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.

simulating dysregulated gene expression in single cell transcriptome data

Dynamic lncRNA causal regulation in autism

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

DECODER-SC is an R-based algorithm for quantifying regulatory execution failure by measuring discordance between transcription factor activity and target gene expression in single-cell RNA-seq data.

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.

Inferring ncRNA synergistic competition

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

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

Meta-analysis of DNA methylation in ART

An R package for multi-dimensional pathway enrichment analysis

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

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

Detecting Regulatory Elements using GRO-seq and PRO-seq