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

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

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.

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

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.

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

Meta-analysis of DNA methylation in ART

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

An R package for multi-dimensional pathway enrichment analysis

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

Detecting Regulatory Elements using GRO-seq and PRO-seq