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Publications

2019

[AFF+19] Alles J, Fehlmann T, Fischer U, Backes C, Galata V, Minet M, Hart M, Abu-Halima M, Grässer FA, Lenhof HP, Keller A, Meese E Author Notes
[HWF+19] Hart M, Walch-Rückheim B, Friedmann KS, Rheinheimer S, Tänzer T, Glombitza B, Sester M, Lenhof HP, Hoth M, Schwarz EC, Keller A, Meese E. miR-34a: a new player in the regulation of T cell function by modulation of NF-κB signaling.Cell Death & Diseasevolume 10, Article number: 46 (2019)

2018

[FLB+18] Fehlmann T, Laufer T, Backes C, Kahramann M, Alles J, Fischer U, Minet M, Ludwig N, Kern F, Kehl T, Galata V, Düsterloh A, Schrörs H, Kohlhaas J, Bals R, Huwer H, Geffers L, Krüger R, Balling B, Lenhof HP, Meese E, Keller A. Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity. RNA Biology, Dec 2018.
[DHA+18] Diener C, Hart M, Alansary D, Poth V, Walch-Rückheim B, Menegatti J, Grässer F, Fehlmann T, Rheinheimer S, Niemeyer BA, Lenhof HP, Keller A, Meese E. Modulation of intracellular calcium signaling by microRNA-34a-5p, Cell Death & Diseasevolume 9, Article number: 1008 (2018).
[KSK+18] Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. The role of TCF3 as potential master regulator in blastemal Wilms tumors. International Journal of Cancer. (in production).
[KFL+18] Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R, for the COSYCONET Study Group.Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development, Genomics Proteomics & Bioinformatics.
[FBA+17] Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, Langseth H, Rounge T, Umu SU, Kahraman M, Laufer T, Haas J, Staehler C, Ludwig N, Hübenthal M, Meder B, Franke A, Lenhof HP, Meese E, Keller A. A high-resolution map of the human small non-coding transcriptome. Bioinformatics. 2018 May 15;34(10):1621-1628. doi: 10.1093/bioinformatics/btx814.
[KSK+18] Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Schick M, Keller U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. REGGAE: a novel approach for the identification of key transcriptional regulators. Bioinformatics. 2018 May 7. doi: 10.1093/bioinformatics/bty372.

2017

[FBA+17] Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, Langseth H, Rounge T, Umu SU, Kahraman M, Laufer T, Haas J, Staehler C, Ludwig N, Hübenthal M, Meder B, Franke A, Lenhof HP, Meese E, Keller A.OXFORD ACADEMIC, Bioinformatics, Volume 34, Issue 10, 15 May 2018, Pages 1621–1628.
[KBK+17] Kehl T, Backes C, Kern F, Fehlmann T, Ludwig N, Meese E, Lenhof HP, Keller A. About miRNAs, miRNA seeds, target genes and target pathways. Oncotarget. 2017 Nov 9;8(63):107167-107175. doi: 10.18632/oncotarget.22363. eCollection 2017 Dec 5.
[BFK+17] Backes C, Fehlmann T, Kern F, Kehl T, Lenhof HP, Meese E, Keller A. miRCarta: a central repository for collecting miRNA candidates. Nucleic acids research 46 (D1), D160-D167. doi: 10.1093/nar/gkx851.
[KSS+17] Kehl T, Schneider L, Schmidt F, Stöckel D, Gerstner N, Backes C, Meese E, Keller A, Schulz MH, Lenhof HP. RegulatorTrail: a web service for the identification of key transcriptional regulators. Nucleic Acids Res. 2017 Jul 3;45(W1):W146-W153. doi: 10.1093/nar/gkx350.
[BKS+17] Backes C., Kehl T., Stöckel D., Fehlmann T., Schneider L., Meese E., Lenhof H.-P., Keller A. miRPathDB: a new dictionary on microRNAs and target pathways. Nucleic Acids Res. 2017 Jan 4;45(D1):D90-D96. doi: 10.1093/nar/gkw926

2016

[BLL+16] Backes C, Ludwig N, Leidinger P, Huwer H, Tenzer S, Fehlmann T, Franke A, Meese E, Lenhof HP, Keller A. Paired proteomics, transcriptomics and miRNomics in non-small cell lung cancers: known and novel signaling cascades. Oncotarget. 2016 Nov 1;7(44):71514-71525. doi: 10.18632/oncotarget.11723.
[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]
[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
[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.

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