ATAC-seq

STARNet enables spatially resolved inference of gene regulatory networks from spatial multi-omics data

STARNet infers gene regulatory networks from spatial multi-omics data, revealing domain-specific regulatory interactions in tissues.

SCRIPT: Predicting Single-cell Long-range Cis-regulation Based on Pretrained Graph Attention Networks

SCRIPT predicts single-cell cis-regulatory relationships using graph attention networks, achieving high accuracy and improving long-range prediction.

Finding ancestry-specific chromatin architecture in Alzheimer's disease

The paper identifies ancestry-specific chromatin architecture differences in Alzheimer's Disease using Hi-C and ATAC-seq data from African and European ancestry individuals.

chronODE: A framework to integrate time-series multi-omics data based on ordinary differential equations combined with machine learning

chronODE integrates time-series multi-omics data using ordinary differential equations and machine learning to model gene and chromatin dynamics during brain development.

Identification of Viral Variants from Functional Genomics Data

The paper presents a pipeline to identify viral variants from functional genomics data, showing it can accurately recover introduced mutations in HSV-1 mutants.

Early, adjuvant-responsive epigenetic programs in B cells imprint subsequent plasma cell survival and the duration of humoral immunity

The paper identifies early epigenetic programs in B cells that influence plasma cell survival and humoral immunity duration, showing that ZBTB20 deficiency affects antibody responses when disrupted early post-immunization.

From Wiring to Firing: Collapse of embryonic identities and emergence of functional diversity during motor neuron maturation

This study tracks the transcriptional and chromatin changes in mouse motor neurons during maturation, revealing dynamic shifts in diversity and functional identity.

Whole-genome single-cell multimodal history tracing to reveal cell identity transition

The paper introduces HisTrac-seq to track cell identity transitions over time using single-cell multi-omics, revealing large-scale 'identity jumps' in mouse brain cells.

In vivo bioreactor matures iPSC-CMs for MLP disease modeling

This study shows that in vivo maturation of MLP-KO iPSC-CMs recapitulates DCM phenotypes, while in vitro maturation does not.

Integrating tDNA Epigenomics and Expression with Codon Usage Unravel an Intricate Connection with Protein Expression Dynamics in Trypanosoma cruzi

The paper investigates codon usage bias and its relationship with protein expression in Trypanosoma cruzi by integrating tRNA sequencing and transcriptomic data.

Comparative evaluation of genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data

This study benchmarks genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data, finding peak-level read coverage as the strongest predictor and proposing an ensemble model to improve concordance with ChIP-seq.

Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.

Mechanisms of the FTO locus association with obesity: Irx3 controls a sumoylation-dependent switch between adipogenesis and osteogenesis

This study identifies IRX3 as a regulator of sumoylation that controls adipogenesis and osteogenesis through epigenetic mechanisms, linking the FTO locus to obesity.

Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

Multi-omic analysis of photoreceptor alterations during early-onset retinal degeneration in Mfrp-/- mice

This study uses multi-omic analysis to identify transcriptional and spatial changes in Mfrp-/- mice, revealing photoreceptor loss and gene regulatory disruptions during retinal degeneration.

Differential Chromatin Architecture and Risk Variants in Deep Layer Excitatory Neurons and Grey Matter Microglia Contribute to Major Depressive Disorder

This study identifies differential chromatin architecture and risk variants in specific brain cell types associated with major depressive disorder.

Metastatic organotropism in small cell lung cancer

This study identifies key cellular programs and pathways driving metastatic organotropism in small cell lung cancer using preclinical models and multiomic profiling.

Chromatin-dependent motif syntax defines differentiation trajectories

The paper identifies chromatin-dependent motif syntax that distinguishes binding patterns of NGN2 and MyoD1 during differentiation, revealing how context-specific chromatin states influence transcription factor specificity.

Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex

The paper identifies genes and regulatory networks driving electrophysiological maturation of neurons in primate prefrontal cortex, with implications for autism.

Mechanisms of Cardiomyocyte Aging

This study identifies molecular mechanisms of cardiomyocyte aging using single-nucleus RNA-seq, ATAC-seq, and epigenetic analyses in mice, revealing DNA methylation and ESRRG as key regulators.

Inflammation-Induced Alternative Splicing in Human Endothelial Cells Reveals Genetic Mechanisms of Cardiovascular Disease Risk

This study identifies inflammation-induced alternative splicing in human endothelial cells and links it to cardiovascular disease risk through genetic mechanisms.

Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression between patients

This study identifies enhancer heterogeneity as a driver of transcriptional differences in KMT2A::AFF1 ALL patients, revealing patient-specific enhancer activity at oncogenes.

A stem cell-based platform for functional analysis of genetic variants in lung disease

This study develops an iPSC-based platform to functionally analyze genetic variants in lung disease, demonstrating its application in diagnosing a variant of uncertain significance in primary ciliary dyskinesia.

The gene regulatory landscape driving mouse gonadal supporting cell differentiation

The paper identifies key transcription factors and regulatory elements involved in mouse gonadal sex determination through integrated transcriptomic and chromatin accessibility analyses.

An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin

The paper develops RoboATAC, an automated ATAC-seq method, to study how TF dosage affects chromatin accessibility and gene expression, finding that DNA sequence predicts dosage sensitivity and nucleosome positioning patterns vary by TF.

Postnatal Abrogation of VEGFR2 Blocks Terminal Cap2 Differentiation by Preventing the Developmental Progression from a Capillary Intermediate Cell State

This study shows that postnatal VEGFR2 abrogation blocks Cap2 differentiation by preventing the transition from Cap1 to CapINT, impairing alveolarization and activating fibroblasts.

An integrated framework for functional dissection of variable expressivity in genetic disorders

The paper develops a framework to study variable expressivity in genetic disorders using 16p12.1 deletion models, showing how genetic background and secondary variants influence gene expression and phenotypes.

SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing

The paper introduces SMAdd-seq, a method to profile chromatin accessibility using small molecule intercalation and nanopore sequencing, and demonstrates its application in yeast.

Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales

The paper uses polymer mechanics and nucleosome positioning to explain genomic contacts, finding that nucleosomes explain 71% of close contacts within 500 kb.

Highly efficient XIST reactivation in female hPSC by transient dual inhibition of TP53 and DNA methylation during Cas9 mediated genome editing

The paper develops a method to efficiently reactivate XIST in female hPSCs by inhibiting TP53 and DNA methylation during Cas9-mediated genome editing.