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Publications

2014

[BRS+14] Backes, C., Rühle, F., Stoll, M., Haas, J., Frese, K., Franke, A., Lieb, W., Wichmann, H.-E., Weis, T., Kloos, W., Lenhof, H.-P., Meese, E., Katus, H., Meder, B., and Keller, A. Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. BMC Genomics. 2014 Jul 22;15(1):622. [Epub ahead of print]
[HNO14] Hellmuth, M., Noll, M., and Ostermeier, L.: Strong Products of Hypergraphs: Unique Prime Factorization Theorems and Algorithms, Discrete Applied Mathematics, 171, 60-71, 2014
[AHH14] Althaus, E., Hildebrandt, A. and Hildebrandt, A.K. A Greedy Algorithm for Hierarchical Complete Linkage Clustering. 1st International Conference on Algorithms for Computational Biology (AlCoB 2014)
[HDL+14] Hildebrandt, A.K., Dietzen, M., Lengauer, T., Lenhof, H.-P., Althaus, E., and Hildebrandt, A. Efficient computation of root mean square deviations under rigid transformations. J Comput Chem. 35(10):765–771, 2014
[HSH+14] Hoang-Vu Dang and Schmidt, B. and Hildebrandt, A. and Hildebrandt, A.K. Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP). ISSN:1066-6192, 2014
[GFK+14] Gerasch, A., Faber, D., Küntzer, J., Niermann, J., Kohlbacher, O., Lenhof, H.-P., and Kaufmann, M.: BiNA: A Visual Analytics Tool for Biological Network Data. PLOS ONE 10.1371, 2014.
[HOS14] Hellmuth, M., Ostermeier, L., and Stadler, P.F.: Unique Square Property, Equitable Partitions, and Product-like Graphs, Discrete Mathematics, 320, 0, 92-103, 2014.
[HHW+14] Hernandez-Rosales, M., Hellmuth M., Wieseke N., and Stadler, P.F.: Simulation of gene family histories, BMC Bioinformatics, 15, Suppl 3, A8, 2014.
[HLS14] Hellmuth, M., Leydold, J., and Stadler, P.F.: Convex Cycle Bases, Ars Math. Contemporanea, 7, 1, 123-140, 2014.

2013

[HWT13] Hellmuth, M., Imrich, W., and Kupka, T.: Partial Star Products: A Local Covering Approach for the Recognition of Approximate Cartesian Product Graphs. Mathematics in Computer Science, 7(3):255-273,2013.
[CEG+13] Cabezas-Wallscheid, N., Eichwald, V., de Graaf, J., Löwer, M., Lehr, H.-A., Kreft, A., Eshkind, L., Hildebrandt, A., Abassi, Y., Heck, R., Dehof, A. K., Ohngemach, S., Sprengel, R., Wörtge, S., Schmitt, S., Lotz, J., Meyer, C., Kindler, T., Zhang, D.-E., Kaina, B., Castle, J. C., Trumpp, A., Sahin, U. and Bockamp, E.: Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model. EMBO Mol Med. doi: 10.1002/emmm.201302661, 2013.
[NSM+13] Nickels, S., Stöckel, D., Mueller, S.C., Lenhof, H.-P., Hildebrandt, A., and Dehof, A.K.: PresentaBALL – a Powerful Package for Presentations and Lessons in Structural Biology. BioVis - 3rd IEEE Symposium on Biological Data Visualization, 2013.
[HEL+13] Hildebrandt, A.K., Althaus, E., Lenhof, H.P., Hung, C.W., Tholey, A., and Hildebrandt, A.: Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. Proceedings of the German Conference on Bioinformatics (GCB), 2013.
[H13] Hellmuth, M.: On the Complexity of Recognizing S-composite and S-prime Graphs, Discrete Appl. Math., 161, 7-8, 1006-1013, 2013.
[SMK+13] Stöckel, D., Müller, O., Kehl, T., Gerasch, A., Backes, C., Rurainski, A., Keller, A., Kaufmann, M., and Lenhof, H.-P.: NetworkTrail - A web service for identifying and visualizing deregulated subnetworks. Bioinformatics 29 (13):1702-03, 2013.
[LBH+13] Li, D., Beisswenger, C., Herr, C., Hellberg, J., Han, G., Zakharkina, T., Voss, M., Wiewrodt, R., Bohle, R.M., Menger, M.D., Schmid, R.M., Stöckel, D., Lenhof, H.-P., and Bals, R.: Myeloid cell RelA/p65 promotes lung cancer proliferation through Wnt/β-catenin signaling in murine and human tumor cells. Oncogene, doi: 10.1038/onc.2013.75, 2013.
[DLL+13] Dehof, A.K., Loew, S., Lenhof, H.-P., & Hildebrandt, A.: NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction. BMC Bioinformatics, 14(1):98, 2013.

2012

[RHH+12] Rosales, M. H., Hellmuth, M., Huber, K. T., Moulton, V., Wieseke, N. & Stadler, P.F. (2012). From Event-Labeled Gene Trees to Species Trees, BMC Bioinformatics, 13, Suppl 19, S6, 2012
[LKL+12] Ludwig, N., Keller, A., Leidinger, P., Harz, C., Backes, C., Lenhof, H.-P. & Meese, E.: Is there a general autoantibody signature for cancer? Eur J Cancer, 48(15):2451-61, 2012.
[SBN+12] Schmitt, J., Backes, C., Nourkami-Tutdibi, N., Leidinger, P., Deutscher, S., Beier, M., Gessler, M., Graf, N., Lenhof, H.-P., Keller, A., and Meese, E.: Treatment-independent miRNA signature in blood of wilms tumor patients. BMC Genomics, 13:379, 2012.
[SHK+12] Schmitt, J., Heisel, S., Keller, A., Leidinger, P., Ludwig, N., Habel, N., Furtwängler, R., Nourkami-Tutdibi, N., Wegert, J., Grundy, P., Gessler, M., Graf, N., Lenhof, H.-P. & Meese, E.: Multicenter study identified molecular blood-born protein signatures for Wilms Tumor. Int J Cancer, 131(3): 673-682, 2012.
[NSM+12] Nickels, S, Sminia, H, Mueller, S, Kools, B, A.K. Dehof, H.-P. Lenhof, and A. Hildebrandt: (2012) ProteinScanAR - An augmented reality web application for high school education in biomolecular life sciences. Proceedings of the 6th International Symposium on Information Visualization in Biomedical Informatics (IVBI 2012).
[GHS12] Gringmann, L., Hellmuth, M. & Stadler, P.F. (2012). The Cartesian Product of Hypergraphs, Journal of Graph Theory, 70, 2, 180-196, 2012
[HGS12] Hellmuth, M., Gringmann, L., Stadler, P.F. (2012). Diagonalized Cartesian Products of S-prime graphs are S-prime, Discrete Mathematics, 312, 1, 74-80, 2012
[BDZ+12] Bogojeska, J., Stöckel, D., Zazzi, Z., Rolf, K., Francesca, I., Michal, R-Z., Lengauer, T. History-alignment models for bias-aware prediction of virological response to HIV combination therapy. AISTATS 2012.

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Recent Publications

1st International Conference on Algorithms for Computational Biology, 01 Jul 2014: A Greedy Algorithm for Hierarchical Complete Linkage Clustering
22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), 14 Feb 2014: Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs