ATAC-seq

ChromSkills enables interpretable and reproducible agentic chromatin data analysis

ChromSkills provides a framework for reproducible and interpretable chromatin data analysis using domain-specific tools guided by LLMs.

Integrative Multi-Omics Analysis Identifies a Functional Enhancer Driving Tumorigenesis in Head and Neck Squamous Cell Carcinoma

The paper identifies a functional enhancer, GH05J001312, that drives tumorigenesis in HNSCC by enhancing TERT expression and affecting cancer-related pathways.

A consensus spinal cord cell type atlas across mouse, macaque, and human

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

Directing stem cell differentiation by chromatin state approximation

The paper uses chromatin state approximation to optimize stem cell differentiation protocols, finding that greedy selection based on ATAC-seq profiles improves erythroblast generation.

Reversible Dissociation of Mitochondrial Complex V Balances Anabolic and Energy-Generating Needs in Cancer

The paper shows that dissociation of mitochondrial Complex V into Fo and F1 domains balances anabolic and energy needs in cancer cells by uncoupling ATP synthesis from TCA cycle activity.

The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements

This study identifies CHD4's role in restricting transcription factor binding to maintain regulatory function and silence cryptic enhancers.

MTFP1 preserves β-cell cristae structure and bioenergetics to ensure insulin release and glucose homeostasis

This study identifies MTFP1 as critical for β-cell mitochondrial structure and function, essential for insulin secretion and glucose homeostasis, and shows its role as a downstream effector of miR-125b.

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

This study identifies CD55 and CD248 as novel surface markers for tendon stem/progenitor cells using single-cell and single-nucleus sequencing in mouse Achilles tendon.

Early microglial priming in Alzheimer's disease revealed by ME-seq

The paper introduces ME-seq, a technology that profiles DNA methylation, gene expression, and chromatin accessibility in single nuclei, revealing early microglial priming in Alzheimer's disease.

Single-cell multiomics identifies key nodes and cis-regulatory elements of the networks specifying the eye domains in zebrafish

The paper uses single-cell multiomics to identify key regulatory nodes and cis-regulatory elements in zebrafish eye development.

Expanded Chromatin Accessibility Mapping Explains Genetic Variation Associated with Complex Traits in Liver

The paper integrates chromatin accessibility data with GWAS to identify regulatory mechanisms underlying blood lipid traits, finding 20% of signals lack proposed mechanisms.

Rectifying Stress into Structural Memory Drives Specialization in Cells and Adaptive Computational Systems

This paper identifies asymmetric-drive rectification as a mechanism converting stress into structural memory, enabling functional specialization in cells and adaptive computational systems.

PETScan: Score-Based Genome-Wide Association Analysis of RNA-Seq and ATAC-Seq Data

PETScan performs genome-wide association analysis of RNA-Seq and ATAC-Seq data using negative binomial models and score tests, achieving faster computation than Wald tests while identifying similar significant gene-peak pairs.

SOX21 Suppresses Glioblastoma Growth by Repressing AP-1 Activity

This study shows SOX21 suppresses glioblastoma stem cells by repressing AP-1 activity, leading to reduced tumor growth and improved survival in mouse models.

FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity

This study identifies FOXA1 mutations in prostate cancer, showing they alter chromatin accessibility and promote tumorigenicity by reprogramming cell fate through interactions with androgen receptor and POU2F1.

The evolution of gene regulation in mammalian cerebellum development

This study identifies conserved and diverged gene regulatory networks in mammalian cerebellum development using single-nucleus gene expression and chromatin accessibility data from six species.

Multi-omics Differential Inference for Functional Interpretation (MoDIFI): A Statistical Framework to Prioritize Cell Lines for Neurodevelopmental Variants

The paper develops MoDIFI, a Bayesian framework to prioritize cell lines and regulatory regions for testing noncoding variants associated with neurodevelopmental disorders.

Chromatin compaction upon CDK12 inhibition drives long gene silencing and a combinatorial lethal dependency on PAF1

This study shows CDK12 inhibition causes chromatin compaction and long gene silencing, revealing a lethal dependency on PAF1 for cell survival in prostate cancer.

Metabolic Repression of Autophagy Drives Inflammation, Pain, and Malodor in Hidradenitis Suppurativa

This study identifies metabolic dysregulation of autophagy in HS, linking mTOR activation and cadaverine to inflammation, pain, and malodor.

EZH2 Inhibition Reshapes 3D Chromatin Architecture to Induce Immunogenic Phenotype in Small Cell Lung Cancer

This study shows that inhibiting EZH2 alters 3D chromatin structure in SCLC, reactivating MHC genes and enhancing immunogenicity.

Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome

This study identifies how genetic and environmental factors shape the human immune cell epigenome through differential methylation and chromatin accessibility changes.

The histone code of love: epigenetics of maturation of gonads in the human blood fluke Schistosoma mansoni

This study analyzes histone modifications, chromatin accessibility, and transcription in Schistosoma mansoni gonads to uncover the histone code governing gene expression and reproductive development.

Establishment of the Saudi Bank of Induced Pluripotent Stem Cells (SBiPSCs): A National Platform for iPSC-Based Research and Therapy

The paper establishes the Saudi Bank of Induced Pluripotent Stem Cells (SBiPSCs) to address underrepresentation of Middle Eastern populations in iPSC resources and supports immunocompatible cell therapies.

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging

The paper builds a cross-species single-cell multi-omics kidney atlas to identify epithelial cells as a driver of epigenetic aging in diseased kidneys.

Endothelial RRM2B-dependent mitochondrial DNA signalling drives doxorubicin-cardiotoxicity

This study identifies endothelial RRM2B-dependent mitochondrial DNA signaling as a driver of doxorubicin-induced cardiotoxicity and shows that Eltrombopag can prevent it.

eTRex Reveals Oncogenic Transcriptional Regulatory Programs Across Human Cancers

The paper develops eTRex, a variational Bayesian model, to analyze 4,819 ATAC-seq datasets and create a pan-cancer atlas of transcriptional regulator profiles, revealing common and context-specific regulators.

Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment

The paper identifies mitochondrial dysfunction in a glaucoma model using single-cell analysis and shows that vitamin B3 treatment protects against IOP elevation.

Human left ventricle circRNA-miRNA-mRNA network analyses reveals a novel proangiogenic role for circNPHP1 under ischemic conditions

This study identifies a circRNA-miRNA-mRNA network in ischemic heart disease, revealing circNPHP1's role in enhancing angiogenesis by sponging miR-221-3p to upregulate VEGF-A and BCL2.