Emanuel Sonder

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

The paper predicts transcription factor binding across 43 human cell types using ATAC-seq data and a new platform, revealing promiscuous occupancy and chromatin contacts.

This study investigates how repeated stress affects molecular responses in the mouse hippocampus, finding widespread habituation without new adaptive responses or baseline gene expression changes.

The paper benchmarks methods for identifying differentially-active transcription factors from ATAC-seq data using curated and simulated datasets, identifying three promising approaches.

The paper validates 30 DNA methylation markers that accurately distinguish precancerous colorectal lesions from normal mucosa across multiple datasets.

This paper meta-analyzes single-cell method benchmarks to identify challenges in extensibility, interoperability, and reproducibility.