TopoICE-R: 3D visualization modeling the topology of DNA recombination. - Isabel K. Darcy; Robert G. Scharein (Bioinform., 2006)

Coloring the Mu transpososome. - Isabel K. Darcy; Jeff Chang; Nathan Druivenga; Colin McKinney; Ram K. Medikonduri; Stacy Mills; Junalyn Navarra-Madsen; Arun Ponnusamy; Jesse Sweet; Travis B. Thompson (BMC Bioinform., 2006)

Modeling protein-DNA complexes with tangles. - Isabel K. Darcy (Comput. Math. Appl., 2008)

Introduction to DNA Topology. - Isabel K. Darcy; Stephen D. Levene; Robert G. Scharein (Discrete and Topological Models in Molecular Biology, 2014)

Tracing patterns and shapes in remittance and migration networks via persistent homology. - Paul Samuel Ignacio; Isabel K. Darcy (EPJ Data Sci., 2019)

Applications of Topological Data Analysis in Oncology. - Anuraag Bukkuri; Noemi Andor; Isabel K. Darcy (Frontiers Artif. Intell., 2021)