Publications

[NKG+10]

Nieselt, K., Kaufmann, M., Gerasch, A., Lenhof, H.-P., Spehr, M., Hesse, S. & Gumhold, S. (2010). Visuelle Analytik biologischer Daten. Informatik Spektrum, Online First™, 29 September 2010.

[MTH+10]

Melchior, K., Tholey, A., Heisel, S., Keller, A., Lenhof, H.-P., Meese, E. & Huber CG. (2010). 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. 2010 Juli 21. [Epub ahead of print].

[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.

[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), NA.

[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].

[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.

[FLK+10]

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.

[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.

[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.

[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.

[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. 

[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. 

[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.

[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.

[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.  

[KBB+07]

Küntzer, J., Backes, C., Blum, T., Gerasch, A., Kaufmann, M., Kohlbacher, O., & Lenhof, H.-P. (2007). BNDB - The Biochemical Network Database.  BMC Bioinformatics, 8, 367.

[KBL07]

Keller, A., Backes, C., & Lenhof, H.-P. (2007). Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics, 8, 290.         

[ERS+07] 

Elnakady, Y. A., Rohde, M., Sasse, F., Backes, C., Keller, A., Lenhof, H.-P., Weissmann, K. J., & Müller, R. (2007). Evidence for the Mode of Action of the Highly Cytotoxic Streptomyces Polyketide Kendomycin. Chembiochem. 8(11), 1261-72. 

[HBR+07]

Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., & Lenhof, H.-P. (2007). Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics, Proceedings - European Conference on Computational Biology ECCB 2006 -, 23(2), e99-103.

[HKL07]

Hildebrandt, A., Kohlbacher, O., & Lenhof, H.-P. (2007). Modeling protein-protein and protein-dna docking. In T. Lengauer (Eds.), Bioinformatics - From Genomes to Therapies (2, pp. 601-644).

[CKD+07]

Comtesse, N., Keller, A., Diesinger, I., Bauer, C., Kayser, K., Huwer, H., Lenhof, H.-P., & 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(12), 2538-44.

[KCL+07]

Keller, A., Comtesse, N., Ludwig, N., Meese, E., & Lenhof, H.-P. (2007). Sepacs--a web-based application for classification of seroreactivity profiles. Nucleic Acids Res., 35, W683-687.

[BKK+07]

Backes, C., Keller, A., Küntzer, J., Kneissl, B., Comtesse, N., Elnakady, Y. A., Müller, R., Meese, E., & Lenhof, H.-P. (2007). Genetrail--advanced gene set enrichment analysis. Nucleic Acids Res., 35, W186-192.

[BKN+06]

Baldes, C., Koenig, P., Neumann, D., Lenhof, H.-P., Kohlbacher, O., & Lehr, C.-M. (2006). Development of a fluorescence-based assay for screening of modulators of human organic anion transporter 1b3 (oatp1b3). European Journal of Pharmaceutics and Biopharmaceutics, 62(1), 39-43.

[MHL+06]

Moll, A., Hildebrandt, A., Lenhof, H.-P., & Kohlbacher, O. (2006). Ballview: a tool for research and education in molecular modeling. Bioinformatics, 22(3), 365-366.

[ACL+06]

Althaus, E., Caprara, A., Lenhof, H.-P., & Reinert, K. (2006). A branch-and-cut algorithm for multiple sequence alignment. Mathematical Programming, 105(2-3), 387-425.

[KBG+06]

Küntzer, J., Blum, T., Gerasch, A., Backes, C., Hildebrandt, A., Kaufmann, M., Kohlbacher, O., & Lenhof, H.-P. (2006). BN++ - A Biological Information System. Journal of Integrative Bioinformatics, 3(2), 34.

[TBH+06]

Toll, H., Berger, P., Hofmann, A., Hildebrandt, A., Oberacher, H., Lenhof, H.-P., & Huber, C. G. (2006). Glycosylation patterns of human chorionic gonadotropin revealed by liquid chromatography-mass spectrometry and bioinformatics. Electrophoresis, 27(13), 2734-46.

[KLC+06]

Keller, A., Ludwig, N., Comtesse, N., Hildebrandt, A., Meese, E., & Lenhof, H.-P. (2006). A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC Bioinformatics (7), 539.

[MHL+05]

Moll, A., Hildebrandt, A., Lenhof, H.-P. & Kohlbacher, O. (2005). BALLView: an object-oriented molecular visualization and modeling framework. J. Comput. Aided Mol. Des., 19(11), 791-800.

[BKL+05]

Backes, C., Küntzer, J., Lenhof, H.-P., Comtesse, N., & Meese, E. (2005). Grabcas: a bioinformatics tool for score-based prediction of caspase- and granzyme b-cleavage sites in protein sequences. Nucleic Acids Res., 33, 208-213.

[CZW+05]

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. (2005). Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets. PNAS, 102(27), 9601-06.

[HBR+04]

Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., & Lenhof, H.-P. (2004). Novel formulation of nonlocal electrostatics. Phys. Rev. Lett., 93(10), 108104.

[DHS+04]

Dönnes, P., Höglund, A., Sturm, M., Comtesse, N., Backes, C., Meese, E., Kohlbacher, O., & Lenhof, H.-P. (2004). Integrative analysis of cancer-related data using cap. FASEB J., 18(12), 1465-7.

[HL04]

Ralf Hofestädt & H.-P. Lenhof (Eds.). (2004). Methoden und innovative anwendungen der informatik und informationstechnik. schwerpunktthema: molekulare bioinformatik. In H.-P. Hofestädt, & H.-P. Lenhof (Eds.), Information technology (it).

[NLL+04]

Neumann, D., Lehr, C., Lenhof, H., & Kohlbacher, O. (2004).  Computational modeling of the sugar-lectin interaction. Advanced DRUG DELIVERY Reviews, 56(4), 437-457.

[LS03]

H.-P. Lenhof & M.-F. Sagot (Eds.). (2003). Proceedings - European Conference on Computational Biology (ECCB) 2003 . In H.-P. Lenhof, & M.-F. Sagot (Eds.), Bioinformatics 19 (Suppl. 2), 1-256.

[NKL+02]

Neumann, D., Kohlbacher, O., Lenhof, H.-P., & Lehr, C.-M. (2002). Lectin-sugar interactions: calculated versus experimental binding energies.   Eur. J. Biochem., 269, 1518-1524.

[SSE+02]

Sirava, M., Schäfer, T., Eiglsperger, M., Kaufmann, M., Kohlbacher, O., Bornberg-Bauer, E., & Lenhof, H.-P. (2002). BioMiner - modeling, analysing, and visualizing biochemical pathways and networks. Bioinformatics, Proceedings of the European Conference on Computational Biology 2002, 18 (Suppl. 2), S219-S230.

[ACL+02]

Althaus, E., Caprara, A., Lenhof, H.-P., & Reinert, K. (2002). Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics. Bioinformatics, Proceedings of the European Conference on Computational Biology 2002, 18 (Suppl. 2), 4-16.

[LL02]

Lengauer, T. & Lenhof, H.-P. (Eds.). (2002). European Conference on Computational Biology 2002. In T. Lengauer, & H.-P. Lenhof (Eds.), (pp. 1-260). Bioinformatics.

[AKL+02]

Althaus, E., Kohlbacher, O., Lenhof, H.-P., & Müller, P. (2002). A combinatorial approach to protein docking with flexible side chains. Journal of Computational Biology, 9(4), 597-612.

[KBM+01]

Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., & Lenhof, H.-P. (2001). A NMR-spectra-based scoring function for protein docking. In D. Sankoff, & T. Lengauer (Eds.), RECOMB 2001 - Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (pp. 169-177). ACM press.

[KBM+01]

Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., & Lenhof, H.-P. (2001). Structure prediction of protein complexes by a NMR-based protein docking algorithm. J. Biomol. NMR, 20, 15-21.

[KL00]

Kohlbacher, O., & Lenhof, H.-P. (2000). BALL - Rapid Software Prototyping in Computational Molecular Biology. Bioinformatics, 16(9), 815-824.

[KLM+00]

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

[BKL00]

Boghossian, N., Kohlbacher, O., & Lenhof, H.-P. (2000). Rapid software prototyping in molecular modeling using the biochemical algorithms library (ball). Journal of Experimental Algorithmics, 5(16).

[JLM+00]

Jung, B., Lenhof, H.-P., Müller, P., & Rüb, C. (2000). Simulating synthetic polymer chains in parallel. Future Generation Computer Systems, Elsevier Special Issues, 16, 513-522.

[BKL99]

Boghossian, N. P., Kohlbacher, O., & Lenhof, H.-P. (1999). BALL: Biochemical Algorithms Library. In J. Vitter, & C. Zaroliagis (Eds.), Lecture Notes in Computer Science (LNCS): Vol. 1668. Algorithm Engineering, 3rd International Workshop, WAE'99, Proceedings (pp. 330-344). Springer.

[KL99]

Kohlbacher, O., & Lenhof, H.-P. (1999). Rapid software prototyping in computational molecular biology. In XX (Ed.), Proceedings of the German Conference on Bioinformatics (GCB'99).

[LMR99]

Lenhof, H.-P., Morgenstern, B., & Reinert, K. (1999). An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics, 15(3), 203-210.

[LRV98]

Lenhof, H.-P., Reinert, K., & Vingron, M. (1998). A polyhedral approach to rna sequence structure alignment. Journal of Computational Biology, 5(3), 517-530.

[VLM97]

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.

[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).

[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).

[JLM+97]

Jung, B., Lenhof, H.-P., Müller, P., & Rüb, C. (1997). Langevin dynamics simulations of macromolecules on parallel computers. Macromol. Theory and Simul., 6, 507-521.

[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). Maintaining a visibility map of spheres while moving the viewpoint on a circle at infinity. Algorithmica, 13, 301-312.

[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). Sequential and parallel algorithms for the k closest pairs problem. Int. J. Comput. Geometry Appl., 5(3), 273-288.

[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.

[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.

[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).

[LS92]

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

[LS91]

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