ATAC-seq

Systematic Multi-Omics Investigation of Androgen Receptor Driven Gene Expression and Epigenetics changes in Prostate Cancer

This study investigates AR-driven gene expression and epigenetic changes in prostate cancer using multi-omics data from LNCaP cells, identifying gene expression shifts and AR binding patterns under androgen deprivation therapy.

Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells

The paper identifies regulatory elements controlling Ets1 expression in B cells but not T cells, using epigenetic and reporter assays in mice.

The epigenetic reader MORC3 is required for T cell development in the thymus

This study shows that MORC3 is essential for T cell development in the thymus, as its loss causes developmental arrest and altered chromatin accessibility in DN1 cells.

Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development

The paper examines how sensory input, sex, and function influence the developmental trajectories of hypothalamic cell types during early life transitions.

Enhancing Radiation-induced Reactive Oxygen Species Generation Through Mitochondrial Transplantation in Human Glioblastoma

This study enhances radiation-induced ROS generation in GBM cells through mitochondrial transplantation, showing increased ROS production and cell death.

Chromatin Changes Associated with Neutrophil Extracellular Trap (NET) Formation in Whole Blood Reflect Complex Immune Signaling

This study compares chromatin accessibility changes during NET formation in whole blood versus isolated neutrophils, finding that whole blood responses show stronger immune pathway activation.

Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model

The paper investigates how exercise affects Alzheimer's disease in mice by analyzing gene expression and chromatin changes, finding that growth factor signaling pathways are key to exercise's benefits.

MOSim: bulk and single-cell multi-layer regulatory network simulator

MOSim generates synthetic bulk and single-cell multi-omics datasets for benchmarking methods that analyze regulatory networks across various omics layers.

Distinct small molecule inhibitors of Kras specifically prime CTLA4 blockade therapy to transcriptionally reprogram Tregs and overcome resistance to suppress pancreas cancer

This study identifies small molecule Kras inhibitors that synergize with anti-CTLA4 therapy to reprogram Tregs and enhance immunotherapy efficacy in PDAC.

The INO80 chromatin remodeling complex regulates histone H2A.Z mobility and the G1-S transition in oligodendrocyte precursors

Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos

The paper identifies the role of Oct4 and Sox2 in establishing the pluripotency network in early mouse embryos through chromatin and transcriptome analysis.

The transcription factor ZNF469 regulates collagen production in liver fibrosis

The paper identifies ZNF469 as a transcription factor regulating collagen production in liver fibrosis through computational analysis and experimental validation.

Basic-Leucine-Zipper Transcription Factors Regulate Selective Molecular Phenotypes in Regulatory T Cells During IL-2-Induced Activation

The paper identifies bZIP transcription factors as key regulators of IL-2-induced Treg activation, linking chromatin accessibility changes to Th1/Th2 molecular phenotypes and metabolic pathways.

CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development

The paper shows that CTCF depletion in mouse rod photoreceptors disrupts chromatin accessibility and gene expression, affecting ~20% of the transcriptome and ~41% of genome accessibility.

SARS-CoV-2 nucleocapsid uniquely disrupts chromatin over pathophysiologically relevant gene promoters

This study shows that SARS-CoV-2 nucleocapsid protein alters chromatin structure at gene promoters linked to immune and metabolic pathways in severe COVID-19.

IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium

This study investigates how IFNγ affects cardiac vascular endothelium by analyzing RNA-seq and ATAC-seq data from iPSC-derived cells, revealing immune-like regulatory changes and GWAS variant overlaps.

C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data

The paper introduces CLaP, a transformer-based model that integrates DNA sequences and ATAC-seq data to improve chromatin modeling, achieving high accuracy in predicting genomic signals and detecting CTCF binding sites.

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes

This study identifies cis-regulatory roles of transposable elements in livestock genomes using multi-omics data and a novel computational framework.

Origin and stepwise improvement of vertebrate lungs

The paper analyzes single-cell RNA sequencing data to show that lung development involves regulatory changes and new genes, with some features specific to bony fishes and mammals.

CHD3 regulates BMP signalling response during cranial neural crest cell specification

This study shows CHD3 regulates BMP signaling during cranial neural crest cell specification by modulating chromatin accessibility and gene expression.

Clonal memory of colitis accumulates and promotes tumor growth

The paper shows that colitis leaves an epigenetic memory in colonic stem cells that promotes tumor growth by enhancing regenerative gene programs and AP-1 activity.

TGIF2 is a major regulator of neural stem cell fate and neurogenic priming

The paper identifies TGIF2 as a key regulator of neural stem cell fate and neurogenic priming through transcriptomic and chromatin analysis in mouse brain development.

Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle

This study shows intermittent fasting changes chromatin accessibility and gene expression in brain and muscle tissues of mice, affecting metabolic and functional pathways.

Canonical and non-canonical PRC1 differentially contribute to the regulation of neural stem cell fate

The paper compares the roles of canonical and non-canonical PRC1 sub-complexes in neural stem cell regulation during neocortex development, finding canonical PRC1 has a more significant impact.

Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade

This study shows that exhausted T cells can form functional memory T cells after antigen clearance, and checkpoint blockade expands these memory clones.

Alternative lipid synthesis in response to phosphate limitation promotes antibiotic tolerance in Gram-negative ESKAPE pathogens

This study shows that phosphate limitation in Gram-negative ESKAPE pathogens triggers alternative lipid synthesis, enabling antibiotic tolerance through reduced interaction with cationic antimicrobial peptides.

Cell signaling pathways discovery from multi-modal data

The paper introduces Incytr, a method for discovering cell signaling pathways from multi-omics data, demonstrating its application in disease contexts and showing its utility for drug discovery and understanding cell communication.

Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data

The paper introduces Consenrich, a method for robust signal recovery from multi-sample functional genomics data, showing improved biological insights in Alzheimer's cohort analysis.

Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions

This study uses single-nucleus multiome sequencing to identify HIV-associated transcriptional and epigenetic changes in brain regions of individuals with HIV, revealing altered glial cell states and pro-inflammatory signaling.

Inference of Transcriptional Regulation From STARR-seq Data

The paper introduces a method to infer functional regulatory sites in enhancer sequences using STARR-seq data, showing it can identify local regulatory sites missed by global approaches.