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[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.
[HRH+12] Hellmuth, M., Rosales, M.-H., Huber, K. T., Moulton, V., Stadler, P.F., Wieseke, N. Orthology Relations, Symbolic Ultrametrics, and Cographs, J. Math. Biol., 2012
[HOS12] Hellmuth, M., Ostermeier, L., Stadler, P.F., Minimum Cycle Bases of Lexicographic Products, Ars Math. Contemporanea, 5, 2, 219–230, 2012
[LLH+12] Laczny, C., Leidinger, P., Haas, J., Ludwig, N., Backes, C., Gerasch, A., Kaufmann, M., Vogel, B., Katus, H.-A., Meder, B., Stahler, C., Meese, E., Lenhof, H.-P., and Keller, A.: miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics,13:36, 2012.
[HOS12] Hellmuth, M., Ostermeier, L., Stadler, P.F., A Survey on Hypergraph Products, Math. Comp. Sci., 6, 1, 1-32, 2012


[BRK+11] Backes, C., Rurainski, A., Klau, G.W., Müller, O., Stöckel, D., Gerasch, A., Küntzer, J., Maisel, D., Ludwig, N., Hein, M., Keller, A., Burtscher, H., Kaufmann, M., Meese, E., and Lenhof, H.-P.: An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res., 40(6):e43, 2011.
[SKN+11] Schmitt, J., Keller, A., Nourkami-Tutdibi, N., Heisel, S., Habel, N., Leidinger, P., Ludwig, N., Gessler, M., Graf, N., Berthold, F., Lenhof, H.-P., and Meese, E.: Autoantibody signature differentiates wilms tumor patients from neuroblastoma patients. PLoS ONE 6(12): e28951, 2011.
[DLH11] Dehof, A.K., Lenhof, H.-P., and Hildebrandt, A.: Predicting Protein NMR Chemical Shifts in the Presence of Ligands and Ions using Force Field-based Features. Proceedings of the German Conference on Bioinformatics (GCB), 2011.
[KLB+11] Keller, A., Leidinger, P., Bauer, A., Elsharawy, A., Haas, A., Backes, C., Wendschlag, A., Giese, N., Tjaden, C., Ott, K., Werner, J., Hackert, T., Ruprecht, K., Huwer, H., Huebers, J., Jacobs, G., Rosenstiel, P., Dommisch, H., Schaefer, A., Müller-Quernheim, J., Wullich, B., Keck, B., Graf, N., Reichrath, J., Vogel, B., Nebel, A., Jager, SU, Staehler, P., Amarantos, I., Biosquerin, V., Staehler, C., Beier, M., Scheffler, M., Büchler, MW., Wischhusen, J., Haeusler, SF, Dietl, J., Hofmann, S., Lenhof, H.-P., Schreiber, S., Katus, HA., Rottbauer, W., Meder, B., Hoheisel, JD., Franke, A. & Meese, E.: Toward the blood-borne miRNome of human diseases. Nat Methods, 8: 841-43, 2011.
[BLL+11] Backes, C., Ludwig, N., Leidinger, P., Harz, C., Hoffmann, J., Keller, A., Meese, E. & Lenhof, H.-P.: Immunogenicity of autoantigens. BMC Genomics, 12:340, 2011.
[SKB+11] Schuler, M., Keller, A., Backes, C., Phillipar, K., Lenhof, H.-P. & Bauer, P.: Transcriptome analysis by Gene Trail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biology, 11:87, 2011.
[KML+11] Küntzer, J., Maisel, D., Lenhof, H.-P., Klostermann, S. & Burtscher H.: The Roche Cancer Genome Database 2.0. BMC Med Genomics, 4:43, 2011.
[KLG+11] Keller, A., Leidinger, P., Gislefoss, R., Haugen, A., Langseth, H., Staehler, P., Lenhof, H.-P. & Meese, E.: Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis. RNA Biol., 8(3): 506-16, 2011.
[LKB+11] Leidinger, P., Keller, A., Borries, A. Huwer, H., Rohling, M. Huebers, J., Lenhof, H.-P. & Meese, E.: Specific peripheral miRNA profiles for distinguishing lung cancer from COPD. Lung Cancer, 74(1): 41-7, 2011.
[DRB+11] Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P. & Hildebrandt, A.: Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 27(13), 2011.


[HDR+10] Hildebrandt, A., Dehof, A.K., Rurainski, A., Bertsch, A., Schumann, M., Toussaint, N.C., Moll, A., Stöckel, D., Nickels, S., Müller, S.C., Lenhof, H.-P. & Kohlbacher, O.: BALL - Biochemical Algorithms Library 1.3. BMC Bioinformatics, 11:531, 2010.
[SER+10] Singh, K.K., Erkelenz, S., Rattay, S., Dehof, A.-K., Hildebrandt, A., Schulze-Osthoff, K., Schaal, H., and Schwerk, C.: Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold. RNA, 2010, 16(12), 2442-2454, 2010.
[MDG+10] Marsalek, L., Georgiev, I., Dehof, A.K., Lenhof, H.-P., Slusallek, P., and Hildebrandt, A.: Real-time Ray Tracing of Complex Molecular Scenes. Proceedings of the IVbm 10 - Information Visualization in Biomedical Informatics, 2010.
[MTH+10] Melchior, K., Tholey, A., Heisel, S., Keller, A., Lenhof, H.-P., Meese, E. & Huber C.G.: Protein-versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples. J Chromatogr A., 1217(40): 6159-68, 2010.
[LKB+10] Leidinger, P., Keller, A., Borries, A., Reichrath, J., Rass, K., Jager, S.U., Lenhof, H.-P. & Meese, E.. (2010). High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer 2010, 10:262.
[FLK+10] Fischer, U., Leidinger, P., Keller, A., Folarin, A., Ketter, R., Graf, N., Lenhof, H.-P. & Meese, E. (2010). Amplicons on chromosome 12q13-21 in glioblastoma recurrences. Int J Cancer, 2010, 126(11):2594-602.
[PGDN+10] M. Phillips, I. Georgiev, A.K. Dehof, L. Marsalek, H.-P. Lenhof, A. Hildebrandt, and P. Slusallek: (2010) Measuring Properties of Molecular Surfaces Using Ray Casting. HiCOMB 2010, Proceedings of 9th International Workshop on High Performance Computational Biology
[LKH+10] Ludwig, N., Keller, A., Heisel, S., Leidinger, P., Rheinheimer, S., Andres, C., Stephan, B., Steudel, W.-I., Donauer, E., Graf, N., Burgeth, B., Weickert, J., Lenhof, H.-P., & Meese, E. (2010). Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%. Int J Cancer, 9999(999A)
[KEL+10] Küntzer, J., Eggle, D., Lenhof, H.-P., Burtscher, H. & Klostermann, S.: The Roche Cancer Genome Database (RCGDB). Hum Mutat. 3(4), 407-13, 2010.