Systematic calibration of a cell signaling network model. - Kyoung Ae Kim; Sabrina L. Spencer; John G. Albeck; John M. Burke; Peter K. Sorger; Suzanne Gaudet; Do Hyun Kim (BMC Bioinform., 2010)

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. - Daniel C. Kirouac; Julio Saez-Rodriguez; Jennifer Swantek; John M. Burke; Douglas A. Lauffenburger; Peter K. Sorger (BMC Syst. Biol., 2012)

Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. - S. Evan Staton; John M. Burke (Bioinform., 2015)