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mutzel:cheminformatics [2015-09-11 13:18]
 mutzel:cheminformatics [2015-09-11 13:18] (current)
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 +====== Cheminformatics ======
 +{{ :​mutzel:​scaffold_hunter.png?​400|Scaffold Hunter - A tool for the visual analysis and exploration of chemical space}}
 +
 +The challenging task in Cheminformatics is to support the drug discovery process by adequate computational methods including largely automated data mining algorithms as well as visual analysis tools. Our research includes algorithms to compare graphs, which are a prerequisite to apply data mining algorithms to structured objects like chemical compounds. Moreover, we develop methods for searching graph databases as well as visual analysis approaches for chemical space.
 +
 +We develop [[http://​scaffoldhunter.sourceforge.net/​|Scaffold Hunter]], a tool for the analysis and exploration of chemical space aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g., for clustering and classification.
 +===== Publications =====
 +  * **[[http://​dx.doi.org/​10.7155/​jgaa.00338|Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics]]** \\ Nils Kriege, Petra Mutzel, Till Schäfer \\ Journal of Graph Algorithms and Applications (JGAA), vol. 18, no. 4, 577-602, 2014.
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 +  * **Explicit versus Implicit Graph Feature Maps: A Computational Phase Transition for Walk Kernels** \\ Nils Kriege, ​ Marion Neumann, Kristian Kersting, Petra Mutzel \\ International Conference on Data Mining (ICDM) 2014, to appear.
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-319-13075-0_7|Enumeration of Maximum Common Subtree Isomorphisms with Polynomial-Delay]]** \\ Andre Droschinsky,​ Bernhard Heinemann, Nils Kriege, Petra Mutzel \\ International Symposium on Algorithms and Computation (ISAAC) 2014, 81-93.
 +
 +  * **On Maximum Common Subgraph Problems in Series-Parallel Graphs** \\ Nils Kriege, Florian Kurpicz, Petra Mutzel \\ International Workshop on Combinatorial Algorithms (IWOCA) 2014, to appear.
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-662-44465-8_43|Finding Maximum Common Biconnected Subgraphs in Series-Parallel Graphs]]** \\ Nils Kriege, Petra Mutzel \\ International Symposium on Mathematical Foundations of Computer Science (MFCS) 2014, 505-516.
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-662-44911-0_6|The Landscape Metaphor for Visualization of Molecular Similarities]]** \\ Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel \\ in: Battiato, S.; Coquillart, S.; Laramee, R. S.; Kerren, A. & Braz, J. (Eds.), Computer Vision, Imaging and Computer Graphics. Theory and Application;​ Communications in Computer and Information Science, 2014, 458, 85-100.
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-319-04657-0_11|SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search]]** \\ Till Schäfer, Petra Mutzel, Nils Kriege \\ International Workshop on Algorithms and Computation (WALCOM) 2014, 90-101
 +
 +  * **Scaffold Hunter: Visual Analysis of Biological Activity Data** \\ Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer \\ German Conference on Chemoinformatics,​ Fulda, Germany, 2013.
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 +  * **[[http://​ls11-www.cs.tu-dortmund.de/​_media/​techreports/​tr13-03.pdf|SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search]]** [Kriege/​etal/​2013] \\ Nils Kriege, Petra Mutzel, Till Schäfer \\ in: Algorithm Engineering Reports, TR13-1-003, TU Dortmund, 2013
 +
 +  * **[[http://​dx.doi.org/​10.1002/​minf.201300087|Visual Analysis of Biological Activity Data with Scaffold Hunter]]** \\ Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer \\ Molecular Informatics,​ WILEY-VCH Verlag, 2013, 32, 964-975
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-642-38241-3_12|Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space]]** \\ Karsten Klein, Nils Kriege, Petra Mutzel \\ in: G. Csurka, M. Kraus, R. Laramee, P. Richard, J. Braz (Eds.), Computer Vision, Imaging and Computer Graphics. Theory and Application;​ Communications in Computer and Information Science, 2013, 359, 176-192
 +
 +  * **[[http://​dx.doi.org/​10.5220/​0004267205150524|MolMap - Visualizing Molecule Libraries as Topographic Maps]]** [Gronemann/​etal/​2013] \\ Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel \\ International Conference on Information Visualization Theory and Applications (IVAPP) 2013, 537-541, **Best Paper Award**.
 +
 +  * **[[http://​dx.doi.org/​10.4230/​OASIcs.GCB.2012.82|Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs]]** \\ Marianna D'​Addario,​ Nils Kriege, Sven Rahmann \\ German Conference on Bioinformatics (GCB) 2012, Jena, Germany, 82-92.
 +
 +  * **[[http://​icml.cc/​discuss/​2012/​542.html|Subgraph Matching Kernels for Attributed Graphs]]** [Kriege/​etal/​2012] \\ Nils Kriege, Petra Mutzel \\ International Conference on Machine Learning (ICML) 2012.
 +
 +  * **[[http://​dx.doi.org/​10.5220/​0003836806260635|Scaffold Hunter - Visual Analysis of Chemical Compound Databases]]** [Klein/​etal/​2012] \\ Karsten Klein, Nils Kriege, Petra Mutzel \\ International Conference on Information Visualization Theory and Applications (IVAPP) 2012, 626-635, **Best Paper Award**.
 +
 +  * **[[http://​dx.doi.org/​10.1109/​ICDE.2011.5767909|CT-Index:​ Fingerprint-based Graph Indexing Combining Cycles and Trees]]** [Klein/​etal/​2011] \\ Karsten Klein, Nils Kriege, Petra Mutzel \\ in: Proceedings of the 27th International Conference on Data Engineering (ICDE) 2011, Hannover, Germany, 1115-1126
 +
 +  * **[[http://​dx.doi.org/​10.1007/​978-3-642-11805-0_47|Scaffold Hunter - Interactive Exploration of Chemical Space]]** \\ Karsten Klein, Nils Kriege, Petra Mutzel, Herbert Waldmann, Stefan Wetzel \\ in: D. Eppstein, E. Gansner (Eds.), 17th Symposium on Graph Drawing 2009, Chicago \\ Lecture Notes in Computer Science 5849, 2010, 426-427
 +
 +  * **[[http://​dx.doi.org/​10.1038/​nchembio.187|Interactive Exploration of Chemical Space with Scaffold Hunter]]** [Wetzel/​etal/​2009a] \\ Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea, Petra Mutzel, Herbert Waldmann\\ Nature Chemical Biology 5, 2009, 581-583
 +
 +==== Theses ====
 +
 +  * **Effiziente Enumerationsalgorithmen für Common Subtree Probleme** \\ Andre Droschinsky,​ Diploma Thesis, 2014
 +
 +  * **Efficient algorithms for the maximum common subgraph problem in partial 2-trees** \\ Florian Kurpicz, Master Thesis, 2014
 +
 +  * **Verfeinerung bitvektorbasierter Filterverfahren zur Substruktursuche in Molekülgraphdatenbanken** \\ Fabian Weißberg, Bachelor Thesis, 2013
 +
 +  * **Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße** \\ Till Schäfer, Diploma Thesis, 2012
 +
 +  * **Entwurf von Oligonukleotid-Bibliotheken für die DNA-Nanotechnologie** \\ Marianna D'​Addario,​ Diploma Thesis, 2011 (Collaboration with [[staff:​rahmann|Prof. Rahmann]] and Prof. Niemeyer, Chemistry)
 +
 +  * **[[http://​ls11-www.cs.tu-dortmund.de/​_media/​techreports/​tr10-01.pdf|Erweiterte Substruktursuche in Moleküldatenbanken und ihre Integration in Scaffold Hunter]]** \\ Nils Kriege \\ in: TR10-1-001, Algorithm Engineering Report, Fakultät für Informatik, TU Dortmund, 2010.\\ Diploma Thesis, TU Dortmund, December 2009.
  
 
Last modified: 2015-09-11 13:18 (external edit)
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