Publications (Lenhof) – Lenhof Group

2023

[23+HZS] Henn, D., Zhao, Sivarajav, D., Trotsyuk, A., Bonham, C.A., Fischer, K.S., Kehl, T., Fehlmann, T., Greco, A.H., Kussie, H.C., Moortgat Illouz, S.E., Padmanabhan, J., Barrera, J.A., Kneser, U., Lenhof H.-P., Januszyk, M., Levi, B., Keller, A., Longaker M.T., Chen, K., Qi, L.S., Gurtner, G.C. Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing. Nature Communications, 2023. DOI: 10.1038/s41467-023-40519-z.

[22+DHK] Diener, C., Hart, M., Kehl, T., Becker-Dorison, A., Tänzer, T., Schub, D., Krammes, L., Sester, M., Keller, A., Unger, M., Walch-Rückheim, B., Lenhof, H.-P., Meese, E. Time-resolved RNA signatures of CD4+ T cells in Parkinson’s disease. Nature Cell Death Discovery, 2023. DOI: 10.1038/s41420-023-01333-0.

2022

[MNS+22] Menegatti, J., Nakel, J.,1, Stepanov, Y.K., Caban, K.M., Ludwig, N., Nord, R., Pfitzner, T., Yazdani, M., Vilimova, M., Kehl, T., Lenhof, H.-P., Philipp, S.E., Meese, E., Fröhlich, T., Grässer, F.A., 1, Hart, M. Changes of Protein Expression after CRISPR/Cas9 Knockout of miRNA-142 in Cell Lines Derived from Diffuse Large B-Cell Lymphoma. Cancers, 2022. DOI: 10.3390/cancers14205031.

[LEG+22] Lenhof, K., Eckhart, L., Gerstner, N., Kehl, T., Lenhof, H.-P. Simultaneous regression and classification for drug sensitivity prediction using an advanced random forest method. Scientific Reports, 2022. DOI: 10.1038/s41598-022-17609-x.

[VKK+22] Vardapour, R., Kehl, T., Kneitz; S., Ludwig, N., Meese, E., Lenhof, H.-P., Gessler, M. The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression patterns and biological processes, Oxford Academic Carcinogenesis, 2022. DOI: 10.1093/carcin/bgab110.

[SZM+22] Schick, M., Zhang, L.,Maurer, S., Maurer, H. C., Isaakaidis, K., Schneider, L., Patra, U., Schunck, K., Rohleder, E., Hofstetter, J., Baluapuri, A., Scherger, A.K., Slotta-Huspenina, J., Hettler, F., Weber, J., Engleitner, T., Maresch, R., Slawska, J., Lewis, R., Istvanffy, R., Habringer, S., Steiger, K., Baiker, A., Oostendorp, R.A.J., Miething, C., Lenhof, H.-P., Bassermann, F., Chapuy, B., Wirth, M., Wolf, E., Rad, R., Müller, S., Keller, U. Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma. Nature Communications, 2022. DOI: 10.1038/s41467-021-27704-8.

2021

[GKL+21] Gerstner, N., Kehl, T., Lenhof, K., Eckhart, L., Schneider, L., Stöckel, D., Backes, C., Meese, E., Keller, A., Lenhof, H.-P. GeneTrail: A Framework for the Analysis of High-Throughput Profiles. Frontiers in Molecular Biosciences, 2021. DOI: 10.3389/fmolb.2021.716544.

[LGK+21] Lenhof, K., Gerstner, N., Kehl, T., Eckhart, L., Schneider, L., Lenhof, H.-P. MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy. Bioinformatics, btab 546, 2021. DOI: 10.1093/bioinformatics/btab546.

[KPL+21] Kern, F., Aparicio-Puerta, E., Li, Y., Fehlmann, T., Kehl, T., Wagner, V., Ray K., Ludwig N., Lenhof, H.-P., Meese, E., Keller A. miRTargetLink 2.0—interactive miRNA target gene and target pathway networks. Nucleic Acids Research, 2021. DOI: org/10.1093/nar/gkab297.

[KKD+21] Kern, F., Krammes, L., Danz, K., Diener, C., Kehl, T., Küchler, O., Fehlmann, T., Kahraman, M., Rheinheimer, S., Aparicio-Puerta, E., Wagner, S., Ludwig, N., Backes, C., Lenhof, H.-P., von Briesen, H., Hart, M., Keller, A., Meese, E. Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Research, 2021. DOI: 10.1093/nar/gkaa1161.

2020

[FKL+20] Fehlmann, T., Kahraman, M., Ludwig, N., Backes, C., Galata, V., Keller, V., Geffers, L., Mercaldo, N., Hornung, D., Weis, T., Kayvanpour, E., Abu-Halima, M., Deuschle, C., Schulte, C., Suenkel, U., von Thaler, A.-K., Maetzler, W., Herr, C., Fähndrich, S., Vogelmeier, C., Guimaraes, P., Hecksteden, A., Meyer, T., Metzger, F., Diener, C., Deutscher, S., Abdul-Khaliq, H., Stehle, I., Haeusler, S., Meiser, A., Groesdonk, H.-V., Volk, T., Lenhof,, H.-P., Katus, H., Balling, R., Meder, B., Kruger, R., Huwer, H., Bals, R., Meese, E., Keller, A. Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients. JAMA Oncology, 2020. DOI: 10.1001/jamaoncol.2020.0001.

[BHS+20] Biederstädt, A., Zonera, H., Schneeweis, C., Schick, M., Schneider, L., Muckenhuber, A., Hong, Y., Siegers, G., Nilsson, L.,Wirth, M., Dantes, Z., Steiger, K., Schunck, K., Langston, S., Lenhof, H.-P., Coluccio, A., Orben, F., Slawska, J., Scherger, A., Saur, D., Müller, S., Rad, R., Weichert, W., Nilsson, J., Reichert, M., Schneider, G., Keller, U. SUMO pathway inhibition targets an aggressive pancreatic cancer subtype. GUT, Januar 2020. DOI: 10.1136/gutjnl-2018-317856.

[HNW-R20] Hart, M., Nickl, L., Walch-Rueckheim, B., Krammes, L., Rheinheimer, S., Diener, C.,Taenzer, T., Kehl, T., Sester, M., Lenhof, H.-P., Keller, A., Meese, E. Wrinkle in the plan: miR-34a-5p impacts chemokine signaling by modulating CXCL10/CXCL11/CXCR3-axis in CD4+, CD8+ T cells, and M1 macrophages. Journal for ImmunoTherapy of Cancer, 2020. DOI: 10.1136/jitc-2020-001617.

[DHK+20] Diener, C., Hart, M., Kehl, T., Rheinheimer, S., Ludwig, N.,Krammes, L., Pawusch, S., Lenhof, K., Tänzer, T., Schub, D., Sester, M., Walch-Rückheim,B., Keller, A., Lenhof, H.-P., Meese, E. Quantitative and time-resolved miRNA pattern of early human T cell activation. Nucleic Acids Research, 2020. DOI: 10.1093/nar/gkaa788.

[GKL+20] Gerstner, N., Kehl, T., Lenhof, K., Müller, A., Mayer, C., Eckhart, L., Grammes, N.L., Diener, C., Hart, M., Hahn, O., Walter, J., Wyss-Coray, T., Meese, E., Keller, A., Lenhof, H.-P. GeneTrail 3: advanced high-throughput enrichment analysis. Nucleic Acids Research, 2020. DOI:10.1093/nar/gkaa306.

2019

[LFK+19] Ludwig, N., Fehlmann, T., Kern, F., Gogol, M., Maetzler, W., Deutscher, S., Gurlit, S.,Schulte,C.,vonThaler, A.-K., Deuschle, C., Metzger, F., Berg, D., Suenkel, U., Keller, V., Backes, C., Lenhof, H.-P., Meese, E., Keller, A. Machine Learning to Detect Alzheimer’s Disease from Circulating Non-coding RNAs. Genomics, Proteomics & Bioinformatics, 2019. DOI:10.1016/j.gpb.2019.09.004.

[KKB+19] Kehl, T., Kern, F., Backes, C., Fehlmann, T., Stöckel, D., Meese, E., Lenhof, H.-P., Keller, A. miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. Nucleic Acids Research, Dezember 2019. DOI: 10.1093/nar/gkz1022.

[KLF+19] Keller, A., Ludwig, N., Fehlmann, T., Kahraman, M., Backes, C., Kern, F., Vogelmeier, CF., Diener, C., Fischer, U., Biertz, F., Herr, C., Jörres, RA., Lenhof, H.-P., Bals, R., Meese, E.Low miR-150-5p and miR-320b Expression Predicts Reduced Survival of COPD Patients. Cells 2019, 8(10), 1162; DOI:10.3390/cells8101162.

[HWK+19] Hart, M., Walch-Rückheim, B., Krammes, K., Kehl, T., Rheinheimer, S., Tänzer, T., Glombitza, B., Sester, M., Lenhof, H.-P., Keller, A., Meese, E. miR-34a as hub of T cell regulation networks. Journal for Immunotherapy of Cancer 7 (1), 187, 2019. DOI: 10.1186/s40425-019-0670-5.

[SKT+19] Schneider, L., Kehl, T., Thedinga, K., Grammes, N. L., Backes, C., Mohr, C., Schubert, B., Lenhof, K., Gerstner, N., Hartkopf. A. D., Wallwiener, M., Kohlbacher, O., Keller, A., Meese, E., Graf, N., Lenhof, H.-P. ClinOmicsTrail bc: a visual analytics tool for breast cancer treatment stratification, Bioinformatics, btz302, 2019. DOI: 10.1093/bioinformatics/btz302.

[FBP+19] Fehlmann, T., Backes, C., Pirritano, M., Laufer, T., Galata, V., Kern, F., Kahraman, M., Gasparoni, G., Ludwig, N., Lenhof, H.-P., Gregersen, H., Francke, R., Meese, E., Simon, M., Keller, A. The sncRNA Zoo: a repository for circulating small noncoding RNAs in animal. Nucleic Acids Research 47 (9), 4431-4441, 2019. DOI: 10.1093/nar/gkz227.

[KSK+19] 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, H.-P. The role of TCF3 as potential master regulator in blastemal Wilms tumors. International Journal of Cancer 144 (6), 1432-1443, 2019. DOI: 10.1002/ijc.31834.

[AFF+19] Alles, J., Fehlmann, T., Fischer, U., Backes, C., Galata, V., Minet, M., Har, M., Abu-Halima, M., Grässer. F.A., Lenhof, H.-P., Keller, A., Meese, E. An estimate of the total number of true human miRNAs. Nucleic Acids Research 47 (7), 3353-3364, 2019. DOI: 10.1093/nar/gkz097.

[HWF+19] Hart, M., Walch-Rückheim, B., Friedmann, K.S., Rheinheimer, S., Tänzer, T., Glombitza, B., Sester, M., Lenhof, H.-P., Hoth, M., Schwarz, E.C., Keller, A., Meese, E. miR-34a: a new player in the regulation of T cell function by modulation of NF-κB signaling. Cell Death & Disease 10 (2), 46, 2019. DOI: 10.1038/s41419-018-1295-1.

[FLB+19] 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, H.-P., Meese, E., Keller, A. Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity. RNA Biology 16 (1), 93-103, 2019. DOI: 10.1080/15476286.2018.1559689.

2018

[DHA+18] Diener, C., Hart, M., Alansary, D., Poth, V., Walch-Rückheim, B., Menegatti, J., Grässer, F., Fehlmann, T., Rheinheimer, S., Niemeyer, B.A., Lenhof, H.-P., Keller, A., Meese, E. Modulation of intracellular calcium signaling by microRNA-34a-5p. Cell Death & Disease 9 (10), 1008, 2018. DOI: 10.1038/s41419-018-1050-7.

[KFL+18] Keller, A., Fehlmann, T., Ludwig, N., Kahraman, M., Laufer, T., Backes, C., Vogelmeier, C., Diener, C., Biertz, F., Herr, C., Jörres, R.A., Lenhof, H.-P., Meese, E., Bals, R., COSYCONET Study Group.Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development. Genomics, Proteomics & Bioinformatics 16 (3), 162-171, 2018. DOI: 10.1016/j.gpb.2018.06.001.

[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, H.-P. REGGAE: a novel approach for the identification of key transcriptional regulators. Bioinformatics. Bioinformatics 34 (20), 3503-3510, 2018. DOI: 10.1093/bioinformatics/bty372.

2017

[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

[FBA+17] Fehlmann, T., Backes, C., Alles, J., Fischer, U., Hart, M., Kern, F., Langseth, H., Rounge, T., Umu, S.U., Kahraman, M., Laufer, T., Haas, J., Staehler, C., Ludwig, N., Hübenthal, M., Meder, B., Franke, A., Lenhof, H.-P., Meese, E., Keller, A. A high-resolution map of the human small non-coding transcriptome. Bioinformatics 34 (10), 1621-1628, 2017. DOI: 10.1093/bioinformatics/btx814.

[KBK+17] Kehl, T., Backes, C., Kern, F., Fehlmann, T., Ludwig, N., Meese, E., Lenhof, H.-P., Keller, A. About miRNAs, miRNA seeds, target genes and target pathways. Oncotarget 8 (63), 107167, 2017. DOI: 10.18632/oncotarget.22363.

[BFK+17] Backes, C., Fehlmann, T., Kern, F., Kehl, T., Lenhof, H.-P., Meese, E., Keller, A. miRCarta: a central repository for collecting miRNA candidates. Nucleic Acids Research 46 (D1), D160-D167, 2017. DOI: 10.1093/nar/gkx851.

[KSS+17] Kehl, T., Schneider, L., Schmidt, F., Stöckel, D., Gerstne,r N., Backes, C., Meese, E., Keller, A., Schulz, M.H., Lenhof, H.-P. RegulatorTrail: a web service for the identification of key transcriptional regulators. Nucleic Acids Research 45 (W1), W146-W153, 2017. DOI: 10.1093/nar/gkx350.

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. International Journal of Molecular Sciences. 2016 Mar 30;17(4). pii: E475. doi: 10.3390/ijms17040475.

[BLL+16] Backes, C., Ludwig, N., Leidinger, P., Huwer, H., Tenzer, S., Fehlmann, T., Franke, A., Meese, E., Lenhof, H.-P., Keller, A. Paired proteomics, transcriptomics and miRNomics in non-small cell lung cancers: known and novel signaling cascades. Oncotarget 7 (44), 71514, 2017. DOI: 10.18632/oncotarget.11723.

[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

[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

[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

[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.

[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

[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]

[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.

2014

[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

[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

[HLS14] Hellmuth, M., Leydold, J., and Stadler, P.F.: Convex Cycle Bases, Ars Math. Contemporanea, 7, 1, 123-140, 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

[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. Jul 22;15(1):622, 2014.

[HMO+15] Hellmuth, M., Marc, T., Ostermeier, L., and Stadler, P. F.: The Relaxed Square Property. Australasian Journal of Combinatorics, 62, 3, 240-270, 2015

[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)

[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.

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.

[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.

[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.

[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.

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.

[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).

[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

[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.

[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.

[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

2011

[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.

[NKG+10] Nieselt, K., Kaufmann, M., Gerasch, A., Lenhof, H.-P., Spehr, M., Hesse, St., and Gumhold, S.: Visuelle Analytik biologischer Daten. Informatik Spektrum, 33(6):559-568, 2010.

[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.

[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.

[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.

[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.

[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.

[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.

2010

[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.

[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)

[BML+10] Backes, C., Meese, E., Lenhof, H.-P., & Keller, A. (2010). A dictionary on microRNAs and their putative target pathways. Nucleic Acids Res. 2010 Mar 18. [Epub ahead of print].

[FRL+10] Jan Fuhrmann, Alexander Rurainski, Hans-Peter Lenhof, and Dirk Neumann. A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem., 31(9), 1911-18, 2010.

[MGD+10] Marsalek, L., Georgiev, I., Dehof, A.K., Lenhof, H.-P., Slusallek, P. & Hildebrandt, A. (2010). Real-Time Ray Tracing of Complex Molecular Scenes. Proceedings of the IVBI 2010 – Information Visualization in Biomedical Informatics.

[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.

[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.

[LKH+10] Leidinger, P., Keller, A., Heisel, S. Ludwig, N., Rheinheimer, S., Klein, V., Andres, C., Staratschek-Jox, A., Wolf, J., Stoelben, E., Stephan, B., Stehle, I., Hamacher, J., Huwer, H., Lenhof, H.-P., & Meese, E. (2010). Identification of lung cancer with high sensitivity and specificity by blood testing. Respiratory Research 2010, 11:18.

2009

[DGMS+09] A. K. Dehof, I. Georgiev, L. Marsalek, D. Stöckel, S. Nickels, H.-P. Lenhof, P. Slusallek and A. Hildebrandt (2009): Visual Computing in Computer Aided Drug Design. Visual Computing Research Conference, Saarbrücken, Germany, 8-10 December 2009

[FLK+09] Fischer, U., Leidinger, P., Keller A., Folarin, A., Ketter, R., Graf, N., Lenhof, H.-P., & Meese, E. (2009). Amplicons on chromosome 12q13-21 in glioblastoma recurrences. Int J Cancer, 126(11):2594-2602.

[DRL+09] Dehof, A. K., Rurainski, A., Lenhof, H.-P., and Hildebrandt, A.: Automated Bond Order Assignment as an Optimization Problem. Proceedings of the German Conference on Bioinformatics (GCB), Lecture Notes in Informatics, 2009.

[LKH+09] Leidinger, P., Keller, A., Heisel, S., Ludwig, N., Rheinheimer, S., Klein, V., Andres, C., Hamacher, J., Huwer, H., Stephan, B., Stehle, I., Lenhof, H.-P., & Meese, E. (2009). Novel autoantigens immunogenic in COPD patients. Respiratory Research 10(1):20.

[LKH+09] Ludwig, N., Keller A., Heisel, S., Leidinger, P., Klein, V., Rheinheimer, S., Andres, C.U., Stephan, B., Steudel, W-I., Graf, N.M., Burgeth, B., Weickert, J., Lenhof, H.-P., & Meese, E. (2009). Improving Seroreactivity-Based Detection of Glioma. Neoplasia, 11 (12): 1383-89.

[KLL+09] Keller, A., Leidinger, P., Lange, J., Borries, A., Schroers, H., Scheffler, M., Lenhof, H.-P., Ruprecht, K. & Meese, E. (2009). Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One, 4(10):e7440.

[MTH+09] Melchior, K., Tholey, A., Heisel, S., Keller, A., Lenhof, H.-P., Meese, E. & Huber C.G. (2009). Proteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography-mass spectrometry-based approaches. J. Proteome Res., 8(19):4604-14.

[KLB+09] Keller, A., Leidinger, P., Borries, A., Wendschlag, A., Wucherpfennig, F., Scheffler, M., Huwer, H., Lenhof, H.-P., & Meese, E. (2009). miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microrarray experiments. BMC Cancer, 9:353.

[KBG+09] Keller, A., Backes, C., Gerasch, A., Kaufmann, M., Kohlbacher, O., Meese, E., & Lenhof, H.-P. (2009). A novel algorithm for detecting differentially regulated paths based on Gene Set Enrichment Analysis. Bioinformatics, 25:2787-94.

[KLH+09] Keller, A., Ludwig, N., Heisel, S., Leidinger, P., Andres, C., Steudel, W.-I., Huwer, H., Burgeth, B., Hein, M., Weickert, J., Meese, E. & Lenhof, H.-P. (2009). Large-scale antibody profiling of human blood sera: The future of molecular diagnosis. Informatik-Spektrum 32(4):332-338.

[AKK+09] Althaus, E., Klau, G.W., Kohlbacher, O., Lenhof, H.-P., & Reinert, K. (2009). Integer Linear Programming in Computational Biology. Lecture Notes in Computer Science (LNCS). Vol. 5760: Efficient Algorithms, 199-218, Springer.

[CSB+09] Chatterjee, I., Schmitt, S., Batzilla, C.F., Engelmann, S., Keller, A., Ring, M.W., Kautenburger, R., Ziebuhr, W., Hecker, M., Preissner, K.T., Bischoff, M., Proctor, R.A., Beck, H.P., Lenhof, H.-P., Somerville, G.A., Herrmann, M. (2009). Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence. Proteomics 9(5), 1152-76.

2008

[KBA+08] Keller, A., Backes, C., Al-Awadhi, M., Gerasch, A., Küntzer, J., Kohlbacher, O., Kaufmann, M., & Lenhof, H.-P. (2008). Gene TrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics (9), 552.

[RHL08] Rurainski, A., Hildebrandt, A., & Lenhof, H.-P. (2008). A consensus line search algorithm for molecular potential energy functions. J Comput Chem. 30 (9), 1499-1509.

[FRL+08] Fuhrmann, J., Rurainski, A., Lenhof, H.-P. & Neumann, D. (2008). A new method for the gradient-based optimization of molecular complexes. J Comput Chem. 30(9), 1371-78.

[KLB+08] Keller, A., Ludwig, N., Backes, C., Romeike, B.F., Comtesse, N., Henn, W., Steudel, W.I., Mawrin, C., Lenhof, H.-P. & Meese, E. (2008). Genome wide expression profiling identifies specific deregulated pathways in meningioma. Int J Cancer, 124(2), 346-351.

[KLC+08] Keller, A., Ludwig, N., Comtesse, N., Henn, W., Steudel, W.I., Lenhof, H.-P. & Meese, E. (2008). Combining gene expression signatures and autoantibody profiles in human meningioma. Gene Ther. 16, 184-189.

[LKC+08] Ludwig, N., Keller, A., Comtesse, N., Rheinheimer, S., Pallasch, C., Fischer U., Fassbender, K., Steudel, W.I., Lenhof, H.-P. & Meese, E. (2008). Pattern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ. Clin Cancer Res. 14(15), 4767-74.

[LKL+08] Leidinger, P., Keller, A., Ludwig, N., Rheinheimer, S., Hamacher, J., Huwer, H., Stehle, I., Lenhof, H.-P. & Meese, E. (2008). Toward an early diagnosis of lung cancer: An autoantibody signature for squamous cell lung carcinoma. Int J Cancer 123(7), 1631-36.

[HKK+08] Heisel, S.M., Ketter, R., Keller, A., Klein V., Pallasch, C.P., Lenhof, H.-P. & Meese, E. (2008). Increased seroreactivity to glioma-expressed antigen 2 in brain tumor patients under radiation. PLoS ONE, 3(5), e2164.

[FKL+08] Fischer, U., Keller, A., Leidinger, P., Deutscher, S., Heisel, S., Urbschat, S., Lenhof, H.-P. & Meese, E. (2008). A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma. Mol Cancer Res., 6(4), 576-84.

2007

[07+KBB] Küntzer, J., Backes, C., Blum, T. Gerasch, A., Kaufmann, M., Kohlbacher, O., Lenhof, H.-P. BNDB – The Biochemical Network Database. BMC Bioinformatics 8, 367 (2007). https://doi.org/10.1186/1471-2105-8-367

[07+KBL] Keller, A., Backes, C., Lenhof, H.-P. Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics 8, 290 (2007). https://doi.org/10.1186/1471-2105-8-290

Elnakady, Y.A., Rohde, M., Sasse, F., Backes, C., Keller, A., Lenhof, H.-P., Weissman, K.J. and Müller, R. (2007), Evidence for the Mode of Action of the Highly Cytotoxic Streptomyces Polyketide Kendomycin. ChemBioChem, 8: 1261-1272. https://doi.org/10.1002/cbic.200700050

[07+KCL] Keller, A., Comtesse, N., Ludwig, N., Meese, E., Lenhof, H.-P., SePaCS—a web-based application for classification of seroreactivity profiles, Nucleic Acids Research, Volume 35, Issue suppl_2, 1 July 2007, Pages W683–W687, https://doi.org/10.1093/nar/gkm262

[07+BKK] Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y.A., Müller, R., Meese, E., Lenhof, H.-P., GeneTrail—advanced gene set enrichment analysis, Nucleic Acids Research, Volume 35, Issue suppl_2, 1 July 2007, Pages W186–W192, https://doi.org/10.1093/nar/gkm323

[07+KKK] Küntzer, J., Kneissl, B., Kohlbacher, O. , Lenhof, H.-P., Abstract analysis of pathways using the BN++ software framework. BMC Syst Biol 1 (Suppl 1), P24 (2007). https://doi.org/10.1186/1752-0509-1-S1-P24

[07+CKD] Comtesse, N., Keller, A., Diesinger, I., Bauer, C., Kayser, K., Huwer, H., Lenhof, H.-P. and Meese, E. (2007), Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26-27 in squamous cell carcinoma of the lung. Int. J. Cancer, 120: 2538-2544. https://doi.org/10.1002/ijc.22585

[07+HBR] Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., Lenhof, H.-P., Electrostatic potentials of proteins in water: a structured continuum approach, Bioinformatics, Volume 23, Issue 2, January 2007, Pages e99–e103, https://doi.org/10.1093/bioinformatics/btl312

[07+HKL] Hildebrandt, A., Kohlbacher, O., Lenhof, H.-P., Modeling Protein‐Protein and Protein‐DNA Docking, Bioinformatics‐From Genomes to Therapies, Wiley‐VCH Verlag GmbH, pp. 601-650, 2007

2006

[06+KLC] Keller, A., Ludwig, N., Comtesse, N. et al. A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC Bioinformatics 7, 539 (2006). https://doi.org/10.1186/1471-2105-7-539

[06+KBG] Küntzer, J., Blum, T., Gerasch, A., Backes, C., Hildebrandt, A., Kaufmann, M., Kohlbacher, O., and Lenhof, H.-P. "BN++ – A Biological Information System" Journal of Integrative Bioinformatics, vol. 3, no. 2, 2006, pp. 148-161. https://doi.org/10.1515/jib-2006-34

[05+MHL] Moll, A., Hildebrandt, A., Lenhof, H.-P. , Kohlbacher, O. BALLView: An object-oriented molecular visualization and modeling framework. J Comput Aided Mol Des 19, 791–800 (2005). https://doi.org/10.1007/s10822-005-9027-x

2005

[05+MHL] Moll, A., Hildebrandt, A., Lenhof, H.-P., Kohlbacher,O. BALLView: a tool for research and education in molecular modeling, Bioinformatics, Volume 22, Issue 3, February 2006, Pages 365–366, https://doi.org/10.1093/bioinformatics/bti818

[05+ACL] Althaus, E., Caprara, A., Lenhof, H.-P., Reinert, K. A branch-and-cut algorithm for multiple sequence alignment.Math. Program. 105, 387–425 (2006). https://doi.org/10.1007/s10107-005-0659-3

[05+BKN] Baldes, C., Koenig, P., Neumann, D., Lenhof, H.-P., Kohlbacher, O., Lehr, C.-M. European Journal of Pharmaceutics and Biopharmaceutics, Volume 62, Issue 1, January 2006, Pages 39-43, https://doi.org/10.1016/j.ejpb.2005.06.001

[05+BKL] Backes, C., Kuentzer, J., Lenhof, H.-P., Comtesse, N., Meese, E. GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences, Nucleic Acids Research, Volume 33, Issue suppl_2, 1 July 2005, Pages W208–W213, https://doi.org/10.1093/nar/gki433

[05+CZW] Comtesse, N., Zippel, A., Walle, S., Monz, D., Backes, C., Fischer, U., Mayer, J., Ludwig, N., Hildebrandt, A., Keller, A., Steudel, W.-I., Lenhof, H.-P., Meese, E. Complex humoral immune response against a benign tumor: Frequent antibody response against specific antigens as diagnostic targets. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES Vol. 102 | No. 27, July 5, 2005, https://doi.org/10.1073/pnas.0500404102

2004

Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., Lenhof, H.-P. Novel Formulation of Nonlocal Electrostatics, Physical Review Letters, 93:10, 104-108, 2004, https://link.aps.org/doi/10.1103/PhysRevLett.93.108104

[04+DHS] Dönnes, P., Höglund, A., Sturm, M., Comtesse, N., Backes, C., Meese, E., Kohlbacher, O. and Lenhof, H.-P. (2004), Integrative analysis of cancer-related data using CAP. The FASEB Journal, 18: 1465-1467. https://doi.org/10.1096/fj.04-1797fje

[04+NLL] Neumann, D., Lehr, C.-M., Lenhof, H.-P., Kohlbacher, O. Computational modeling of the sugar–lectin interaction. Advanced drug delivery reviews, 2004, 56:4, pp. 437-457, https://doi.org/10.1016/j.addr.2003.10.019

2002

[02+ACL] Althaus, E., Caprara, A., Lenhof, H.-P., Reinert, K. Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. Bioinformatics, Vol. 18: Suppl. 2, S4-S16, 2002.

Šırava, M., Schäfer, T., Eiglsperger, M., Kaufmann, M., Kohlbacher, O., Bornberg-Bauer, E., Lenhof, H.-P. BioMiner—modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics, 18: Suppl. 2, pp. S219-S230. 2002.

[02+NKL] Neumann, D., Kohlbacher, O., Lenhof, H.-P. and Lehr, C.-M. (2002), Lectin–sugar interaction. European Journal of Biochemistry, 269: 1518-1524. https://doi.org/10.1046/j.1432-1033.2002.02800.x

2001

[01+KBM] Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., Lenhof, H.-P. Structure prediction of protein complexes by an NMR-based protein docking algorithm. J Biomol NMR 20, 15–21 (2001). https://doi.org/10.1023/A:1011216130486

[01+KBM] Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., Lenhof, H.-P. A NMR-spectra-based scoring function for protein docking. RECOMB 2001, pp. 184-192. 2001

2000

Boghossian, N.P., Kohlbacher, O., Lenhof, H.-P. Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL). ACM J. Exp. Algorithmics 5 (2000), 16–es. https://doi.org/10.1145/351827.384258

[KL00] Kohlbacher, O., & Lenhof, H.-P. (2000). BALL - Rapid Software Prototyping in Computational Molecular Biology. Bioinformatics, 16(9), 815-824. Proc. of the GCB 1999.

[KLM+00] Kececioglu, J., Lenhof, H.-P., Mehlhorn, K., Mutzel, P., & Vingron, M. (2000). A polyhedral approach to sequence alignment problems. Discrete Applied Mathematics, 104, 143-186.

Althaus, E., Kohlbacher, O., Lenhof, H.-P., Müller, P. 2000. A combinatorial approach to protein docking with flexible side-chains. In Proceedings of the fourth annual international conference on Computational molecular biology (RECOMB '00). Association for Computing Machinery, New York, NY, USA, 15–24. https://doi.org/10.1145/332306.332319

[00+JLR] Jung, B., Lenhof, H.-P., Müller, P., Rüb, C. Simulating synthetic polymer chains in parallel. Future Generation Computer Systems, Volume 16, Issue 5, March 2000, Pages 513-522, https://doi.org/10.1016/S0167-739X(99)00138-7

1999

[99+JLM] Jung, B., Lenhof, H.-P., Müller, P., Rüb, C. (1999). Simulating synthetic polymer chains in parallel. In: Sloot, P., Bubak, M., Hoekstra, A., Hertzberger, B. (eds) High-Performance Computing and Networking. HPCN-Europe 1999. Lecture Notes in Computer Science, vol 1593. Springer, Berlin, Heidelberg . https://doi.org/10.1007/BFb0100561

[99+KL] Kohlbacher, O., & Lenhof, H.-P. (1999). Rapid Software Prototyping in Computational Molecular Biology. In Proceedings of the German Conference on Bioinformatics (GCB'99)(pp. 81-92). Braunschweig, Germany: GBF-Braunschweig / Dep. of Bioinformatics.

[99+BCF] Burkhardt, S., Crauser, A., Ferragina, P., Lenhof, H.-P., Rivals, E., Vingron, M. Q-gram based database searching using a suffix array (QUASAR). Proc. of RECOMB 1999. pp. 77-83.

[99+LMR] Lenhof, H.-P., Morgenstern, B., Reinert, K. An exact solution for the segment-to-segment multiple sequence alignment problem., Bioinformatics, Volume 15, Issue 3, March 1999, Pages 203–210, https://doi.org/10.1093/bioinformatics/15.3.203

1998

[98+LRV] Lenhof, H.-P., Reinert, K., Vingron, M. A polyhedral approach to RNA sequence structure alignment. J Comput Biol. 1998 Fall;5(3):517-30. doi: 10.1089/cmb.1998.5.517. PMID: 9773347.

[LRV98] Lenhof, H.-P., Reinert, K., & Vingron, M. (1998). A polyhedral approach to RNA sequence structure alignment. Proc. of RECOMB 98, pp. 153-162.

1997

[97+JLM] Jung, B., Lenhof, H.-P., Müller, P. and Rüb, C. (1997), Langevin dynamics simulations of macromolecules on parallel computers. Macromol. Theory Simul., 6: 507-521. https://doi.org/10.1002/mats.1997.040060213

[97+VLM] Vingron, M., Lenhof, H.-P., & Mutzel, P. (1997). Computational molecular biology. In Annotated Bibliographies in Combinatorial Optimization, M.Dell'Amico, F. Maffioli, & S. Martello (Eds.) (pp. 445-471). John Wiley and Sons, ISBN: 047196574X.

[Len97] Lenhof, H.-P. (1997). New contact measures for the protein docking problem. Proc. of the First Annual International Conference on Computational Molecular Biology RECOMB 1997 (pp. 182-191).

[RLM+97] Reinert, K., Lenhof, H.-P., Mutzel, P., Mehlhorn, K., & Kececioglu, J.D. (1997). A branch-and-cut algorithm for multiple sequence alignment. RECOMB 1997 (241-250).

1995

[Len95] Lenhof, H.-P. (1995). An algorithm for the protein docking problem. German Conference on Bioinformatics, 18, 125-139.

[LS95] Lenhof, H.-P., & Smid, M. (1995). Sequential and parallel algorithms for the k closest pairs problem. Int. J. Comput. Geometry Appl., 5(3), 273-288.

[DLS+95] Datta, A., Lenhof, H.-P., Schwarz, C., & Smid, M. (1995). Static and dynamic algorithms for the k-point clustering problems. Journal of Algorithms, 19, 474-503.

[LS95] Lenhof, H.-P., & Smid, M. (1995). Maintaining a visibility map of spheres while moving the viewpoint on a circle at infinity. Algorithmica, 13, 301-312.

1994

[LS94] Lenhof, H.-P., & Smid, M. (1994). Using persistant data structures for adding range restrictions to searching problems. RAIRO Theoretical Informatics and Application, 28, 25-49.

1993

[LS93] Lenhof, H.-P., & Smid, M. (1993). An optimal construction method for generalized convex layers. International Journal of Computational Geometry & Applications, 3(3), 245-267.

1992

[LS92] Lenhof, H.-P., & Smid, M. (1992). Enumerating the k closest pairs optimally. Annual Symposium on Foundations of Computer Science (FOCS) (pp. 380-386).

[LS92] Lenhof, H.-P., & Smid, M. (1992). Maintaining the visibility map of spheres while moving the viewpoint on a circle at infinity. Third Scandinavian Workshop on Algorithm Theory (SWAT) (pp. 388-398).

1991

[LS91] Lenhof, H.-P., & Smid, M. (1991). An optimal construction method for generalized convex layers. International Symposium on Algorithms (ISA) (pp. 349-363).

Publications (Lenhof Group)