Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. - Melody K. Morris; Julio Saez-Rodriguez; David C. Clarke; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2011)

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. - Camille Terfve; Thomas Cokelaer; David Henriques; Aidan MacNamara; Emanuel J. V. Gonçalves; Melody K. Morris; Martijn P. van Iersel; Douglas A. Lauffenburger; Julio Saez-Rodriguez (BMC Syst. Biol., 2012)

Benchmarking network algorithms for contextualizing genes of interest. - Abby Hill; Scott Gleim; Florian Kiefer; Frederic Sigoillot; Joseph Loureiro; Jeremy L. Jenkins; Melody K. Morris (PLoS Comput. Biol., 2019)