that BETi or HOXA10 knockdown represses the HOX-signature and reduces stemness features.

An organismal view of newborn cell dynamics in mammalian aging

The paper uses TrackerSci to analyze newborn cell dynamics across 21 mouse tissues at different ages, showing how aging affects cell renewal and composition.

Globular domain histone H3R131C mutation remodels chromatin accessibility to promote oncogenic transcriptional programs

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

ACLY integrates metabolism and chromatin accessibility to enable B Cell activation and humoral immunity

This study shows ACLY links metabolism to chromatin accessibility in B cells, essential for activation and humoral immunity.

Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States

This study identifies two epigenetically distinct cell states in leiomyosarcoma using single-nucleus multiome sequencing and spatial transcriptomics, linking them to clinical outcomes and therapeutic vulnerabilities.

Integration of Alzheimer's GWAS, 3D genomics, and single-cell CRISPRi non-coding screen implicates causal variants in a microglial enhancer regulating TSPAN14.

Mutations Causative of CPEO Differentially Engage Innate Immunity Sensors

This study shows that mutations in RNASEH1 and Twinkle trigger innate immune activation through different mitochondrial nucleic acid release mechanisms, leading to paracrine inflammation in CPEO.

Chromatin landscape and epigenetic heterogeneity of acute myeloid leukemia

This study identifies 16 AML subgroups based on chromatin accessibility profiles using ATAC-seq in 1,563 cases, revealing epigenetic heterogeneity and its clinical and therapeutic implications.

Single-cell multi-omic integration analysis prioritizes druggable genes and reveals cell-type-specific causal effects in glioblastomagenesis

The paper integrates GWAS with single-cell multi-omics to identify druggable genes and cell-type-specific causal effects in glioblastoma development.

Personalized multi-assay profiling of respiratory motile ciliopathies and mRNA therapy

This study develops a personalized multi-assay platform using nasal epithelial cells to assess ciliary function and therapeutic response in primary ciliary dyskinesia.