Clifford A. Meyer

scATAnno automatically annotates scATAC-seq data using reference atlases, outperforming existing methods across multiple datasets.

The paper expands the DNA motif lexicon of transcriptional regulatory code by identifying composite elements and using a deep learning model to predict their activity and impact of variants.

This study investigates transcription factor dynamics during human enteroendocrine cell differentiation, finding that oscillations of ASCL1 and NEUROD1 enable accurate cell type diversification.

MetaTiME identifies data-driven meta-components in tumor immune microenvironment scRNA-seq data to annotate cell states and reveal transcriptional regulators.

MIRA jointly models gene expression and chromatin accessibility in single cells to infer regulatory circuits and lineage trees during development.

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

SELMA estimates intrinsic cleavage biases in bulk and single-cell chromatin accessibility data, improving analysis accuracy and cell clustering in single-cell ATAC-seq.

CHIPS is a Snakemake pipeline for processing chromatin profiling data, providing quality control metrics and reproducible analysis workflows for ChIP-seq, ATAC-seq, and DNase-seq experiments.

The paper identifies two classes of transcription factors based on their regulatory range and shows that long-range TFs' activity depends on chromatin state.

Lisa predicts transcriptional regulators of gene sets by integrating chromatin accessibility and ChIP-seq data to identify relevant regulators.

The paper introduces MAGeCK-NEST, a method to improve CRISPR screen analysis by integrating PPI data and refining sgRNA design, leading to better hit calling and library design.

MACS calls ChIP-Seq peaks by estimating tag shift from Watson/Crick strand offsets and testing enrichment against a locally adaptive Poisson background, improving specificity and binding-site resolution.