Ph.D. studentRoom: MI 01.09.042
Institut für Informatik / I12
85748 Garching b. München, Germany
Fax number: +49 (89) 289-19414
machine learning, data mining, bio-/cheminformatics, toxicology, small molecule representations, in silico drug discovery, algorithms for small molecules, graph algorithms, chemical and biological similarity of small molecules
I am currently finishing my PhD thesis in the Machine Learning and Data Mining in Bioinformatics group in a collaborative project with the global research-based biopharmaceutical company AstraZeneca. The project is about small molecule similarity in quantitative structure activity relationships (QSARs) and how to improve those for various toxicological endpoints on publically available and AstraZeneca in-house datasets. The working title of my PhD thesis is Small Molecule Similarity for In silico toxicology prediction.
I also worked two and a half years as an algorithm and REST webservice developer and researcher on the EU FP7 project OpenTox (Project-No.: HEALTH-F5-2008-200787). The overall objective of the OpenTox project was to develop a framework that provides a unified access to toxicity data, (Q)SAR models, procedures supporting validation and additional information that helps with the interpretation of (Q)SAR predictions. I was responsible for algorithm and web service development and implementation as well as involved in infrastructure and API design. Additionally, I was in the organizing team of the international conference: Innovation in Predictive Toxicology: OpenTox InterAction Meeting 2011 held in Munich.
I am also a alumni of the CeDoSIA class of 2008. CeDoSIA is a facultiy graduate school for computer science in the TUM Graduate School, that offers additional soft skill training for PhD candidates. Before joining Professor Kramer's lab, I studied Bioinformatics in the joint diploma program of Technische Universität München and Ludwig-Maximilians-Universität München and wrote my diploma thesis in collaboration with the biotech company 4SC AG in Martinsried. The topic of the thesis was Machine learning based prediction of compound behavior in metabolism relevant Cytochromes P450.
- Member of the organizing team of the international conference Innovation in Predictive Toxicology: OpenTox InterAction Meeting 2011, Munich, Germany.
- IEEE International Conference on Data Mining (ICDM-2008, 2009)
- ACM Symposium on Applied Computing (SAC-2009 Data Mining Track, 2010)
- European Conference on Machine Learning/European Conference on Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD-2008, 2010, 2011)
- International Conference on Discovery Science (DS-2008, DS-2011)
- International Workshop on Mining and Learning with Graphs (MLG-2008, 2009)
- SIAM International Conference on Data Mining (SDM-2009, 2010)
- AAAI-10 Special Track on Artificial Intelligence and Bioinformatics (AIB-2010)
- International Conference on Extending Database Technology (EDBT-2012)
- BMC Bioinformatics
Selected Talks and Tutorials:
- Fast Conditional Density Estimation for Quantitative Structure-Activity Relationships, at the 24th AAAI Conference on Artificial Intelligence (2010), Atlanta, GA
- Machine learning based prediction of compound behavior in CYP 3A4, CYP 2D6 and CYP 2C9, at the 4th Russian-Bavarian Conference on Biomedical Engineering (2008), Moscow
- Girschick, T, Buchwald, F and Kramer, S (2010), Combining Local and Global Chemical Distance Measures for Quantitative Structure-Activity Relationships, 18th European Symposium on Quantitative Structure-Activity Relationships, Rhodes, Greece
- Seeland, M, Girschick, T, Buchwald, F and Kramer, S (2010), Clustering Structure Databases Using Frequent Substructure Mining, 18th European Symposium on Quantitative Structure-Activity Relationships, Rhodes, Greece
- Proseminar Bioinformatik (SS 2009, SS2011)
- Hauptseminar Bioinformatik (WS 08/09, WS 09/10, SS 2010, WS 10/11)
- Programmierpraktikum Bioinformatik (WS 08/09)
- Tutor Machine Learning and Data Mining in Bioinformatics (WS09/10)
- S. Seemayer; "Significant Similarities of Small Molecules in 3D", 2011. (Master Thesis)
- K. Ciosek; "Teilüberwachtes Lernen mit Untergraphen" (in German) [Semi-supervised learning with Subgraphs], 2010 (Master Thesis)
- M. Stransky; "Conditional Density Estimation with Continuous Intervals", 2010. (Bachelor Thesis)
- S. Seemayer; "Molecular Paths - a Novel Structural Descriptor for Small Molecule Similarity", 2009. (Bachelor Thesis)