ATAC-seq

Vaccinia virus infection induces concurrent alterations in host chromatin architecture, accessibility, and gene expression

This study shows that vaccinia virus infection causes coordinated changes in host chromatin structure, accessibility, and gene expression over time.

JMnorm: a novel Joint Multi-feature normalization method for integrative and comparative epigenomics

JMnorm improves normalization of epigenetic data by jointly normalizing multiple features across cell types and conditions, preserving biological relationships and enhancing downstream analysis.

Transcription dosage compensation does not occur in Down syndrome

The paper shows that transcriptional dosage compensation is absent in Down syndrome using real and simulated data, and highlights issues with standard analysis methods.

Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis

This study identifies dynamic chromatin accessibility changes during osteosarcoma metastasis to the lung, revealing epigenetic states critical for metastatic colonization and new therapeutic targets.

The chromatin landscape of the euryarchaeon Haloferax volcanii

This study uses ATAC-seq to map the chromatin accessibility of Haloferax volcanii and finds that promoter accessibility does not correlate with transcriptional activity, and archaeal chromatin is similarly accessible to eukaryotic chromatin.

In vivo silencing of regulatory elements using a single AAV-CRISPRi vector

This paper develops an AAV-based CRISPRi system to silence gene expression in cardiac myocytes, showing dose-dependent reduction of Nppa expression in vitro and in vivo.

Transcriptomics and chromatin accessibility in multiple African population samples

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

Development of a novel aging clock based on chromatin accessibility

This paper develops an aging clock using chromatin accessibility data from PBMCs and shows it correlates with transcriptional changes during aging.

cisDynet: an integrated platform for modeling gene-regulatory dynamics and networks

cisDynet is a platform for analyzing chromatin accessibility data, integrating preprocessing, downstream analysis, and visualization to uncover gene regulatory networks and GWAS variant associations.

DeLoop: a deep learning model for chromatin loop prediction from sparse ATAC-seq data

DeLoop predicts CTCF-mediated chromatin loops from sparse ATAC-seq data, outperforming existing models under low read depth conditions.

A Neanderthal Origin of Genetic Variants Associated with Asthma

The paper identifies Neanderthal-derived genetic variants associated with asthma and shows one variant disrupts glucocorticoid receptor binding to an IL33 enhancer.

Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer

The paper identifies AP1 transcription factor dichotomy and CD68+ macrophages as drivers of intratumoral subtype co-existence and therapy response in pancreatic cancer.

Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data

This study benchmarks seven methods for integrating unpaired and paired scRNA-seq and snATAC-seq data, finding that multiome data improve cell type annotation but require sufficient cell numbers.

GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership

This paper introduces GoM DE, a differential expression analysis method that allows cells to have partial membership in multiple groups, improving the interpretation of structure in single-cell sequencing data.

Functional interrogation of twenty type 2 diabetesassociated genes using isogenic hESC-derived β-like cells

This study functionally interrogates 20 T2D-associated genes using isogenic hESC-derived β-like cells, identifying variants and genes linked to insulin production and lipotoxicity sensitivity.

Yes1-mediated Cul9 phosphorylation promotes the metabolic reprogramming in gastric cancer

This study identifies Yes1-mediated Cul9 phosphorylation as a driver of metabolic reprogramming in gastric cancer, revealing a feedback loop with therapeutic implications.

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells

Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings

The paper investigates how the Hox gene Ubx is restricted to hindwings in butterflies by analyzing chromatin structures and CRISPR perturbations, revealing silencing and insulating sequences.

Multi-omic profiling of the developing human cerebral cortex at the single cell level

The paper profiles gene expression and chromatin accessibility in 45,549 cortical nuclei across 6 developmental timepoints to study cell fate determination and neuropsychiatric disease mechanisms.

Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells.

The paper investigates chromatin changes in human endothelial cells under inflammatory stress using ATAC-seq and RNA-seq, finding correlations between chromatin accessibility and gene expression related to endothelial dysfunction.

Epigenetic insights into GABAergic development in Dravet Syndrome iPSC and therapeutic implications

This study investigates epigenetic changes in GABAergic development using DS iPSCs and shows that VPA can rescue some chromatin abnormalities.

Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia

This study identifies convergent epigenetic evolution in AML relapse using ATAC-seq and mtscATAC, showing that epigenetic changes drive relapse independent of genetic mutations.

Single cell expression and chromatin access of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential pivotal controller of a ribosome regulon

The paper maps transcriptional and chromatin changes during the Toxoplasma gondii lytic cycle, identifying AP2XII-8 as a key regulator of a ribosome regulon.

Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

The paper develops a chromatin accessibility and gene expression atlas of human breast tissues from 92 donors of diverse genetic ancestry, identifying 10 cell types and ancestry-dependent gene expression patterns.

DegCre: Probabilistic association of differential gene expression with regulatory regions

DegCre associates differential gene expression with regulatory regions using probabilistic correlation analysis across perturbation data.

Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming

The paper uses deep learning to analyze chromatin accessibility and gene expression during reprogramming, revealing how TF concentrations and motif syntax influence cis-regulatory networks.

MINI-AC: Inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles

MINI-AC infers plant gene regulatory networks using bulk or single-cell accessible chromatin data, outperforming existing methods in identifying TF binding sites and revealing cell-type specific regulators.

Notch signaling and Bsh homeodomain activity are integrated to diversify Drosophila lamina neuron types

The paper shows Notch signaling differentially specifies L4 and L5 Drosophila lamina neuron fates by modulating Bsh's chromatin accessibility and gene activation.

Interleukin 11 therapy causes acute heart failure and its use in patients should be reconsidered

This paper identifies direct cardiomyocyte toxicities of IL11 therapy, showing it causes acute heart failure by activating JAK/STAT3, which questions its continued use in patients.

TRANSPOSABLE ELEMENTS ALTER GENE EXPRESSION AND MAY IMPACT RESPONSE TO CISPLATIN THERAPY IN OVARIAN CANCER

This study investigates how transposable elements (TEs) affect gene expression and response to cisplatin therapy in ovarian cancer cell lines.