The eleventh Cold Spring Harbor conference on Systems Biology: Global Regulation of Gene Expression will be held at Cold Spring Harbor Laboratory and begin at 7:30 pm on Tuesday, March 15 and run through lunch on Saturday, March 19, 2016. The conference is intended to foster cross-disciplinary exchange of ideas and expertise between experimentalists and computational biologists interested in the organization and control of complex transcription networks in eukaryotes. While a number of speakers have been invited, please note that the majority of oral presentations will be drawn from openly submitted abstracts.