Methodological advances have in recent years given us unprecedented information on the molecular details of living cells. However, it remains a challenge to integrate and jointly analyze all available data and literature on individual drugs and proteins, their mutual interactions, and associations with diseases. My lectures and associated exercises will cover the following three topics: 1) constructing networks of proteins and chemicals through large-scale data integration, 2) text mining of associations, and 3) hands-on analysis of biological networks. As examples of the data-integration approach, I will introduce the participants to the STRING and STITCH databases, which are used by over ten thousand users around the world every week. I will present general approaches and tools for automatic text mining of biomedical literature and other unstructured text. Finally, I will illustrate how networks can be used as a scaffold for other data and teach how to use Cytoscape for network analysis and visualization.



Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU), from where he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology based protein function prediction. During this time, he also developed methods for visualization of microbial genomes, pattern recognition in promoter regions, and microarray analysis. From 2003 to 2008, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining, integration of large-scale experimental datasets, and analysis of biological interaction networks. Since 2009, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a founder, owner and scientific advisor of Intomics A/S. He is a co-author of more than 150 scientific publications that have in total received more than 15,000 citations. He was awarded the Lundbeck Foundation Talent Prize in 2003, his work on cell-cycle research was named “Break-through of the Year” in 2006 by the magazine Ingeniøren, his work on text mining won the first prize in the “Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences” in 2009, and he was awarded the Lundbeck Foundation Prize for Young Scientists in 2010.