Computational Drug Repositioning with Networks, Structures, Text & Ontologies
Previous and Current Research
Developing a drug costs in the order of a billion USD and takes some 10 years. Drug repositioning tries to reduce cost and time by applying drugs that are already on the market to new uses. With the avalanche of publicly available data on compounds, genes, proteins, and diseases and their relationships, there is a tremendous need for computational approaches to organize and analyze this data and finally predict novel uses. In our group we are specifically focusing on developing algorithms and analysis pipelines using networks, protein structures, text-mining and ontologies for this purpose. We currently focus on pancreas cancer as application, where we have a wealth of experimental data from collaborations with the medical faculty.
Future Projects and Goals
We currently focus on prediction of pancreas cancer drugs and biomarkers using graph algorithms, protein structures, and text-mining. We experimentally validate predictions with simple assay.
Simone Daminelli, V Joachim Haupt, Matthias Reimann, and Michael Schroeder
Drug Repositioning through Incomplete Bi-cliques in an Integrated Drug-Target-Disease Network
Integrative Biology (2012)
Christof Winter, Janine Roy, Glen Kristiansen, Stephan Kersting, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert, Marcus Bahra, Hans J. Schlitt, Utz Settmacher, Helmut Friess, Markus Büchler, Hans-Detlev Saeger, Michael Schroeder, Robert Grützmann, and Christian Pilarsky
Prediction of Survival and Response to Adjuvant Therapy in Pancreatic Cancer
PLoS Computational Biology (2012)
Jörg-Christian Heinrich, Anne Tuukkanen, Michael Schroeder, Torsten Fahrig, and Rudolf Fahrig
RP101 (Brivudine) binds to heat shock protein HSP27 (HSPB1) and enhances survival in animals and pancreatic cancer patients.
Journal of Cancer Research and Clinical Oncology, 137(9):1349–61 (2001)
Joachim Haupt and Michael Schroeder
Old Friends in new Guise: Repositioning of known Drugs with Structural Bioinformatics.
Briefings in Bioinformatics, 12(4):312–26 (2011)
Loic Royer, A Francis Stewart, and Michael Schroeder
Evaluating Coverage and Accuracy of Protein Interaction Datasets with Network Compression
PLoS One (2012)