Emek focuses on integrating rich, detailed pathway information and using the resulting "cell maps" to answer cancer biology problems in conjunction with omic data. His work runs the gamut on Pathway Informatics, from pathway curation, visualization, NLP, data standardization and integration to machine learning, mechanistic assembly and simulation. He led the development of the BioPAX standard for pathway information and built an extensive software stack for aggregating and using pathway information from all major public data sources. These efforts resulted in Pathway Commons, a resource with more than 2 million interactions and more than 400,000 highly-detailed reactions of human pathways. Pathway Commons is the largest process-level pathway database.