His principal research interests are in computational and systems biology, including predictive simulations of biological processes, integrated molecular profiling of disease states, gene regulation by small RNAs, structural genomics and the development of multiplex cancer therapy. He is a leader in community efforts to create an open-source
information resource for biological pathways.

Previously, Sander served as Chief Information Science Officer with Millennium Pharmaceuticals, as Senior Scientist at the European Bioinformatics Institute in Cambridge, England, as founding chair of the department of Biocomputing at the European Molecular Biology Laboratory.
From 1995 until 2004 he was chief editor of the leading journal Bioinformatics, and is now an academic editor of the open access journal PLoS Computational Biology.