Ethan J. Armand

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

The paper creates a single-cell atlas of transcription and chromatin states in the human brain, identifying regulatory programs and linking them to neuropsychiatric disorders.

GAME: Genomic API for Model Evaluation

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.

Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery

The paper investigates how chromatin architecture, mediated by histone modifiers and loop-extrusion machinery, influences gene regulation in mouse embryonic stem cells under different conditions.

SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis

SnapATAC2 is a fast, scalable dimensionality reduction tool for single-cell omics data that improves accuracy and efficiency in capturing cellular heterogeneity across multiple modalities.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

The paper identifies gene-CRE pairs in mouse brain cells by integrating single-cell transcriptomes and epigenomes, controlling for gene co-expression.

Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

The paper analyzes gene regulatory programs in the neocortex of rodents and primates using single-cell multiomics, finding rapid evolution of cell type-specific gene expression and TE-driven cCREs.

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.