ATAC-seq

Semi-parametric Empirical Bayes Method for Multiplet Detection in snATAC-seq with Probabilistic Multi-omic Integration

SEBULA detects multiplets in snATAC-seq using a semi-parametric empirical Bayes model and integrates with scRNA-seq data, showing superior performance on benchmark datasets.

Diverse processes drive the origination and maturation of super-enhancers and super-silencers during a vast evolutionary timescale of a bicistronic gene

The paper analyzes the evolutionary development of regulatory elements in the human bicistronic gene SMIM45, identifying diverse mechanisms for the formation of super-enhancers and super-silencers over millions of years.

HIRA-SETDB1-H3K9me3 axis regulate chromatin architecture in chronic myeloid leukemia cells

This study shows that the HIRA-SETDB1-H3K9me3 axis regulates chromatin architecture in CML cells, affecting proliferation and differentiation.

Unified imputation of missing data modalities and features in multi-omic data via shared representation learning

MIMIR is a deep learning framework that imputes missing modalities and features in multi-omic data using shared representation learning, outperforming existing methods on pan-cancer data.

AR suppression rewires a SOX4 regulatory program to promote enzalutamide resistance in prostate cancer

The paper identifies a SOX4-driven regulatory program that promotes enzalutamide resistance in prostate cancer by rewiring gene regulation following AR suppression.

Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES

CANDIES denoises and integrates spatial multi-omics data using a conditional diffusion model and contrastive learning, improving downstream analysis tasks.

A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease

This study identifies a MEF2C transcription factor network that regulates endothelial cell proliferation in diabetic kidney disease and shows that SGLT2i treatment can reverse its dysregulation.

Multi-omic phenotyping of MAPT V337M neurons reveals early changes in axonogenesis and tau phosphorylation

The paper uses multi-omic analysis to study MAPT V337M neurons, finding altered axonogenesis and tau phosphorylation, with p38 MAPK pathway involvement in tau phosphorylation in V337M neurons.

Hepatic gene replacement restores energy metabolism and doubles the survival in mouse model of GRACILE syndrome, a neonatal mitochondrial disease

This study uses gene replacement in a mouse model of GRACILE syndrome to show improved energy metabolism and doubled survival through liver-specific correction of a mitochondrial complex III deficiency.

Mosaic integration of spatial multi-omics with SpaMosaic

SpaMosaic integrates spatial multi-omics data using contrastive learning and graph neural networks, improving spatial domain identification and missing modality imputation across diverse datasets.

Gene regulatory co-option drives birdsong neural circuit specialization

The paper identifies gene regulatory co-option as a mechanism driving the evolution of specialized neural circuits in birdsong by analyzing gene expression and chromatin accessibility in songbird brains.

A single cell multi-omic analysis identifies molecular and gene-regulatory mechanisms dysregulated in the developing Down syndrome neocortex

This study uses single-nucleus multi-omics to analyze the developing Down syndrome neocortex, identifying dysregulated molecular and gene-regulatory mechanisms affecting neurogenesis and cell specification.

Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex

This study uses single-nucleus multiomic sequencing to analyze gene expression and chromatin accessibility in the Down syndrome prefrontal cortex, revealing widespread dysregulation in metabolic, synaptic, and neuroinflammatory pathways.

Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double-strand breaks reveals specific gene expression programs

The paper examines chromatin accessibility changes at DNA double-strand breaks (DSBs) in single cells, revealing resection-dependent remodeling and associated gene expression programs.

Single-cell multi-omic analysis of mesenchymal cells reveals molecular signatures and putative regulators of lung allograft fibrosis

CAD variants act through ox-LDL-induced enhancer remodelling to alter VSMC gene programmes

The paper identifies CAD risk variants that alter VSMC gene programs via ox-LDL-induced enhancer remodelling using multi-omics approaches.

Specification of the interstitial cell lineage in the fetal mouse ovary requires balanced Notch signaling

The paper identifies Notch signaling as critical for specifying the interstitial lineage in fetal mouse ovaries through single-nucleus transcriptomics and lineage tracing.

Bioengineered yeast tethered respiratory supercomplexes reveal mechanisms governing efficient substrate utilization

This study engineers yeast to express a tethered respiratory supercomplex, revealing its role in optimizing electron flux and metabolic plasticity through substrate-specific interactions.

Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

The paper uses single-cell RNA sequencing and ATAC-seq to analyze host responses to HCoV-229E infection, revealing heterogeneous transcriptional and regulatory changes across infected cells.

Multiomic screening platform uncovers the impact of histone mutations on chromatin and cell fate

This study develops CHANCLA, a multiomic platform to screen oncohistones, revealing their impact on chromatin and cell fate through functional and structural analyses.

FOXP-stabilization of the Il2ra super-enhancer structure augments Treg fitness

The paper shows FOXP1 and FOXP4 maintain the peripheral Treg pool by regulating chromatin structure at the Il2ra locus to sustain CD25 expression.

Fruitless produces diverse neuronal sex differences by editing lineage-programmed chromatin landscapes

The paper investigates how the Fruitless transcription factor generates sex-specific neuronal differences by interacting with lineage-programmed chromatin landscapes in Drosophila.

Decoding Single-Cell Omics of Perturbation Responses Using DeSCOPE

DeSCOPE is a variational autoencoder framework for predicting genetic perturbation responses across multiple omics modalities, outperforming baselines in unseen gene and cell type scenarios.

A multi-omic atlas in the African turquoise killifish reveals increased glucocorticoid signaling as a hallmark of brain aging

This study creates a multi-omic atlas of brain aging in African turquoise killifish, identifying glucocorticoid signaling activation as a key feature of aging and showing its inhibition can reverse aging phenotypes.

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

This study shows FOXA1 maintains cell polarity and limits lysosome biogenesis in lung adenocarcinoma by regulating transcriptional circuits and interacting with TFE3.

Rete Ridge Topography as a Determinant of Epidermal Stem Cell Identity: Implications for Skin Aging

This study shows that the concave topography of rete ridges influences epidermal stem cell differentiation and function, with changes in topography contributing to skin aging.

SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation

SCOPE identifies fate-decision states and regulatory drivers in single-cell differentiation by localizing branchpoints and epigenetic priming across developmental processes.

Early Epigenetic and Metabolic Responses to the Adipocyte Secretome Reveal Stress-Adaptive States in Triple-Negative Breast Cancer

This study identifies how adipocyte secretome induces metabolic and epigenetic changes in TNBC cells, promoting stress-adaptive states through chromatin remodeling and metabolic reprogramming.

Brain cell type nuclei enrichment without fixative for nanoCUT&Tag and other omics approaches

The paper introduces a workflow for cell-type-specific epigenomic profiling of brain cells using nanoCUT&Tag and FANS, applicable to unfixed human and mouse brain tissue.

Assessing molecular gene by treatment interactions using a population of neural progenitors exposed to valproic acid and lithium

The paper exposes human neural progenitors to valproic acid and lithium, identifying gene by treatment interactions linked to psychiatric disorder risk and folate metabolism.