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Publications

2017

[KSS+17] Kehl, T., Schneider, L., Schmidt, F., Stöckel, D., Gerstner, N., Backes, C., Meese, E., Keller, A., Schulz, M. H. and Lenhof, H.-P.: RegulatorTrail: a web service for the identification of key transcriptional regulators. Nucl. Acids Res. (2017). doi: 10.1093/nar/gkx350.
[BKS+16] Backes, C., Kehl, T., Stöckel, D., Fehlmann, T., Schneider, L., Meese, E., Lenhof, H.-P., and Keller, A.: miRPathDB: a new dictionary on microRNAs and target pathways. Nucl. Acids Res. (2016). doi: 10.1093/nar/gkw926.

2016

[HW16] Hellmuth, M., and Wieseke, N.: From Sequence Data incl. Orthologs, Paralogs, and Xenologs to Gene and Species Trees. Chapter in Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods, Ed. Pierre Pontarotti, Springer, p. 373-392, ISBN 978-3-319-41323-5, 2016
[HHO+16] Hammack, R.H., Hellmuth, M., Ostermeier, L. and Stadler, P.F.: Associativity and non-associativity of some hypergraph products. Mathematics in Computer Science, 10(3), 403-408, 2016
[SSK+16] Schneider, L., Stöckel, D., Kehl, T., Gerasch, A., Ludwig, N., Leidinger, P., Huwer, H., Tenzer, S., Kohlbacher, O., Hildebrandt, A., Kaufmann, M., Gessler, M., Keller, A., Meese, E., Graf, N., and Lenhof, H.-P.: DrugTargetInspector: An assistance tool for patient treatment stratification. Int J Cancer. 2016 Apr 1;138(7):1765-76. doi: 10.1002/ijc.29897.
[LWB+16] Ludwig, N., Werner, T.V., Backes, C., Trampert, P., Gessler, M., Keller, A., Lenhof, H.-P., Graf, N., and Meese E.: Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes. Int J Mol Sci. 2016 Mar 30;17(4). pii: E475. doi: 10.3390/ijms17040475.
[TLB+16] Tenzer, S., Leidinger, P., Backes, C., Huwer, H., Hildebrandt, A., Lenhof, H.-P., Wesse, T., Franke, A., Meese, E., and Keller, A.: Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase. Oncotarget. 2016 Feb 22. doi: 10.18632/oncotarget.7562. [Epub ahead of print]
[HL16] Hellmuth, M., and Lehner, F.: Fast Factorization of Cartesian products of (Directed) Hypergraphs. Theor. Comp. Sci, 615, 1-11, 2016
[MBM+16] Marx, A., Backes, C., Meese, E., Lenhof, H.-P., and Keller, A.: EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon-Mann-Whitney Test. Genomics Proteomics Bioinformatics. 2016 Feb;14(1):55-61. doi: 10.1016/j.gpb.2015.11.004. [Epub 2016 Jan 29]
[SKT+16] Stöckel, D., Kehl, T., Trampert, P., Schneider, L., Backes, C., Ludwig, N., Gerasch, A., Kaufmann, M., Gessler, M., Graf, N., Meese, E., Keller, A., Lenhof, H.P.,: Multi-omics Enrichment Analysis using the GeneTrail2 Web Service. Bioinformatics 2016; doi: 10.1093/bioinformatics/btv770

2015

[SST+15] Stöckel, D., Schmidt, F., Trampert, P., and Lenhof, H.-P.: CausalTrail: Testing hypothesis using causal Bayesian networks. F1000Research 2015, 4(ISCB Comm J):1520, doi: 10.12688/f1000research.7647.1
[DKN+15] Dirnberger, M., Kehl, T, and Neumann, A.: NEFI: Network Extraction From Images. Scientific Reports (2015). doi: 10.1038/srep15669
[DOT+15] Dietzen, M., Kalinina, O.V., Taskova, K., Kneissl, B., Hildebrandt, A.-K., Jaenicke, E., Decker, H., Lengauer, T., and Hildebrandt, A.:Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces. Proteins: Structure, Function, and Bioinformatics. 2015
[HSH+15] Hoang-Vu, D., Schmidt, B., Hildebrandt, A., Tran, T.T. and Hildebrandt, A.-K: CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm International Journal of High Performance Computing Applications, 2015
[MBK+15] Mueller, S.C., Backes, C. , Kalinina, O. V., Meder, B., Stöckel, D., Lenhof, H.-P., Meese, E. and Keller, A. BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms. Genome Medicine. 2015, 7:65, DOI:10.1186/s13073-015-0190-y
[HW15] Hellmuth, M. and Wieseke, N.: On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions In D. Xu, D. Du & D. Du (Eds.), Computing and Combinatorics, Springer International Publishing. Lecture Notes in Computer Science, 9198, pp. 609-623, 2015
[LKM+15] Leidinger, P., Keller, A., Milchram, L., Harz, C., Hart, M., Werth, A., Lenhof, H.-P., Weinhäusel, A., Keck, B., Wullich, B., Ludwig, N., and Meese, E.: Combination of Autoantibody Signature with PSA Level Enables a Highly Accurate Blood-Based Differentiation of Prostate Cancer Patients from Patients with Benign Prostatic Hyperplasia. PLoS One. 2015 Jun 3;10(6):e0128235. doi: 10.1371/journal.pone.0128235. eCollection 2015.
[BCF+15] Berkemer, S., Chaves, R., Fritz, A., Hellmuth, M., Hernandez-Rosales, M., and Stadler, P.F.: Spiders can be recognized by counting their legs. Mathematics in Computer Science, DOI=10.1007/s11786-015-0233-1, 2015
[LNB+15] Ludwig, N., Nourkami-Tutdibi, N., Backes, C., Lenhof, H.-P., Graf, N., Keller, A., and Meese, E. Circulating serum miRNAs as potential biomarkers for nephroblastoma. Pediatr Blood Cancer, Wiley Periodicals, Inc.; 2015 March 18 doi: 10.1002/pbc.25481. [Epub ahead of print]
[HM15] Hellmuth, M. and Marc, T.: On the Cartesian Skeleton and the Factorization of the Strong Product of Digraphs. J. Theor. Comp. Sci, 565, 0, 16-29, 2015
[GKN+15] Gerasch, A., Küntzer, J., Niermann, P., Stöckel, S., Kaufmann, M., Kohlbacher, O., Lenhof, H.-P., Network-based interactive navigation and analysis of large biological datasets, it - Information Technology. Volume 57, Issue 1, Pages 37–48, ISSN (Online) 2196-7032, ISSN (Print) 1611-2776, DOI: 10.1515/itit-2014-1076, January 2015
[HWL+15] Hellmuth, M., Wieseke, N., Lechner, M., Lenhof, H.-P., Middendorf, M., and Stadler, P.F.: Phylogenomics with Paralogs. Proceedings of the National Academy of Sciences (PNAS), 112/7: 2058-63, 2015.
[SL15] Stöckel, D. and Lenhof, H.-P.: Detecting Dysregulated Processes and Pathways. Chapter 14, 309-324 in Nucleic Acids as Molecular Diagnostics. Edited by Andreas Keller and Eckart Meese (First Edition, Wiley-VCH Verlag, ISBN: 978-3-527-33556-5), 2015.

2014

[HIK15] Hellmuth, M., Imrich, W., Kupka, T.: Fast Recognition of Partial Star Products and Quasi Cartesian Products Ars Math. Contemporanea, 9:2 (233-252), 2015
[AKH+14] Hildebrandt, A. K., Stöckel D., Fischer, N. M., de la Garza, L., Krüger, J., Nickels, S., Röttig, M., Schärfe, C., Schumann, M., Thiel, P., Lenhof, H.-P., Kohlbacher, O., and Andreas Hildebrandt, ballaxy: web services for structural bioinformatics, Bioinformatics 2014, doi: 10.1093/bioinformatics/btu574

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