Detecting Regulatory Elements using GRO-seq and PRO-seq

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

An R package for multi-dimensional pathway enrichment analysis

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Meta-analysis of DNA methylation in ART

Data analysis for the manuscript, "Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus", Zacharias et al., Comm Biol, 2025

Data analysis for the manuscript, "Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus", Zacharias et al., Comm Biol, 2025

Dynamic lncRNA causal regulation in autism

Inferring ncRNA synergistic competition

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.

Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.

simulating dysregulated gene expression in single cell transcriptome data

A resource of gene expression signatures derived from the DEE2 dataset (http://dee2.io)

An R package for multi-dimensional pathway enrichment analysis (legacy repo)

Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"

Identification and characterization of m6A regulatory genes in soybean.