The second Challenges in Computational Biology meeting will focus during 2 days on the topic of Gene Expression Data Analysis. It will take place on 1-2 December 2016 at the Institute of Molecular Biology (IMB) located on the campus of the Johannes Gutenberg University of Mainz (JGU), Germany. It aims at fostering international cross-disciplinary interactions between experimentalists and computational biologists interested in understanding the organisation and regulation of gene expression. The main questions to be discussed are what is the current status and limitations of related computational methods and resources, which methods and resources are being currently developed, and what are the challenges and developments needed in the field.