Labrat LIMS: An Extensible Framework for Developing Laboratory Information Management, Analysis, and Bioinformatics Solutions for Microarrays. - Marcus R. Breese; Matthew J. Stephens; Jeanette N. McClintick; Matthew W. Grow; Howard J. Edenberg (SAC, 2003)

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. - Marcus R. Breese; Yunlong Liu (Bioinform., 2013)

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. - Jacob Pfeil; Lauren M. Sanders; Ioannis N. Anastopoulos; A. Geoffrey Lyle; Alana S. Weinstein; Yuanqing Xue; Andrew Blair; Holly C. Beale; Alex Lee; Stanley G. Leung; Phuong T. Dinh; Avanthi Tayi Shah; et al. (PLoS Comput. Biol., 2020)