Spencer Halberg

A Framework for Benchmarking Pathway Reconstruction Algorithms

This paper benchmarks 14 pathway reconstruction algorithms across 822 datasets using a standardized framework to evaluate performance, similarity, and computational efficiency.

A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen

This paper constructs a gene regulatory network for Aspergillus fumigatus using RNA-seq data, validates it with experimental cases, and provides an online resource called GRAsp.

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

This paper introduces scMTNI, a framework to infer cell type-specific gene regulatory networks on cell lineages using scRNA-seq and scATAC-seq data, showing its effectiveness on simulated and real datasets.