Publications

The following list contains selected publications of the CBI Saar members.
 
2012

• Alcaraz, N., Kucuk, H., Weile, J., Wipat, A., and Baumbach, J. (2012). KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Internet Mathematics, 2012, 7:299-313.
   
• Cerdeira, L. T., Carneir, A. R., Ramos, R. T. J., de Almeida, S. S., D'Afonseca Vivian,, Schneider, M. P. C., Baumbach, J., Tauch, A., McCulloch, J. A., Azevedo, V. A. C., and Silva, A. (2012). Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Journal of Microbiological Methods, 2012, 86:218-23.
   
• Mikeev, L., Wolf, V. (2012). Parameter Estimation for Stochastic Hybrid Models of Biochemical Reaction Networks. Proceedings of the 15th International Conference on Hybrid Systems: Computation and Control (HSCC12), 2012.
   
• Pauling, J., Roettger, R., Tauch, A., Azevedo, V., and Baumbach, J. (2012). CoryneRegNet 6.0âUpdated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research, 2012, 40:D610-D614.
   

 
2011

• Ahmad, M., Gu, W., Geyer, T., and Helms, V. (2011). Adhesive water networks facilitate binding of protein interfaces (Abstract). Nature Communications, Vol. 2, Article no. 261.
   
• Andreychenko, A. , Mikeev, L., Spieler, D., and Wolf, V.(2011). Parameter Identification for Markov Models of Biochemical Reactions. Proceedings of the 23rd International Conference on Computer Aided Verification (CAV11), 2011.
   
• Andreychenko, A., Crouzen, P., Wolf, V.(2011). On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models. Proceedings of the 9th International Workshop on Quantitative Aspects of Programming Languages (QAPL11), 2011.
   
• Aranda, B., Blankenburg, H., Kerrien, S., Brinkman, F. S., Ceol, A., Chautard, E., Dana, J. M., De Las Rivas, J., Dumousseau, M., Galeota, E., Gaulton, A., Goll, J., Hancock, R. E. W., Isserlin, R., Jimenez, R. C., Kerssemakers, J., Khadake, J., Lynn, D. J., Michaut, M., O'Kelly, G., Ono, K., Orchard, S., Prieto, C., Razick, S., Rigina, O., Salwinski, L., Simonovic, M., Velankar, S., Winter, A., Wu, G., Bader, G. D., Cesareni, G., Donaldson, I. M., Eisenberg, D., Kleywegt, G. J., Overington, J., Ricard-Blum, S., Tyers, M., Albrecht, M., and Hermjakob, H. (2011). PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods, 2011, 8:528-529.
   
• Backes, C., Ludwig, N., Leidinger, P., Harz, C., Hoffmann, J., Keller, A., Meese, E. & Lenhof, H.-P. (2011). Immunogenicity of autoantigens. BMC Genomics, 2011 Jul 4; 12(1):340. [E-pub ahead of print].
   
• 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. & Lenhof, H.-P. (2011). An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res., 2011 Dec. 30 [E-pub ahead of print].
   
• Baumbach, J. (2011). RhizoRegNet-A database of rhizobial transcription factors and regulatory networks.. J Biotechnol., 2011, 155(1):127-134.
   
• Carbon-Mangels, M. and Hutter, M.C. (2011). Selecting relevant descriptors for classification by Bayesian estimates: A comparison with decision trees and support vector machines approaches for disparate data sets. Journal of Molecular Informatics, Vol. 30, p. 885-895.
   
• Dayar, T., Hermanns, H., Spieler, D., and Wolf, V.(2011). Bounding the Equilibrium Distribution of Markov Population Models. Numerical Linear Algebra with Applications, 2011.
   
• Dayar, T., Sandmann, W., Spieler, D., and Wolf, V. (2011). Infinite LevelDependent QBDs and Matrix Analytic Solutions for Stochastic Chemical Kinetics. Advances in Applied Probability, 2011, 43.4.
   
• Dehof, A.K., Lenhof, H.-P. & Hildebrandt, A. (2011). 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).
   
• Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011 January 17 [E-pub ahead of print].
   
• Didier, F., Henzinger, T. A., Mateescu, M., and Wolf, V.(2011). Approximation of Event Probabilities in Noisy Cellular Processes. Journal of Theoretical Computer Science, 2011, 412(21).
   
• Doncheva, N. T., Klein, K., Domingues, F. S., and Albrecht, M. (2011). Analyzing and visualizing residue networks of protein structures. Trends in Biochemical Sciences, 2011, 36:179-182.
   
• Emig, D., Kacprowski, T., and Albrecht, M. (2011). Measuring and analyzing tissue specificity of human genes and protein complexes. EURASIP Journal on Bioinformatics and Systems Biology, 2011, 2011:5.
   
• Emig, D., Sander, O., Mayr, G., and Albrecht, M. (2011). Structure collisions between interacting proteins. PLoS ONE, 2011, 6:e19581.
   
• Emig, D., and Albrecht, M. (2011). Tissue-specific proteins and functional implications. Journal of Proteome Research, 2011, 10:1893-1903.
   
• Erdmann, F., Schäuble, N., Lang, S., Jung, M., Honigmann, A., Ahmad, M., Dudek, J., Benedix, J., Harsmann, A., Kopp, A., Helms, V., Cavalié, A., Wagner, R., and Zimmermann, R. (2011). Interaction of calmodulin with Sec61 limits Ca2+ leakage from the endoplasmic reticulum. EMBO Journal, Vol. 30, p. 17-31.
   
• Eyrisch, S., Medina-Franco, J.L., and Helms, V. (2011). Transient pockets on XIAP-BIR2: towards the characterization of putative binding sites of small-molecule XIAP inhibitors. Journal of Molecular Modeling. [E-pub ahead of print]
   
• Feuerbach, L., Lyngso, R. B., Lengauer, T., and Hein, J. (2011). Reconstructing the ancestral germline methylation state of young repeats. Molecular Biology and Evolution, 2011, 28:1777-1784.
   
• Geyer, T. (2011). Many-particle Brownian and Langevin dynamics simulations with the Brownmove package. BMC Biophysics, Vol. 4:7.
   
• Gu, W., Zhou, B., Geyer, T., Hutter, M., Fang, H., and Helms, V. (2011). Design eines steuerbaren molekularen Protonenkanals. Angewandte Chemie International Edition (EN) Vol. 50, p. 768-771. Design of a gated molecular proton channel.Angewandte Chemie (DE) Vol. 123, p. 794-797.
   
• Hayat, S., Park, Y., and Helms, V. (2011). Statistical analysis and exposure status classification of transmembrane beta barrel residues.Computational Biology and Chemistry, Vol. 35, p. 96-107.
   
• Hayat, S., Walter, P., Park, Y., and Helms, V. (2011) Prediction of the exposure status of transmembrane beta barrel residues from protein sequence (Abstract).Journal of Bioinformatics and Computational Biology Vol. 9, p. 43-65.
   
• Helms, V. and Gu, W. (2011). Proton travel in green fluorescent protein. In: Jung, G. (Ed.) Fluorescent Proteins 1. Springer, p. 171-181.
   
• Henzinger, T. A., Jobstmann, B., and Wolf, V.(2011). Formalisms for Specifying Markovian Population Models. International Journal of Foundations of Computer Science, 2011, 22(4).
   
• Hutter, M.C. (2011). Determining the degree of randomness of descriptors in linear regression equations with respect to the data size. Journal of Chemical Information and Modeling. [E-pub ahead of print]
   
• Hutter, M.C. (2011). Graph-based similarity concepts in virtual screening (Abstract). Future Medicinal Chemistry, Vol. 3, p. 485-501.
   
• Jusoh, S.A. and Helms, V. (2011). Helical integrity and microsolvation of transmembrane domains from Flaviviridae envelope glycoproteins. BBA Biomembranes,Vol. 1808, p. 1040-1049.
   
• Katoen, J.-P., Klink, D., Leucker, M, and Wolf, V.(2011). Three-Valued Abstraction for Probabilistic Systems. Journal on Logic and Algebraic Programming, 2011, :155.
   
• 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. (2011). Toward the blood-borne miRNome of human diseases. Nat Methods 2011 Sep. 4 [E-pub ahead of print].
   
• Keller, A., Leidinger, P., Gislefoss, R., Haugen, A., Langseth, H., Staehler, P., Lenhof, H.-P. & Meese, E. (2011). Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis. RNA Biol., 2011 May 1;8(3) [E-pub ahead of print].
   
• Krol, E., Blom, J., Winnebald, J., Berhoerster, A., Barnett, M. J., Goesmann, A., Baumbach, J., and Becker, A. (2011). RhizoRegNet-A database of rhizobial transcription factors and regulatory networks.. Journal of Biotechnology, 2011, 155:127-34.
   
• Küntzer, J., Maisel, D., Lenhof, H.-P., Klostermann, S. & Burtscher H. (2011). The Roche Cancer Genome Database 2.0. BMC Med Genomics, 2011 May 17;4(1):43 [E-pub ahead of print].
   
• Lapin, M., Mikeev, L., Wolf, V.(2011). SHAVE Stochastic Hybrid Analysis of Markov Population Models. Proceedings of the 14th International Conference on Hybrid Systems: Computation and Control (HSCC11), 2011.
   
• Lawyer, G., Altmann, A., Thielen, A., Zazzi, M., Sonnerborg, A., and Lengauer, T. (2011). HIV-1 mutational pathways under multidrug therapy.. AIDS Research and Therapy, 2011, 8:1-13.
   
• Lee, P.-H. and Helms, V. (2011). Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues. Proteins: Structure, Function, and Bioinformatics. [E-pub ahead of print]
   
• Leidinger, P., Keller, A., Borries, A. Huwer, H., Rohling, M. Huebers, J., Lenhof, H.-P. & Meese, E. (2011). Specific peripheral miRNA profiles for distinguishing lung cancer from COPD. Lung Cancer, 2011 March 7 [E pub ahead of print].
   
• Lutsik, P., Feuerbach, L., Arand, J., Lengauer, T., Walter, J., and Bock, C. (2011). BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Research, 2011, 39:W551-W556.
   
• Ly, T.T.B., Khatri, Y., Zapp, J., Hutter, M.C. and Bernhardt, R. (2011, accepted). CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase. Applied Microbiology and Biotechnology.
   
• Metzger, J., Schaadt, N., Hayat; S., and Helms, V. (2011). Predicting structural and functional properties of membrane proteins from protein sequence. Annual Reports in Computational Chemistry, Vol. 7, p. 39-64. Ed. Wheeler, R.A.
   
• Mikeev, L., Sandmann W., Wolf, V.(2011). Efficient Calculation of Rare Event Probabilities in Markovian Queueing Networks. Proceedings of the 5th International ICST Conference on Performance Evaluation Methodologies and Tools (VALUETOOLS11), 2011.
   
• Morris, J. H., Apeltsin, L., Newman, A. M., Baumbach, J., Wittkop, T., Su, G., Bader, G. D., and Ferrin, T. E. (2011). clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape. BMC Bioinformatics, 2011, 12:436.
   
• Ramos, R. T., Carneiro, A. R., Baumbach, J., Azevedo, V., Schneider, M. P., and Silva, A. (2011). Analysis of quality raw data of second generation sequencers with Quality Assessment Software. BMC Research Notes, 2011, 4:130.
   
• Reiss, S., Rebhan, I., Backes, P., Romero-Brey, I., Erfle, H., Matula, P., Kaderali, L., Poenisch, M., Blankenburg, H., Hiet, M., Longerich, T., Diehl, S., Ramírez, F., Balla, T., Rohr, K., Kaul, A., Bühler, S., Pepperkok, R., Lengauer, T., Albrecht, M., Eils, R., Schirmacher, P., Lohmann, V., and Bartenschlager, R. (2011). Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host & Microbe, 2011, 9:32-45.
   
• Reuter, S., Oette, M., Wilhelm, F. C., Beggel, B., Kaiser, R., Balduin, M., Schweitzer, F., Verheyen, J., Adams, O., Lengauer, T., Faetkenheuer, G., Pfister, H., and Haeussinger, D. (2011). Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.. Medical Microbiology and Immunology, 2011, 200:51-51.
   
• Reuter, S., Oette, M., Wilhelm, F. C., Beggel, B., Kaiser, R., Balduin, M., Schweitzer, F., Verheyen, J., Adams, O., Lengauer, T., Faetkenheuer, G., Pfister, H., and Haeussinger, D. (2011). Prevalence and characteristics of hepatitis B and C virus infections in treatment-na\"ive HIV-infected patients. Medical Microbiology and Immunology, 2011, 200:39-49.
   
• Ruiz, J. C., D'Afonseca, V., Silva, A., Ali, A., Pinto, A. C., Santos, A. R., Rocha, A. A. M. C., Lopes, D. O., Dorella, F. A., Pacheco, L. G. C., Costa, M. P., Turk, M. Z., Seyffert, N., Moraes, P. M. R. O., Soares, S. C., Almeida, S. S., Castro, T. L. P., Abreu, V. A. C., Trost, E., Baumbach, J., Tauch, A., Schneider, M. P. C., McCulloch, J., Cerdeira, L. T., Ramos, R. T. J., Zerlotini, A., Dominitini, A., Resende, D. M., Coser, E. M., Oliveira, L. M., Pedrosa, A. L., Vieira, C. U., Guimaraes, C. T., Bartholomeu, D. C., Oliveira, D. M., Santos, F. R., Rabelo, E. M., Lobo, F. P., Franco, G. R., Costa, A. F., Castro, I. M., Dias, S. R., Ferro, J. A., Ortega, J. M., Paiva, L. V., Goulart, L. R., Almeida, J. F., Ferro, M. I., Carneiro, N. P., Falcao, P. R. K., Grynberg, P., Teixeira, S. M. R., Brommonschenkel, S., Oliveira, S. C., Meyer, R., Moore, R. J., Miyoshi, A., Oliveira, G. C., and Azevedo, V. (2011). vidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains. PLoS One, 2011, 6:e18551.
   
• Saigo, H., Altmann, A., Bogojeska, J., Müller, F., Nowozin, S., and Lengauer, T. (2011). Learning from Past Treatments and Their Outcome Improves Prediction of In Vivo Response to Anti-HIV Therapy. Statistical Applications in Genetics and Molecular Biology, 2011, 10:Article 6.
   
• Santos, A. R., Santos, M. A., Baumbach, J., McCulloch, J. A., Oliveira, G. C., Silva, A., Miyoshi, A., and Azevedo, V. (2011). A singular value decomposition approach for improved taxonomy classification of biological sequences. BMC Genomics, 2011, 12:S11.
   
• Schelhorn, S., Mestre, J., Zotenko, E., and Albrecht, M. (2011). Inferring physical protein contacts from large-scale purification data of protein complexes. Molecular & Cellular Proteomics, 2011, 10:M110.004929.
   
• Schmitt, J., Keller, A., Nourkami-Tutdibi, N., Heisel, S., Habel, N., Leidinger, P., Ludwig, N., Gessler, M., Graf, N., Berthold, F., Lenhof, H.-P. & Meese, E. (2011). Autoantibody signature differentiates wilms tumor patients from neuroblastoma patients. PLoS One, 2011 Dec. 16 [E-pub ahead of print].
   
• 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. (2011). Multicenter study identified molecular blood-born protein signatures for Wilms Tumor. Int J Cancer, 2011 Sep. 12 [E-pub ahead of print].
   
• Schuler, M., Keller, A., Backes, C., Phillipar, K., Lenhof, H.-P. & Bauer, P. (2011). Transcriptome analysis by Gene Trail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biology, 2011, 11:87.
   
• Singh, N.K., Goodman, A., Walter, P., Helms, V., and Hayat, S. (2011). TMBHMM: A frequency-profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues. Future Medicinal Chemistry, Vol. 3, p. 485-501
   
• Thielen, A., Lengauer, T., Swenson, L. C., Dong, W. W., McGovern, R. A., Lewis, M., James, I., Heera, J., Valdez, H., and Harrigan, P. R. (2011). Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially. Antiviral Therapy, 2011, in press:0.
   
• Tolosi, L., and Lengauer, T. (2011). Classification with correlated features: unreliability of feature ranking and solutions. Bioinformatics, 2011, 27:1986-1994.
   
• Walter, P., Ulucan, Ö., Metzger, J., and Helms, V. (2011, accepted). Bioinformatics of protein-protein interfaces and small molecule effectors. Current Bioinformatics
   
• Wittkop, T., Emig, D., Truss, A., Albrecht, M., Böcker, S., and Baumbach, J. (2011). Comprehensive cluster analysis with Transitivity Clustering. Nature Protocols, 2011, 6:285-295.
   
• Wittkop, T., Emig, D., Truss, A., Albrecht, M., Böcker, S., and Baumbach, J. (2011). Comprehensive cluster analysis with Transitivity Clustering. Nature Protocols, 2011, 6:285-95.
   
• Wittkop, T., Rahmann, S., Roettger, R., Boecker, S., and Baumbach, J. (2011). Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. Internet Mathematics, 2011, 7:255-73.
   
• Ziller, M. J., Müller, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Boyle, P., Epstein, C. B., Bernstein, B. E., Lengauer, T., Gnirke, A., and Meissner, A. (2011). Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types. PLoS Genetics, 2011, 7:e1002389.
   
• Zimmermann, R., Eyrisch, S., Ahmad, M., and Helms, V. (2011) Protein translocation across the ER membrane.BBA - Biomembranes, Vol. 1808, p. 912-924.
   

 
2010

• Albrecht, M. (2010). Color blindness. Nature Methods, 2010, 7:775.
   
• Altmann, A., Tolosi, L., Sander, O., and Lengauer, T. (2010). Permutation importance: an unbiased feature importance measure. Bioinformatics, 2010, 26:1340-1347.
   
• 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. [E-pub ahead of print].
   
• Baumbach, J. (2010). On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks. Nucleic Acids Research, 2010, 38:7877-7884.
   
• Berwanger, A., Eyrisch, S., Schuster, I., Helms, V., and Bernhardt, R. (2010). Polyamines: Naturally occurring small molecule modulators of electrostatic protein-protein interactions. Journal of Inorganic Biochemistry, Vol. 104, 118-125.
   
• Bogojeska, J., Bickel, S., Altmann, A., and Lengauer, T. (2010). Dealing with sparse data in predicting outcomes of HIV combination therapies. Bioinformatics, 2010, 26:2085-2092.
   
• Bozek, K., and Lengauer, T. (2010). Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evolutionary Biology, 2010, 10:186,1-186,15.
   
• Brunner, S., Hurni, S., Streckeisen, P., Mayr, G., Albrecht, M., Yahiaoui, N., and Keller, B. (2010). Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. The Plant Journal, 2010, 64:433-445.
   
• Devanathan, R., Venkatnathan, A., Rousseau, R., Dupuis, M., Frigato, T., Gu, W., Helms, V. (2010). Atomistic simulation of water percolation and proton hopping in nafion fuel cell membrane.Journal of Physical Chemistry B, Vol. 114, p. 13681-13690.
   
• Däumer, M., Awerkiew, S., Sierra Aragon, S., Kartashev, V., Poplavskaja, T., Klein, R., Sichtig, N., Thielen, B., Lengauer, T., Roomp, K., Pfister, H., and Kaiser, R. (2010). Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source. AIDS Research and Human Retroviruses, 2010, 26:275-278.
   
• Ellinghaus, E., Ellinghaus, D., Stuart, P. E., Nair, R. P., Debrus, S., Raelson, J. V., Belouchi, M., Fournier, H., Reinhard, C., Ding, J., Li, Y., Tejasvi, T., Gudjonsson, J., Stoll, S. W., Voorhees, J. J., Lambert, S., Weidinger, S., Eberlein, B., Kunz, M., Rahman, P., Gladman, D. D., Gieger, C., Wichmann, H. E., Karlsen, T. H., Mayr, G., Albrecht, M., Kabelitz, D., Mrowietz, U., Abecasis, G. R., Elder, J. T., Schreiber, S., Weichenthal, M., and Franke, A. (2010). Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2. Nature Genetics, 2010, 42:991-995.
   
• Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B. R., and Albrecht, M. (2010). AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research, 2010, 38:W755-W762.
   
• 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.
   
• Franke, A., Balschun, T., Sina, C., Ellinghaus, D., Häsler, R., Mayr, G., Albrecht, M., Wittig, M., Buchert, E., Nikolaus, S., Gieger, C., Wichmann, H. E., Sventoraityte, J., Kupcinskas, L., Onnie, C. M., Gazouli, M., Anagnou, N. P., Strachan, D., McArdle, W. L., Mathew, C. G., Rutgeerts, P., Vermeire, S., Vatn, M. H., Krawczak, M., Rosenstiel, P., Karlsen, T. H., and Schreiber, S. (2010). Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). Nature Genetics, 2010, 42:292-294.
   
• Fuhrmann, J., Rurainski, A., Lenhof, H.-P., & Neumann, D. (2010). A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem., 31(9), 1911-18.
   
• Geyer, T., Mol, X., Blaß, S., and Helms, V. (2010). Bridging the gap: Linking molecular simulations and systemic descriptions of cellular compartments.PLoS ONE 5(11): e14070.
   
• Helms, V., Hayat, S., and Metzger, J. (2010). Predicting the burial/exposure status of transmembrane residues in helical membrane proteins. In: Structural Bioinformatics of Membrane Proteins, Ed. D. Frishman, Springer.
   
• 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. (2010). BALL - Biochemical Algorithms Library 1.3. BMC Bioinformatics, 2010, 11:531.
   
• Hutter, B., Bieg, M. Helms, V., and Paulsen, M. (2010). Divergence of imprinted genes during mammalian evolution. BMC Evolutionary Biology, 10:116.
   
• Hutter, B., Bieg, M., Helms, V., and Paulsen, M. (2010). Imprinted genes show unique patterns of sequence conservation.BMC Genomics, 11:649.
   
• Hutter, M. (2010). Book review: Molecular Descriptors for Chemoinformatics (2nd. Ed.).ChemMedChem, Vol. 5, p. 306-307.
   
• Jusoh, S.A., Welsch, C., Siu, S.W.I., Böckmann, R.A., and Helms, V. (2010). Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus.Journal of Molecular Modelling, Vol. 16, p. 1625-1637.
   
• Kathri, Y., Girhard, A., Romankiewicz, A., Ringle, M., Hannemann, F., Urlacher, V.B., Hutter, M., and Bernhardt, R. (2010). Regioselective Hydroxylation of Norisoprenoids by CYP109D1 from Sorangium cellulosum So ce56.Appl. Microbiol. Biotechnol., Vol. 88, p. 485-495.
   
• Küntzer, J., Eggle, D., Lenhof, H.-P., Burtscher, H. & Klostermann, S. (2010). The Roche Cancer Genome Database (RCGDB). Hum Mutat. 31, 1-7.
   
• Lange, C. M., Roomp, K., Dragan, A., Nattermann, J., Michalk, M., Spengler, U., Weich, V., Lengauer, T., Zeuzem, S., Berg, T., and Sarrazin, C. (2010). HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection. Journal of Hepatology, 2010, 53:1022-1028.
   
• 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.
   
• 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.
   
• Lengauer, T., Altmann, A., Thielen, A., and Kaiser, R. (2010). Chasing the AIDS Virus. Communications of the ACM, 2010, 53:66-74.
   
• 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.
   
• 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.
   
• 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].
   
• Mihm, U., Hofmann, W., Welsch, C., Polta, A., Lengauer, T., Zeuzem, S., Sarrazin, C., and Herrmann, E. (2010). Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome. Journal of Viral Hepatitis, 2010, 17:217-221.
   
• 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.
   
• Phillips, M., Georgiev, I, Dehof, A.K., Nickels, S., Marsalek, L., Lenhof, H.-P., Hildebrandt, A. & Slusallek, P. (2010). Measuring Properties of Molecular Surfaces Using Ray Casting. Proceedings of 9th International Workshop on High Performance Computational Biology.
   
• Ramírez, F., and Albrecht, M. (2010). Finding scaffold proteins in interactomes. Trends in Cell Biology, 2010, 20:2-4.
   
• Roomp, K., Antes, I., and Lengauer, T. (2010). Predicting MHC class I epitopes in large datasets. BMC Bioinformatics, 2010, 11:90,1-90,11.
   
• Schaadt, N., Christoph, J., and Helms, V. (2010). Classifying substrate specifities of membrane transporters from arabidopsis thaliana.Journal of Chemical Information and Modeling, Vol. 50, p. 1899-1905.
   
• Schlicker, A., Lengauer, T., and Albrecht, M. (2010). Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics, 2010, 26:i561-i567.
   
• Schlicker, A., and Albrecht, M. (2010). FunSimMat update: new features for exploring functional similarity. Nucleic Acids Research, 2010, 38:D244-D248.
   
• Thielen, A., Sichtig, N., Kaiser, R., Lam, J., Harrigan, P. R., and Lengauer, T. (2010). Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120. Journal of Infectious Diseases, 2010, 202:1435-1443.
   
• Wang, L., Siu, S., Gu, W., and Helms, V. (2010). Downhill binding energy surface of the barnase-barstar complex. Biopolymers, Vol. 93, p. 977-985.
   
• Weisser, H., Altmann, A., Sierra, S., Incardona, F., Struck, D., Sönnerborg, A., Kaiser, R., Zazzi, M., Tschochner, M., Walter, H., and Lengauer, T. (2010). Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction. PLoSOne, 2010, 5:e9044,1-e9044,10.
   
• Welker, M., Welsch, C., Meyer, A., Antes, I., Albrecht, M., Forestier, N., Kronenberger, B., Lengauer, T., Piiper, A., Zeuzem, S., and Sarrazin, C. (2010). Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper. Protein Science, 2010, 19:1327-1336.
   
• Wittkop, T., Emig, D., Lange, S., Rahmann, S., Albrecht, M., Morris, J. H., Böcker, S., Stoye, J., and Baumbach, J. (2010). Partitioning biological data with transitivity clustering. Nature Methods, 2010, 7:419-420.
   
• Zazzi, M., Kaiser, R., Sönnerborg, A., Struck, D., Altmann, A., Prosperi, M. C. F., Rosen-Zvi, M., Petroczi, A., Peres, Y., Schülter, E., Boucher, C., Brun-Vezinet, F., Harigan, R., Morris, L., Obermeier, M., Perno, F., Shafer, R., Vandamme, A., van Laethem, K., Wensing, A., Lengauer, T., and Incardona, F. (2010). Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study). HIV Medicine, 2010, Early View:1-8.
   

 
2009

• 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.
   
• Altmann, A., Däumer, M., Beerenwinkel, N., Peres, Y., Schülter, E., Büch, J., Rhee, S., Sönnerborg, A., Fessel, W. J., Shafer, R. W., Zazzi, M., Kaiser, R., and Lengauer, T. (2009). Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation. The Journal of Infectious Diseases, 2009, 199:999-1006.
   
• Altmann, A., Sing, T., Vermeiren, H., Winters, B., Van Craenenbroeck, E., Van der Borght, K., Rhee, S., Shafer, R. W., Schülter, E., Kaiser, R., Peres, Y., Sönnerborg, A., Fessel, W. J., Incardona, F., Zazzi, M., Bacheler, L., Van Vlijmen, H., and Lengauer, T. (2009). Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype. Antiviral Therapy, 2009, 14:273-283.
   
• Blankenburg, H., Finn, R. D., Prliç, A., Jenkinson, A. M., Ramírez, F., Emig, D., Schelhorn, S., Büch, J., Lengauer, T., and Albrecht, M. (2009). DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics, 2009, 25:1321-1328.
   
• Blankenburg, H., Ramírez, F., Büch, J., and Albrecht, M. (2009). DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Research, 2009, 37:W122-W128.
   
• Bock, C., Halachev, K., Büch, J., and Lengauer, T. (2009). EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biology, 2009, 10:R14.1-R14.14.
   
• Bozek, K., Thielen, A., Sierra, S., Kaiser, R., and Lengauer, T. (2009). V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.. PLoS One, 2009, 4:e7387:1-e.7387:14.
   
• 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.
   
• Dehof, A.K., Rurainski, A., Lenhof, H.-P., & Hildebrandt, A. (2009). Automated Bond Order Assignment as an Optimization Problem. Lecture Notes in Informatics (LNI) - Proceedings German Conference on Bioinformatics GCB 2009, 201-209.
   
• Erdmann, F., Jung, M., Eyrisch, S., Lang, S., Helms, V., Wagner, R., and Zimmermann, R. (2009). Lanthanum ions inhibit the mammalian Sec61 complex in its channel dynamics and protein transport activity. (Abstract). FEBS Letters, Vol. 583, p. 2359-2364.
   
• Eyrisch, S. and Helms, V. (2009). What induces pocket openings on protein surface patches involved in protein-protein interactions? Journal of Computer-Aided Molecular Design, Vol. 23, p. 73-86.
   
• 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.
   
• Geyer, T. and Winter, U. (2009). An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations. Journal of Chemical Physics, Vol. 130, 114905.
   
• Gu, W. and Helms, V. (2009). Tightly connected water wires facilitate fast proton uptake at the proton entrance of proton pumping proteins. Journal of the American Chemical Society, Vol. 131, p. 2080-2081.
   
• Hartmann, C., Antes, I., and Lengauer, T. (2009). Docking and scoring with alternative side-chain conformations. Proteins: Structure, Function, and Bioinformatics, 2009, 74:712-726.
   
• Hutter, M. C. (2009). In Silico Prediction of Drug Properties. Current Medicinical Chemistry, Vol. 16, p. 189-202.
   
• Hutter, M.C. (2009). QSAR - Old And New Directions in Ed. M.Springborg, RSC Publishing, Cambridge UK, 2009. Chemical Modelling: Applications and Theory, Vol. 6, p. 112-130.
   
• 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.
   
• 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.
   
• 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.
   
• 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.
   
• Krier, M. and Hutter, M. C. (2009). Bioisosteric similarity of molecules based on structural alignment and observed chemical replacements in drugs. Journal of Chemical Information and Modeling, Vol. 49, p. 1280-1297.
   
• Lauck, F., Helms; V., and Geyer, T. (2009). Graph measures reveal fine structure of complexes forming in multiparticle simulations. Journal of Chemical Theory and Computation, Vol. 5, p. 641-648.
   
• 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.
   
• Lengauer, T., Altmann, A., and Thielen, A. (2009). Bioinformatische Unterstützung der Auswahl von HIV Therapien. Informatik Spektrum, 2009, 32:320-331.
   
• Lengauer, T., Sierra, S., and Kaiser, R. (2009). Resistenzbestimmung. MMW Fortschritte in der Medizin, 2009, 151:74-75.
   
• Lengauer, T., and Kaiser, R. (2009). Computerjagd auf das AIDSVIRUS. Spektrum der Wissenschaft, 2009, 08:62-67.
   
• 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.
   
• McHardy, A. C., and Adams, B. (2009). The role of genomics in tracking the evolution of influenza A virus. PLoS Pathog, 2009, 5:e1000566.
   
• 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.
   
• Mihm, U., Ackermann, O., Welsch, C., Herrmann, E., Hofmann, W. P., Grigorian, N., Welker, M. W., Lengauer, T., Zeuzem, S., and Sarrazin, C. (2009). Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C. Journal of Hepatology, 2009, 50:49-58.
   
• Schüffler, P., Mikeska, T., Waha, A., Lengauer, T., and Bock, C. (2009). MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays. Genome Biology, 2009, 10:R105:1-R105:10.
   
• Spaar, A., Flöck, D., and Helms, V. (2009). Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution. Biophysical Journal, Vol. 96, p. 1721-1732.
   
• Trignetti, M., Sing, T., Svicher, V., Santoro, M. M., Forbici, F., D'Arrigo, R., Bellocchi, M. C., Santoro, M., Marconi, P., Zaccarelli, M., Trotta, M. P., Bellagamba, R., Narciso, P., Antinori, A., Lengauer, T., Perno, C. F., and Ceccherini-Silberstein, F. (2009). Dynamics of NRTI resistance mutations during therapy interruption. AIDS Research and Human Retroviruses, 2009, 25:57-64.
   
• Wang, L., Stumm, B., and Helms, V. (2009). Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction. Journal of Computational Chemistry, Vol. 31, p. 847-854
   
• Winter, U. and Geyer, T. (2009). Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions. Journal of Chemical Physics, 131, 104102.
   

 
2008

• Ahmad, M., Gu, W., and Helms, V. (2008). Mechanismus der schnellen Peptiderkennung durch SH3-Domänen (DE). Angewandte Chemie, Vol. 120, p. 7738-7742; Mechanism of Fast Peptide Recognition by SH3 Domains (EN). Angewandte Chemie International Edition, Vol. 47, p. 7626-7630.
   
• Altmann, A., Rosen-Zvi, M., Prosperi, M., Aharoni, E., Neuvirth, H., Sönnerborg, A., Schülter, E., Büch, J., Struck, D., Peres, Y., Incardona, F., Kaiser, R., Zazzi, M., and Lengauer, T. (2008). Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy. PLoS ONE, 2008, 3:e3470.
   
• Assenov, Y., Ramírez, F., Schelhorn, S., Lengauer, T., and Albrecht, M. (2008). Computing topological parameters of biological networks. Bioinformatics, 2008, 24:282-284.
   
• Bock, C., Walter, J., Paulsen, M., and Lengauer, T. (2008). Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Research, 2008, 36:e55.
   
• Bock, C., and Lengauer, T. (2008). Computational epigenetics. Bioinformatics, 2008, 24:1-10.
   
• Bogojeska, J., Alexa, A., Altmann, A., Lengauer, T., and Rahnenführer, J. (2008). Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics, 2008, 24:2391-2392.
   
• Bogojeska, J., Lengauer, T., and Rahnenführer, J. (2008). Stability analysis of mixtures of mutagenetic trees. BMC Bioinformatics, 2008, 9:165-181.
   
• Emig, D., Cline, M. S., Klein, K., Kunert, A., Mutzel, P., Lengauer, T., and Albrecht, M. (2008). Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks. Journal of Integrative Bioinformatics, 2008, 5:101-115.
   
• Emig, D., Cline, M. S., Lengauer, T., and Albrecht, M. (2008). Integrating expression data with domain interaction networks. Bioinformatics, 2008, 24:2546-2548.
   
• Eyrisch, S. and Helms, V. (2008). Designing Binding Pockets on Protein Surfaces using the A* Algorithm. GCB 2008.
   
• 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.
   
• Franke, A., Balschun, T., Karlsen, T. H., Sventoraityte, J., Nikolaus, S., Mayr, G., Domingues, F. S., Albrecht, M., Nothnagel, M., Ellinghaus, D., Sina, C., Onnie, C. M., Weersma, R. K., Stokkers, P. C. F., Wijmenga, C., Gazouli, M., Strachan, D., McArdle, W. L., Vermeire, S., Rutgeers, P., Rosenstiel, P., Krawczak, M., Vatn, M. H., IBSEN study group, t., Mathew, C. G., and Schreiber, S. (2008). Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis. Nature Genetics, 2008, 40:1319-1323.
   
• 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.
   
• 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.
   
• Helms, V. (2008). Principles of Computational Cell Biology - From Protein Complexes to Cellular Networks. Wiley-VCH.
   
• Hutter, B., Paulsen, M., and Helms, V. (2008). Identifying CpG islands by different computational techniques (Abstract). OMICS: A Journal of Integrative Biology.
   
• Jenkinson, A. M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R. D., Hermjakob, H., Hubbard, T. J. P., Jimenez, R. C., Jones, P., Kähäri, A., Kulesha, E., Macías, J. R., Reeves, G. A., and Prliç, A. (2008). Integrating biological data - the Distributed Annotation System. BMC Bioinformatics, 2008, 9:S3.1-7.
   
• 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.
   
• 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.
   
• 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.
   
• 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.
   
• 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.
   
• Park, Y. and Helms, V. (2008). MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon. Bioinformatics, Vol. 24, p. 1819-1820.
   
• Park, Y. and Helms, V. (2008). Prediction of the translocon-mediated membrane insertion free energies of protein sequences. Bioinformatics, Vol. 24, p. 1271-1277.
   
• 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.
   
• Schelhorn, S., Lengauer, T., and Albrecht, M. (2008). An integrative approach for predicting interactions of protein regions. Bioinformatics, 2008, 24:i35-i41.
   
• Schlicker, A., and Albrecht, M. (2008). FunSimMat: a comprehensive functional similarity database. Nucleic Acids Research, 2008, 36:D434-D439.
   
• Schluttig, J., Alamanova, D., Helms, V., and Schwarz, U. S. (2008). Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches. Journal of Chemical Physics, Vol. 129, 155106.
   
• Schneider, N., Jäckels, C., Andres, C., and Hutter, M. (2008). Gradual in Silico Filtering for Druglike Substances. Journal of Chemical Information and Modeling, Vol. 48, p. 613-628.
   
• Van Ooijen, G., Mayr, G., Albrecht, M., Cornelissen, B. J. C., and Takken, F. L. W. (2008). Transcomplementation, but not physical association of the CC-NB-ARC and LRR domains of tomato R protein Mi-1.2 is altered by mutations in the ARC2 subdomain. Molecular Plant, 2008, 1:401-410.
   
• Van Ooijen, G., Mayr, G., Kasiem, M. M. A., Albrecht, M., Cornelissen, B. J. C., and Takken, F. L. W. (2008). Structure-function analysis of the NB-ARC domain of plant disease resistance proteins. Journal of Experimental Botany, 2008, 59:1383-1397.
   
• Weinhold, N., Sander, O., Domingues, F. S., Lengauer, T., and Sommer, I. (2008). Local function conservation in sequence and structure space. PLoS Computational Biology, 2008, 4:e1000105.
   
• Welsch, C., Domingues, F. S., Susser, S., Antes, I., Hartmann, C., Mayr, G., Schlicker, A., Sarrazin, C., Albrecht, M., Zeuzem, S., and Lengauer, T. (2008). Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV. Genome Biology, 2008, 9:R16.
   
• Zhu, H., Sommer, I., Lengauer, T., and Domingues, F. S. (2008). Alignment of Non-Covalent Interactions at Protein-Protein Interfaces. PLoS ONE, 2008, 3:e1926.
   

 
2007

• Backes, C., Keller, A., Küntzer, J., Kneissl, B., Comtesse, N., Elnakady, Y. A., Müller, R., Meese, E., and Lenhof, H.-P. Genetrail--advanced gene set enrichment analysis. Nucleic Acids Res., 34, D108-D110 (2007)
   
• Comtesse, N., Keller, A., Diesinger, I., Bauer, C., Kayser, K., Huwer, H., Lenhof, H.-P., and Meese, E. 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 (2007)
   
• Elnakady, Y. A., Rohde, M., Sasse, F., Backes, C., Keller, A., Lenhof, H.-P., Weissmann, K. J., and Müller, R. Evidence for the Mode of Action of the Highly Cytotoxic Streptomyces Polyketide Kendomycin. Chembiochem., 8(11), 1261-1272 (2007)
   
• Eyrisch, S. and Helms, V. Transient Pockets on Protein Surfaces Involved in Protein-Protein Interaction. J. Med. Chem., 50, 3457 - 3464, (2007)
   
• Geyer, T., Lauck, F., and Helms, V. Molecular Stochastic Simulations of Chromatophore Vesicles from Rhodobacter Sphaeroides. Journal of Biotechnology, 129, 212-228 (2007)
   
• Gu, W., Frigato, T., Straatsma, T.P., and Helms, V. Angewandte Chemie, Dynamisches Protonierungsgleichgewicht der in Wasser gelösten Essigsäure, 46, 2939-2943, (German version); Dynamic Protonation Equilibrium of Solvated Acetic Acid, 119, 2997-3001 (English version) (2007)
   
• Hampe, J., Franke, A., Rosenstiel, P., Till, A., Teuber, M., Huse, K., Albrecht, M., Häsler, R., Sipos, B., Mayr, G., de la Vega, F. M., Briggs, J., Günther, S., Prescott, N. J., Onnie, C. M., Fölsch, U. R., Lengauer, T., Platzer, M., Mathew, C. G., Krawczak, M., and Schreiber, S. A genome-wide association scan of non-synonymous SNPs identifies a susceptibility variant for Crohn disease in the autophagy-related 16-like (ATG16L1) gene Nature Genetics 39,2 207-211 (2007)
   
• Hansen, S., Henning, A., Naegel, A., Heisig, M., Wittum, G., Neumann, D., Kostka, K. H., Lehr, C.-M., and Schaefer, U. F. In-silico model of skin penetration based on experimentally determined input parameters. I. Experimental determination of partition and diffusion coefficients. Eur. J. Pharm. Biopharm. In press (2007)
   
• Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., and Lenhof, H.-P. Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics 23(2):e99-103 (2007)
   
• Hildebrandt, A., Kohlbacher, O., and Lenhof, H.-P. Modeling protein-protein and protein-dna docking. In T. Lengauer (Eds.), Bioinformatics - From Genomes to Therapies (2, pp. 601-644) (2007)
   
• Hussong, R. and Hildebrandt, A. The Isotope Wavelet: A Signal Theoretic Framework for Analyzing Mass Spectrometry Data. Miscellaneous publication (2007)
   
• Hutter, M. C. Separating Drugs from Nondrugs: A Statistical Approach Using Atom Pair Distributions. J. Chem. Inf. Model., 47, 186-194 (2007)
   
• Keller, A., Comtesse, N., Ludwig, N., Meese, E., and Lenhof, H.-P. Sepacs--a web-based application for classification of seroreactivity profiles. Nucleic Acids Res., 35 (Suppl. 2), W683-W687 (2007)
   
• Naegel, A., Hansen, S., Neumann, D., Lehr, C.-M., Schaefer, U. F., Wittum, G., and Heisig, M. In-silico model of skin penetration based on experimentally determined input parameters. II. Mathematical modelling of in-vitro diffusion experiments Identification of critical input parameters. Eur. J. Pharm. Biopharm. In press (2007)
   
• Park, Y. and Helms, V. On the Derivation of Propensity Scales for Predicting Exposed Transmembrane Residues of Helical Membrane Proteins. Bioinformatics, 23, 701-708 (2007)
   
• Pertuit, D., Moulari, B., Betz, Th., Nadaradjane, A., Neumann, D., Ismaïli, L., Refouvelet, B., Pellequer, Y., and Lamprecht, A. 5-amino salicylic acid bound nanoparticles for the therapy of inflammatory bowel disease J. Contr. Rel. Under revision (2007)
   
• Sander, O., Sing, T., Sommer, I., Low, A. J., Cheung, P. K., Harrigan, P., Lengauer, T., and Domingues, F. S. Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage PLoS Computational Biology 3, 3 e58 (2007)
   
• Schlicker, A., Huthmacher, C., Ramirez, F., Lengauer, T., and Albrecht, M. Functional evaluation of domain-domain interactions and human protein interaction networks Bioinformatics 23, 7 859-865 (2007)
   
• Schulz, W. A., Alexa, A., Jung, V., Hader, C., Hoffmann, M. J., Yamanaka, M., Fritzsche, S., Wlazinski, A., Müller, M., Lengauer, T., Engers, R., Florl, A. R., Wullich, B., and Rahnenführer, J. Factor integration analysis from chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer Molecular Cancer 6 14 (2007)
   
• Schulz-Trieglaff, O., Hussong, R., Gröpl, C., Hildebrandt, A., and Reinert, K. A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. In: Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007). Springer (2007)
   
• Walter, P., Ansari, S., and Helms, V. The ABC (Analysing Biomolecular Contacts) Database. Journal of Integrative Bioinformatics, 4(1), 50 (2007)
   
• Weiss, B., Schneider, M., Taetz, S., Neumann, D., Schaefer, U. F., and Lehr, C.-M. Coupling of biotin-(polyethyleneglycolide)amine to poly(D, L-lactide-co-glycolide) nanoparticles for versatile surface modification. Bioconjugate Chem. In press (2007)
   
• Welker, M.-W., Hofmann, W.-P., Welsch, C., von Wagner, M., Hermann, E., Lengauer, T., Zeuzem, S., and Sarrazin, C. Correlation of nonstructural (NS)4B amino acid variations with initial viral kinetics during interferon alpha-based therapy in HCV 1b-infected patients Journal of Viral Hepatitis 14, 5 338-349 (2007)
   

 
2006

• Alexa, A., Rahnenführer, J., and Lengauer, T. Improved significance scoring of functional groups from gene expression data by decorrelating GO graph structure Bioinfor3 1600-1607 (2006)
   
• Althaus, E., Caprara, A., Lenhof, H.-P., and Reinert, K. A branch-and-cut algorithm for multiple sequence alignment. Mathematical Programming, 105(2-3), 387-425 (2006)
   
• Altmann, A., Beerenwinkel, N., Sing, T., Savenkov, I., Däumer, M., Kaiser, R., Rhee, S.-Y., Fessel, J., Shafer, R., and Lengauer, T. Improved prediction of response to anti-HIV combination therapy using probabilistic genetic barriers Antiviral Therapy 12, 2 169-178 (2006)
   
• Andres, C. and Hutter, M. C. CNS Permeability of Drugs Predicted by a Decision Tree. QSAR Comb. Sci., 25, 305-309 (2006)
   
• Antes, I., Siu, S., and Lengauer, T. DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations Bioinformatics 22, 14 e16-e24 (2006)
   
• Baldes, C., Koenig, P., Neumann, D., Lenhof, H.-P., Kohlbacher, O., and Lehr, C.-M. Development of a fluorescence-based assay for screening of modulators of human Organic Anion Transporter 1B3 (OATP1B3) Eur. J. Pharm. Biopharm. 62(1):39-43 (2006)
   
• Bock, C., Paulsen, M., Tierling, S., Mikeska, T., Lengauer, T., and Walter, J. CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure PLoS Genetics 2, 3 e26 (2006)
   
• Gepp, M. and Hutter, M. C. Determination of hERG Channel Blockers Using a Decision Tree. Bioorg. Med. Chem., 14, 5325-5332 (2006)
   
• Geyer, T. and Helms, V. A Spatial Model of the Chromatophore Vesicles of Rhodobacter Sphaeroides and the Position of the Cytochrome bc1 Complex. Biophysical Journal, 91, 921-926 (2006)
   
• Geyer, T. and Helms, V. Reconstruction of a Kinetic Model of the Chromatophore Vesicles from Rhodobacter Sphaeroides. Biophysical Journal, 91, 927-937 (2006)
   
• Heil, B., Lichtenberg, J. Ludwig. H., and Lengauer, T. Computational recognition of potassium channel sequences Bioinformatics 22, 13 1562-1568 (2006)
   
• Helms, V. Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules. ChemPhysChem, 8, 23-33 (2006)
   
• Herzog, E., Frigato, T., Helms, V., and Lancaster, C.R.D. Energy Barriers of Proton Transfer Reactions between Amino Acid Side Chain Analogs and Water from ab initio Calculations. Journal of Computational Chemistry, 27, 1534-1547 (2006)
   
• Hildebrandt, A., Kohlbacher, O., and Lenhof, H.-P. Modeling Protein-Protein and Protein-DNA Interactions. In: Bioinformatics - From Genomes to Drugs, edited by Thomas Lengauer. Wiley-VCH, chapter 17 (2006)
   
• Hutter, B., Helms, V., and Paulsen, M. Tandem Repeats in the CpG Islands of Imprinted Genes. Genomics, 88, 323-332 (2006)
   
• Hutter, M. C. Stability of the Guanine-Cytosine Radical Cation in DNA Base Pair Triplets. Chem. Phys., 326, 240-245 (2006)
   
• Keller, A., Ludwig, N., Comtesse, N., Hildebrandt, A., Meese, E., and Lenhof, H.-P. A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC Bioinformatics (7), 539 (2006)
   
• Kerzmann, A., Neumann, D., and Kohlbacher, O. SLICK - Scoring and energy functions for protein-carbohydrate interactions J. Chem. Inf. Model. 46(4):1635-1642 (2006)
   
• Kämper, A., Apostolakis, J., Rarey, M., Marian, C. M., and Lengauer, T. Fully automated flexible docking of ligands into synthetic receptors using forward and inverse docking strategies Journal of Chemical Information and Modeling 46, 2 903-911 (2006)
   
• Küntzer, J., Blum, T., Gerasch, A., Backes, C., Hildebrandt, A., Kaufmann, M., Kohlbacher, O., and Lenhof, H.-P. BN++ - A Biological Information System. In: Proceedings of the 3rd International Workshop Integrative Bioinformatics. Rothamsted Research (2006)
   
• 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, 3(2), 34 (2006)
   
• Lamprecht, A., Koenig, P., Ubrich, N., Maincent, P., and Neumann, D. Low molecular weight heparin nanoparticles: mucoadhesion and behaviour in Caco-2 cells Nanotechnology 17(15):3673-3680 (2006)
   
• Lange, E., Gröpl, C., Reinert, K., Kohlbacher, O., and Hildebrandt, A. High-Accuracy Peak Picking of Proteomics Data using Wavelet Techniques. In: Proceedings of the Pacific Symposium on Biocomputing (PSB 2006) (2006)
   
• Lehmann, C., Däumer, M., Boussaad, I., Sing, T., Beerenwinkel, N., Lengauer, T., Schmeisser, N., Wyen, C., Fätkenheuer, G., and Kaiser, R. Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART Journal of Clinical Virology 37, 4 300-304 (2006)
   
• Löhbach, C., Neumann, D., Lehr, C.-M., and Lamprecht, A. Human vascular endothelial cells in primary cell culture for the evaluation of nanoparticle bioadhesion J. Nanosci. Nanotechnol. 6(9-10):3303-3309 (2006)
   
• Maydt, J. and Lengauer, T. Recco: Recombination analysis using cost optimization Bioinformatics 22, 9 1064-1071 (2006)
   
• Mihm, U., Grigorian, N., Welsch, C., Herrmann, E., Kronenberger, B., Teuber, G., von Wagner, M., Hofmann, W.-P., Albrecht, M., Lengauer, T., Zeuzem, S., and Sarrazin, C. Amino acid variations in HCV p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C Antiviral Therapy 11, 4 507-519 (2006)
   
• Moll, A., Hildebrandt, A., Lenhof, H.-P., and Kohlbacher, O. BALLView: A tool for research and education in molecular modeling. Bioinformatics 22(3):365-366 (2006)
   
• Moll, A., Hildebrandt, A., Lenhof, H.-P., and Kohlbacher, O. BALLView: An object-oriented molecular visualization and modeling framework. J. Comput.-Aided Mol. Des. 19(11):791 (2006)
   
• Neumann, D., Kohlbacher, O., Merkwirth, C., and Lengauer, T. A fully computational model for predicting percutaneous drug absorption J. Chem. Inf. Model 46(1):424-429 (2006)
   
• Park, Y. and Helms, V. Assembly of Transmembrane Helices of Simple Polytopic Membrane Proteins from Sequence Conservation Patterns. Proteins: Structure, Function, and Bioinformatics, 64, 895-905 (2006)
   
• Park, Y. and Helms, V. How Strongly do Sequence Conservation Patterns and Empirical Scales Correlate with Exposure Patterns of Transmembrane Helices of Membrane Proteins? Biopolymers, 83, 389-399 (2006)
   
• Plotz, G., Welsch, C., Giron-Monzon, L., Friedhoff, P., Albrecht, M., Pilper, A., Biondi, R., Lengauer, T., Zeuzem, S., and Raedle, J. Mutations in the MutS? interaction interface of MLH1 can abolish DNA mismatch repair Nucleic Acids Research 34, 22 574-6586 (2006)
   
• Sander, O., Sommer, I., and Lengauer, T. Local protein structure prediction using discriminative models BMC Bioinformatics 7, 1 Article 14 (2006)
   
• Schlicker, A., Domingues, F., Rahnenführer, J., and Lengauer, T. A new measure for functional similarity of gene products based on gene ontology BMC Bioinformatics 7, 1 Article 302 (2006)
   
• Siu, S. W. I. and Böckmann, R. A. Electric Field Effects on Membranes: Gramicidin A as a Test Ground Journal of Structural Biology , accepted (2006)
   
• Sommer, I., Toppo, S., Sander, O., Lengauer, T., and Tosatto, S. C. E. Improving the quality of protein structure models by selecting from alignment alternatives BMC Bioinformatics 7 , Article 346 (2006)
   
• Spaar, A. and Helms, V. Ionic Strength Effects on the Association Funnel of Barnase and Barstar Investigated by Brownian Dynamics Simulations. Journal of Non-Crystalline Solids, 352, 4437-4444 (2006)
   
• Spaar, A., Dammer, C., Gabdoulline, R.R., Wade, R.C., and Helms, V. Diffusional Encounter of Barnase and Barstar. Biophyical Journal, 90, 1913-1924 (2006)
   
• Steffen, A., Kämper, A., and Lengauer, T. Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm Journal of Chemical Information and Modeling 46, 4 1695-1703 (2006)
   
• Stirnimann, C. U., Rozhkova, A., Grauschopf, U., Böckmann, R. A., Glockshuber, R., Capitani, G., and Grütter, M. G. High resolution structures of Escherichia coli cDsbD in different redox states: a combined crystallographic, biochemical and computational study J.Mol.Biol. 358 , 829-845 (2006)
   
• Svicher, V., Sing, T., Santoro, M. M., Forbici, F., Rodgriguez-Barrios, F., A,, Bertoli,, Beerenwinkel, N., Bellocchi, M. C., Gago, F., d'Arminio Monforte, A., Antinori, A., Lengauer, T., Ceccherini-Silberstein, F., and Perno, C. F. Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors Journal of Virology 80, 14 7186-7198 (2006)
   
• Tameling, W. I. M., Vossen, J. H., Albrecht, M., Lengauer, T., Berden, J. A., Haring, M. A., Cornelissen, B. J. C., and Takken, F. L. W . Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation Plant Physiol 140, 4 1233-1245 (2006)
   
• Toll, H., Berger, P., Hofmann, A., Hildebrandt, A., Oberacher, H., Lenhof, H.-P., and Huber, C. G. Glycosylation patterns of human chorionic gonadotropin revealed by liquid chromatography-mass spectrometry and bioinformatics. Electrophoresis 27(13):2734-2746 (2006)
   
• Velagapudi, V. R., Wittmann, C., Lengauer, T., Talwar, P., and Heinzle, E. Metabolic high-content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains Process Biochemistry 41, 10 2170-2179 (2006)
   
• Yin, J., Beerenwinkel, N., Rahnenführer, J., and Lengauer, T. Model selection for mixtures of mutagenetic trees Statistical Applications in Genetics and Molecular Biology 5, 1 Article 17 (2006)
   
• Zhu, H., Domingues, F. S., and Lengauer, I. Sommer. T. Analysis and prediction of protein-protein-interaction types BMC Bioinformatics 7, 1 Article 27 (2006)
   
• de Groot, B. L., Böckmann, R. A., and Grubmüller, H. Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe Physik in unserer Zeit 37 , 73-79 (2006)
   

 
2005

• Albrecht, M., Choubey, D., and Lengauer, T. The HIN domain of IFI-200 proteins consists of two OB folds Biochemical and Biophysical Research Communications 327, 3 679-687 (2005)
   
• Albrecht, M., Huthmacher, C., Tosatto, S. C. E., and Lengauer, T. Decomposing protein networks into domain-domain interactions, Proceedings of the Fourth European Conference on Computational Biology (ECCB 2005) Bioinformatics 21, Suppl. 2 ii220-ii221 (2005)
   
• Ansari, S. and Helms, V. Statistical Analysis of Predominantly Transient Protein-Protein Interfaces. Proteins: Structure, Function, and Bioinformatics, 61(2), 344 - 355 (2005)
   
• Antes, I., Merkwirth, C., and Lengauer, T. POEM: Parameter optimization using ensemble methods: application to target specific scoring functions Journal of Chemical Information and Modeling 45, 5 1291-1302 (2005)
   
• Backes, C., Küntzer, J., Lenhof, H.-P., Comtesse, N., and Meese, E. Grabcas: a bioinformatics tool for score-based prediction of caspase- and granzyme b-cleavage sites in protein sequences. Nucleic Acids Res., 33, 208-213 (2005)
   
• Beerenwinkel, N., Däumer, M., Sing, T., Rahnenführer, J., Lengauer, T., Selbig, J., Hoffmann, D., and Kaiser, R. Estimating HIV evolutionary pathways and the genetic barrier to drug resistance Journal of Infectious Diseases 191, 11 1953-1960 (2005)
   
• Beerenwinkel, N., Rahnenführer, J., Däumer, M., Hoffmann, D., Kaiser, R., Selbig, J., and Lengauer, T. Learning multiple evolutionary pathways from cross-sectional data Journal of Computational Biology 12, 6 584-598 (2005)
   
• Beerenwinkel, N., Rahnenführer, J., Kaiser, R., Hoffmann, D., Selbig, J., and Lengauer, T. Mtreemix: a software package for learning and using mixture models of mutagenetic trees Bioinformatics 21, 9 2106-2107 (2005)
   
• Beerenwinkel, N., Sing, T., Lengauer, T., Rahnenführer, J., Roomp, K., Savenkov, I., Fischer, R., Hoffmann, D., Selbig, J., Korn, K., Walter, H., Berg, T., Braun, P., Fätkenheuer, G., Oette, M., Rockstroh, J., Kupfer, B., Kaiser, R., and Däumer, M. Computational methods for the design of effective therapies against drug resistant HIV strains Bioinformatics 21, 21 3943-3950 (2005)
   
• Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J., and Lengauer, T. BiQ Analyzer: Visulaization and quality control for DNA methylation data from bisulphite sequencing Bioinformatics 21, 21 4067-4068 (2005)
   
• Bojunga, J., Welsch, C., Antes, I., Albrecht, M., Lengauer, T., and Zeuzem, S. Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency Human Genetics 117, 6 558-564 (2005)
   
• Böckmann, R. A. and Caflisch, A. Spontaneous Formation of Detergent Micelles around the Outer Membrane Protein OmpX Biophys. J. 88 , 3191-3204 (2005)
   
• Castellano, S., Lobanov, A. V., Chapple, C., Novolesov, S. V., Albrecht, M., Hua, D., Lescure, A., Lengauer, T., Krol, A., Gladyshev, V. N., and Guigo, R. Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the novel SelJ family Proceedings of the National Academy of Sciences 102, 45 16188-16193 (2005)
   
• 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., and Meese, E. Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets. PNAS, 102(27), 9601-06 (2005)
   
• Costello, C. M., Mah, N., Häsler, R., Rosenstiel, P., Waetzig, G. H., Hahn, A., Lu, T., Gurbuz, Y., Nikolaus, S., Albrecht, M., Hampe, J., Lucius, R., Klöppel, G., Eickhoff, H., Lehrach, H., Lengauer, T., and Schreiber, S. Dissection of inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes PLoS Medicine 2, 8 e199 (2005)
   
• Förster-Waldl, E., Riemer, A. B., Dehof, A. K., Neumann, D., Brämswig, K., Boltz-Nitulescu, G., Pehamberger, H., Zielinski, C. C., Scheiner, O., Pollak, A., Lode, H., and Jensen-Jarolim, E. Isolation and structural analysis of peptide mimotopes for the disialoganglioside GD2, a neuroblastoma tumor antigen Mol. Immunol. 42(3):319-325 (2005)
   
• Geyer, T. and Tannor, D.J. A Mapping Approach to Synchronization in the "Zaifman Trap": II. The observed Bunch. Journal of Physics B: Atomic, Molecular, and Optical Physics, 38, 3423-2446 (2005)
   
• Gu, W. and Helms, V. Dynamical Binding of Proline-rich Peptides to their Recognition Domains (Abstract). Biochimica and Biophysica Acta (Proteins and Proteomics), 1754, 232-238 (2005)
   
• Gu, W., Kofler, W., Antes, I., Freund, C., and Helms, V. Alternative Binding Modes of Proline-rich Peptides Binding to the GYF-Domain. Biochemistry, 44, 6404-6415 (2005)
   
• Hahn, A., Rahnenführer, J., Talwar, P., and Lengauer, T. Confirmation of human protein interaction data by human expression data BMC Bioinformatics 6, 1 12 (2005)
   
• Helms V., Hutter M. C., and Gu, W. Was hat das Eiweiß in einem Computer zu suchen? Magazin Forschung, 28-32 (2005)
   
• Hessler, G., Zimmermann, M., Matter, H., Evers, A., Naumann, T., Lengauer, T., and Rarey, M. Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach Journal of Medicinal Chemistry 48, 21 6575-6584 (2005)
   
• Merkwirth, C. and Lengauer, T. Automatic Generation of complementary descriptors with molecular graph networks Journal of Chemical Information and Modeling 45, 5 1159-1168 (2005)
   
• Moll, A., Hildebrandt, A., Kerzmann, A., Lenhof, H.-P., and Kohlbacher, O. BALLView - An Open Source Tool for Molecular Modeling and Visualization. In: Tagungsband zum doIT Software-Forschungstag 2005, edited by D. Spath, K. Haasis, D. Klumpp. MFG Stiftung, Stuttgart, pages 203-214 (2005)
   
• Moll, A., Hildebrandt, A., Lenhof, H.-P., and Kohlbacher, O. BALLView: an object-oriented molecular visualization and modeling framework. J. Comput. Aided Mol. Des., 19(11), 791-800 (2005)
   
• Olkhova, E., Helms, V., and Michel, H. Titration Behaviour of Residues at the Entrance of the D-pathway of Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Continuum Electrostatic Calculations. Biophysical Journal, 89, 2324 - 2331 (2005)
   
• Piotukh, K., Gu, W., Kofler, M., Helms, V., and Freund, C. Cyclophilin A Binds to Linear Peptide Motifs Containing a Consensus that is Present in many Human Proteins. Journal of Biological Chemistry, 280(25), 23668-23674 (2005)
   
• Rahnenführer, J., Beerenwinkel, N., Wullich, B., Schulz, W. A., Hartmann, C., von Deimling, A., and Lengauer, T. Estimating cancer survival and clinical outcome based on genetic tumor progression scores Bioinformatics 21, 10 2438-2446 (2005)
   
• Ralser, M., Albrecht, M., Nonhoff, U., Lengauer, T., Lehrach, H., and Krobitsch, S. Ataxin-2 interacts with the cytoplasmatic poly(A)-binding protein 1 and is implicated in RNA-processing pathways Journal of Molecular Biology 346, 1 203-214 (2005)
   
• Ralser, M., Nonhoff, U., Albrecht, M., Lengauer, T., Wanker, E. E., Lehrach, H., and Krobitsch, S. Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways Human Molecular Genetics 14, 19 2893-2909 (2005)
   
• Sarrazin, C., Mihm, U., Herrmann, E., Welsch, C., Albrecht, M., Sarrazin, U., Traver, S., Lengauer, T., and Zeuzem, S. Replication enhancing mutations of the Hepatitis C virus replicon: Prevalence and clinical significance in patients with chronic Hepatitis C Journal of Infectious Diseases 192, 10 1710-1719 (2005)
   
• Shakya, S.K., Gu, W., and Helms, V. Molecular Dynamics Simulation of Truncated Bovine Adrenodoxin. Biopolymers, 78(1), 9-20 (2005)
   
• Sing, T., Sander, O., Beerenwinkel, N., and Lengauer, T. ROCR - Visualizing classifier performance in R erscheint in Bioinformatics 21, 20 3940-3941 (2005)
   
• Spaar, A. and Helms, V. Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase: Barstar. Journal of Chemical Theory and Computation, 1(4), 723-736 (2005)
   
• Staritzbichler, R., Gu, W. and Helms, V. Are Solvation Free Energies of Homogeneous Helical Peptides Additive? Journal of Physical Chemistry B, 109 (140), 19000-19007 (2005)
   
• Ulmschneider, S., Müller-Vieira, U., Klein, C., Antes, I., Lengauer, T., and Hartmann, R. W. Synthesis and evaluation of imidalzolymethylene-tetrahydronaphtalenes and -indanes: Potent inhibitors of Aldosterone Synthase Journal of Medicinal Chemistry 48, 6 1796-1805 (2005)
   
• Valentonyte, R., Hampe, J., Huse, K., Rosenstiel, P., Albrecht, M., Stenzel, A., Nagy, M., Gaede, K. I., Franke, A., R,, Haeseler,, Koch, A., Lengauer, T., Seegert, D., Reiling, N., Ehlers, S., Schweinger, E., Platzer, M., Krawczak, M., Müller-Querheim, J., Schürmann, M., and Schreiber, S. Sarcoidosis is associated with a truncating splice site mutation in BTNL2 Nature Genetics 37, 4 357-364 (2005)
   
• Wemmert, S., Ketter, R., Rahnenführer, J., Beerenwinkel, N., Strowitzki, M., Feiden, W., Hartmann, C., Lengauer, T., Stockhammer, F., Zang, K. D., Meese, E., Steudel, W.-I., von Deimling, A., and Urbschat, S. Patients with high grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment Neoplasia 7, 10 883-893 (2005)
   
• van Duist, M. J., Albrecht, M., Gaichino, D., Lengauer, T., Podswiadek, M. De marchi. M., and Punzi, L. A new CARD15 variant in Blau syndrome European Journal of Human Genetics 13, 6 742-747 (2005)
   

 
2004

• Albrecht, M. and Lengauer, T. Novel Sm-like proteins with long C-terminal tails and associated methyl tranferases FEBS Letters 569, 1-3 18-26 (2004)
   
• Albrecht, M. and Lengauer, T. Survey on PABC recognition motif PAM2 Biochem. Biophys .Res. Comm. 316, 1 129-138 (2004)
   
• Albrecht, M., Golatta, M., Wüllner, U., and Lengauer, T. Structural and functional analysis of Ataxin-2 and Ataxin-3 European Journal of Biochemistry 271, 15 3155-3170 (2004)
   
• Böckmann, R. A. and Grubmüller, H. Multistep Binding of Divalent Cations to Phospholipid Bilayers: A Molecular Dynamics Study Angew. Chemie Int. Ed. 43(8) , 1021-1024 Angew. Chemie 116(8) , 1039-1042 (2004)
   
• Domingues, F. S., Lengauer, T., Sommer, I., Protein structure prediction and databases. Nature Encyclopedia of the Human Genome, 4, 864-867 (2004)
   
• Domingues, F., Rahnenführer, J., and Lengauer, T. Automated clustering of ensembles of alternative models in protein structure databases Protein Engineering, Design and Selection 17, 6 537-543 (2004)
   
• Dönnes, P., Höglund, A., Sturm, M., Comtesse, N., Backes, C., Meese, E., Kohlbacher, O., and Lenhof, H.-P. Integrative analysis of cancer-related data using cap. FASEB J., 18(12), 1465-7 (2004)
   
• Flöck, D. and Helms, V.,. A Brownian Dynamics Study: The Effect of a Membrane Environment on an Electron Transfer System. Biophysical Journal, 87, 65-74 (2004)
   
• Geyer, T. and Tannor, D.J.,. A Mapping Approach to Synchronization in the "Zajfman Trap": Stability Conditions and the Synchronization Mechanism. Journal of Physics B: Atomic, Molecular and Optical Physics, 37(1), 73-92 (2004)
   
• Geyer, T., Gorba, C., and Helms, V.,. Interfacing Brownian Dynamics Simulations. Journal of Chemical Physics, 120, 4573-4580 (2004)
   
• Geyer, T.,. Electron Impact Double Ionization of Helium from Classical Trajectory Calculations. Journal of Physics B, 37(6),1215-1235 (2004)
   
• Gorba, C., Geyer, T., and Helms, V.,. Brownian Dynamics Simulations of Simplified Cytochrome c Molecules in the Presence of a Charged Surface. Journal of Chemical Physics, 121, 457-464 (2004)
   
• Gu, W., Rahi, S.J., and Helms, V.,. Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model. Journal of Physical Chemistry B, 108, 5806-5814 (2004)
   
• Hannemann, A., Schön, J. C., Jansen, M., Putz, H., and Lengauer, T. Modelling amorphous Si3B3N7,: Structure and elastic properties Physical Review B 70, 14 144201 (2004)
   
• Hildebrandt, A., Blossey, R., Rjasanow, S., Kohlbacher, O., and Lenhof, H.-P. Novel formulation of nonlocal electrostatics. Phys. Rev. Lett., 93(10), 108104 (2004)
   
• Hofestädt, R. and H.-P. Lenhof. Methoden und innovative anwendungen der informatik und informationstechnik. schwerpunktthema: molekulare bioinformatik. In H.-P. Hofestädt and H.-P. Lenhof (Eds.), Information technology (it) (2004)
   
• Hofmann, W. P., Herrmann, E., Kronenberger, B., Merkwirth, C., Welsch, C., Lengauer, T., Zeuzem, S., and Sarrazin, C. Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes Blood 104, 4 1228-1229 (2004)
   
• Hutter, M. C. and Hartmann R. W. QSAR of Human Steroid 5?-Reductase Inhibitors: Where are the differences between isoenzyme type 1 and 2? QSAR Comb. Sci., 23, 406-415 (2004)
   
• Merkwirth, C., Mauser, H., Schulz-Gasch, T., Roche, O., Stahl, M., and Lengauer, T. Ensemble methods for classification in cheminformatics Journal Chemical Information and Computer Science 44,6 1971-1978 (2004)
   
• Neumann, D., Lehr, C., Lenhof, H., and Kohlbacher, O. Computational modeling of the sugar-lectin interaction. Advanced DRUG DELIVERY Reviews, 56(4), 437-457 (2004)
   
• Olkhova, E., Hutter, M. C., Lill, M. A., Helms, V., and Michel H. Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations. Biophys. J., 86, 1873-1889 (2004)
   
• Park, Y., Elsner, M., Staritzbichler, R., and Helms, V.,. Novel Scoring Function for Modeling Structures of Oligomers of Transmembrane alpha-helices. Proteins: Structure, Function, and Bioinformatics, 57(3), 577-585 (2004)
   
• Pöhlmann, T., Böckmann, R. A., Grubmüller, H., Uchanska-Ziegler, B., Ziegler, A., and Alexiev, U. Differential Peptide Dynamics is Linked to MHC Polymorphism J. Biol. Chem. 279(27) , 28197-28201 (2004)
   
• Rahnenführer, J., Domingues, F. S., Maydt, J., and Lengauer, T. Calculating the statistical significance of changes in pathway activity from gene expression data Statistical Applications in Genetics and Molecular Biology 3, 1 Article 16 (2004)
   
• Sommer, I., Rahnenführer, J., Domingues, F. S., de Lichtenberg, U., and Lengauer, T. Predicting protein structure classes from function predictions Bioinformatics 20, 5 770-776 (2004)
   
• Stoll, M., Corneliussen, B., Costello, C. M., Waetzig, G. H., Mellgard, B., Koch, W. A., Rosenstiel, P., Albrecht, M., Croucher, P. J. P., Seegert, D., Nikolaus, S., Hampe, J., Lengaur, T., Pierrou, S., Foelsch, U. R., Mathew, C. G., Lagerstrom-Fermer, M., and Schreiber, S. Generic variation in DLF5 confers susceptibility to inflammatory bowel disease Nature Genetics 36, 5 476-480 (2004)
   
• von Öhsen, N., Sommer, I., Zimmer, R., and Lengauer, T. Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures Bioinformatics 20, 14 2228-2235 (2004)
   

 
2003

• Albrecht, M., Domingues, F. S., Schreiber, S., and Lengauer, T. Identification of mammalian orthologs associates PYPAF5 with distinct functional roles FEBS Letters 538 1-3 173-177 (2003)
   
• Albrecht, M., Domingues, F. S., Schreiber, S., and Lengauer, T. Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2 FEBS Letters 554 3 520-528 (2003)
   
• Albrecht, M., Hoffmann, D., Evert, B. O., Schmitt, I., Wüllner, U., Lengauer T. Structural modeling of ataxin-3 reveals distant homology to adaptins. Proteins: Structure, Function, and Genetics 50, 355-370 (2003)
   
• Albrecht, M., Lengauer, T. Pyranose oxidase identified as member of the GMC oxidoreductase family. Bioinformatics, 19, 1216-1220 (2003)
   
• Albrecht, M., Lengauer, T., Schreiber, S. Disease-associated variantsd in PYPAF1 and NOD2 result in similar alterations of conserved sequence. FEBS Letters, 19, 2171-2175 (2003)
   
• Albrecht, M., Lengauer, T., and Schreiber, S. Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence FEBS Letters 538 173-177 (2003)
   
• Beerenwinkel, N., Däumer, M., Oette, M., Korn, K., Hoffmann, D., Kaiser, R., Lengauer, T., Selbig, J., and Walter, H. Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes Nucleic Acids Res. 31, 13 3850-3855 (2003)
   
• Beerenwinkel, N., Lengauer, T., Däumer, M., Kaiser, R., Walter, H., Korn, K., Hoffmann, D., Selbig, J. Methods for optimizing antiviral combination therapies. to appear in Proc. 11th International Conference on Intelligent Systems for Molecular Biology (ISMB2003) (2003)
   
• Burkhardt, S., Kärkkäinen, J. Better filtering with gapped q-grams. Fundamenta Informaticae, 56(1-2), 51-70 (2003)
   
• Böckmann, R. A. and Grubmüller, H. Conformational Dynamics of the F1-ATPase Beta-Subunit: A Molecular Dynamics Study Biophys. J. 85(3) , 1482-149 (2003)
   
• Böckmann, R. A., Hac, A., Heimburg, T., and Grubmüller, H. Effect of Sodium Chloride on a Lipid Bilayer Biophys. J. 85(3) , 1647-1655 (2003)
   
• Corrie, J. E. T., Barth, A., Munasinghe, V. R. N., Trentham, D. R., and Hutter M. C. Photolytic Cleavage of 1-(2-Nitrophenyl)ethyl Ethers Involves Two Parallel Pathways and Product Release Is Rate-Limited by Decomposition of a Common Hemiacetal Intermediate. J. Am. Chem. Soc., 125, 8546-8554 (2003)
   
• Csögör, Z., Nacken, M., Sameti, M., Lehr, C. M. Schmidt H, Modified silica particles for gene delivery. Materials Science and Engineering C23, 93-97 (2003)
   
• Domingues F. S., Lengauer T. Protein Function from Sequence and Structure Data. Applied Bioinformatics 2 (1): 3-12, (2003)
   
• Fuchs, S., Hollins, A. J., Laue, M., Schäfer, U. F., Roemer, K., Gumbleton, M., Lehr, C.M. Differentiation of human alveolar epithelial cells in primary culture. Morphological characterisation and expression of caveolin-1 and Sp C. Cell and Tissue Research, 311(1), 31-45 (2003)
   
• Geyer, T., and Rost, J.M.,. Dynamical Stabilization of Classical Multi-Electron Targets against Autoionization. Journal of Physics B: Atomic, Molecular and Optical Physics, 36, L107-L112 (2003)
   
• Gorba, C., and Helms, V.,. Diffusional Dynamics of Cytochrome c Molecules in the Presence of a Charged Surface. Soft Materials, 1, 187-204 (2003)
   
• H.-P. Lenhof and M.-F. Sagot. Proceedings - European Conference on Computational Biology (ECCB) 2003. In H.-P. Lenhof, and M.-F. Sagot (Eds.), Bioinformatics 19 (Suppl. 2), 1-256 (2003)
   
• Handel, S., Jose, J. Monitoring the surface display of recombinant proteins by cysteine labeling and flow cytometry. Chembiochem, 4, 396-405 (2003)
   
• Hans, M.A., Heinzle, E., Wittmann, C. Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol. Bioeng., 82(2), 143-151 (2003)
   
• Hartmann, R. W., Müller, U., Ehmer, P. B. Discovery of selective CYP11B2 (aldosterone synthase) inhibitors for the therapy of congestive heart failure and myocardial fibrosis. Eur. J. Med. Chem., 38, 363-366 (2003)
   
• Hildebrandt, A., Kohlbacher, O., Blossey, R., and Lenhof, H.-P. Using nonlocal electrostatics for solvation free energy computations: ions and small molecules. Preprint (2003)
   
• Hutter, M. C. Prediction of Blood-Brain Barrier Permeation Using Quantum Chemically Derived Information. J. Comput.-Aided Mol. Des., 17, 415-433 (2003)
   
• Hutter, M. C. and Helms, V. Mechanism of Phosphoryl Transfer in Kinases Investigated by Semiempirical Calculations. International Journal of Quantum Chemistry, 95, 479-486 (2003)
   
• Hutter, M. C. and Helms, V. Mechanism of Phosphoryl Transfer in Kinases Investigated by Semiempirical Calulations. Int. J. Quant. Chem., 95, 479-486 (2003)
   
• Hutter, M. C., Prediction of Blood-Brain Barrier Permeation Using Quantum Chemically Derived Information. Journal of Computer-Aided Molecular Design, 17(7), 415-433 (2003)
   
• Jaeckle, E., Schaefer, U. F., Loth, H. Comparison of effects of different ointment bases on the penetration of ketoprofen through heat-separated human epidermis and artificial lipid barriers. J. Pharm. Sciences, 9 (7), 1396-1406 (2003)
   
• Krebs, J., Helms, V., Griesinger, C. und Carafoli, E.,. The Regulation of the Calcium Signal by Membrane Pumps. Helv. Chim. Acta, 86, 3875-3888 (2003)
   
• Mathur, S., Hassel, M., Steiner, F., Hollemeyer, K., Hartmann, R.W. Development of a new approach for screening combinatorial libraries using MALDI-TOF MS and HPLC-ESI-MS/MS. J. Biomol. Screening, 8, 136-148 (2003)
   
• Strobel, S. Robust and fast computation of molecular surfaces. Diploma thesis, Saarland University (2003)
   
• Talwar, P., Wittmann, C., Heinzle, E., and Lengauer, T. Software tool for automated processing of 13C labeling data from mass spectrometric data BioTechniques 35, 6 (2003)
   
• Zachariae, U., Helms, V., and Engelhardt, H., .. Multistep Mechanism of Chloride Translocation in a Strongly Anion-Selective Porin Channel. Biophysical Journal, 85, 954-962 (2003)
   
• de Groot, Bert L., Frigato,T., Helms, V., and Grubmüller, H.,. The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel. Journal of Molecular Biology, 333, 279-293 (2003)
   
• Öhsen von, N., Sommer, I., Zimmer, R. Profile-profile alignment: A powerful tool for protein structure prediction. Pacific Symposium on Biocomputing (PSB) 8, 252-263 (2003)
   

 
2002

• Albrecht, M., Hanisch, D., Zimmer, R., Lengauer, T. Improving fold recognition of protein threading by experimental distance constraints. In Silico Biology 2, 325-337 (2002)
   
• Althaus, E., Caprara, A., Lenhof, H.-P., Reinert, K. Multiple sequence alignment with arbitrary gap costs: computing an optimal solution using polyhedral combinatorics. Proceedings of the European Conference on Computational Biology (ECCB 2002) Bioinformatics 18 Supp. 2, 4-16 (2002)
   
• Althaus, E., Kohlbacher, O., Lenhof, H.-P., Müller, P. A combinatorial approach to protein docking with flexible side-chains. J. Comput. Biol. 9, 597-612 (2002)
   
• Antes, I., Thiel, W., Gunsteren van, W. F. Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of glu46 deprotonation and mutation. Europ. Biophys. J. 31, 504-520 (2002)
   
• Bechtel S., Belkina, N., Bernhardt, R. The effect of amino-acid substitutions l112P, D147E and K152N in CYP1B2 on the catalytic activities of the enzyme. Eur. J. Biochem. 269, 1118-1127 (2002)
   
• Beerenwinkel, N., Lengauer, T., Däumer, M., Sierra, S., Schmidt, B., Walter, H., Korn, K., Oette, M., Fätkenheuer, G., Rockstroh, J. Hoffmann, D., Kaiser, R., Selbig, J. Geno2pheno is predictive of short-term virological response. In: Proc. from the 5th Int. Workshop on HIV Drug Resistance & Treatment Strategies. Antiviral Therapy 7, 98 (2002)
   
• Beerenwinkel, N., Lengauer, T., Schmidt, B., Walter, H., Kaiser, R., Hoffmann, D., Korn, K., Selbig, J. Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype. Proc. Natl. Acad. Sci. USA 99, 8271-8276 (2002)
   
• Beerenwinkel, N., Lengauer, T., Schmidt, B., Walter, H., Kaiser, R., Hoffmann, D., Korn, K., Selbig, J. Quantitative phenotype prediction by support vector machines. In: Proc. from the 5th Int. Workshop on HIV Drug resistance & Treatment Strategies. Antiviral Therapy 7, 97 (2002)
   
• Beilke, D., Weiss, R., Löhr, F., Pristovsek, P., Hannemann, F., Bernhardt, R., Rüterjans, H. A new electron transport mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin. Biochemistry 41, 7969-7978 (2002)
   
• Betscheider, D., Ray, S., Zangen, D., Schultheiss, E., Lengauer, T., Jose, J. A new model for an inhibitor of human cathepsin G by bacterial surface display library screening and protein-peptide docking. In: Poster Abstracts of the Europ. Conf. on Comp. Biology 2002, (Eds. T. Lengauer, H.-P. Lenhof, R. Christmann, Saarbrücken Germany, P13 (2002)
   
• Biwer, A, Antranikian, G, Heinzle, E. Enzymatic production of cyclodextrins. Appl. Microbiol. Biotechnol. 59, 609-617 (2002)
   
• Boizinov, D., Rahnenführer, J. Unsupervised technique for robust target separation and analysis of Microarray spots through adaptive pixel clustering. Bioinformatics 18, 747-756 (2002)
   
• Brechtel, E., Huwig, A., Giffhorn, F. L-Glucitol catabolism in Stenotrophomonas maltophilia Ac. Appl. Environ. Microbiol. 68, 582-587 (2002)
   
• Bureik, M., Schiffler, B., Hiraoka, Y., Vogel, F., Bernhardt, R. Functional expression of human mitochondrial CYP11B2 in fission yeast and identification of a new internal electron transfer protein, etp1. Biochemistry 41, 2311-2321 (2002)
   
• Burkhardt, S. Filter Algorithms for Approximate String Matching. Ph.D. thesis, Universität des Saarlandes, (2002)
   
• Burkhardt, S., Kärkkäinen, J. One-gapped q-gram filters for levenshtein distance. In: Proc. 13th Annual Symp. on Combinatorial Pattern Matching. LNCS 2373, (Eds.) A. Apostolico, M. Takeda. Springer, Berlin, 225-234 (2002)
   
• Böckmann, R. A. and Grubmüller, H. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase Nature Struct. Biol. 9 , 198-202 (2002)
   
• Bülow, H. E., Bernhardt, R. Analyses of the CYP11B gene family in the guinea pig suggest the existence of aprimordial CYP11B gene with aldosterone synthase activity. Eur. J. Biochem. 269, 3838-3846 (2002)
   
• Comtesse, N., Niedermayer, I., Glass, B., Heckel, D., Maldener, E., Nastainczyk, W., Feiden, W., Meese, E. MGEA6 is tumor-specific overexpressed and frequently recognized by patient-serum antibodies. Oncogene 20, 239-247 (2002)
   
• Crauser, A., Ferragina, P. A theoretical and experimental study on the construction of suffix arrays in external memory. Algorithmica 32, 1-35 (2002)
   
• D. Neumann, A. Kerzmann, O. Kohlbacher. Modelling the sugar-lectin interaction by computer-simulated docking. In Abstracts of the 20th Interlec Meeting/, May 20.-25.2002, Copenhagen/Denmark (2002)
   
• Deprez, E., Gill, E., Helms, V., Wade, R.C. and Hoa, G. H. H. Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin. J. Inorg. Biochem., 91, 597-606 (2002)
   
• Dönnes, P., Elofsson, A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3, 25 (2002)
   
• Ehmer, P. B., Bureik, M., Bernhardt, R., Müller, U., Hartmann, R. W. Development of a test system for inhibitors of human aldosterone synthase (CYP11B2): screening in fission yeast and evalutation of selectivity in V79 cells. J. Steroid Biochem. Mol. Biol. 81, 173-179 (2002)
   
• Ehrhardt, C., Fuchs, S., Abu-Dahab, R., Schaefer, U. F., Lehr, C. M. Arzneistoffabsorption durch die Lungenschleimhaut . Zellkulturmodelle und partikuläre Arzneistoffträger. In: G. Scheuch .Aerosole in der Inhalationstherapie VI.. dustriTBmed, München (2002)
   
• Ehrhardt, C., Kneuer, C., Fiegel, J., Hanes J., Schäfer, U., Kim, K. J., Lehr, C. M. Influence of apical fluid volume on the development of functional cellular junctions in the human epithelial cell line 16HBE140-: implications for the use of this cell line as an in vitro model for bronchial drug absorption studies. Cell Tissue Res. 308, 391-400 (2002)
   
• Flöck, D. and Helms, V. Protein-protein docking of electron transfer complexes. cytochrome c oxidase and cytochrome c. PROTEINS: Structure, Function, and Genetics 47, 75-85 (2002)
   
• Freimund, S., Baldes, L., Huwig, A., F. Giffhorn, F. Enzymatic synthesis of D-glucosone 6-phosphate (D-arabino-hexos-2-ulose 6-(dihydrogen phosphate)) and NMR analysis of its isomeric forms. Carbohydr. Res. 337, 1585-1587 (2002)
   
• Freudenberg, J., Zimmer, R., Lengauer, T. A new method for unification of existing protein structure- and sequence-families. In Silico Biology 2, 0031 (2002)
   
• Haas J., Lehr C. M. Developments in the area of bioadhesive drug delivery systems. Expert Opin. Biol. Ther. 2, 287-298 (2002)
   
• Handel, S., Jose, J. Surface display of active sorbitol dehydrogenase in Escherichia coli. Biocat2002, International Congress on Biocatalysis, Hamburg, Germany, P013 (2002)
   
• Hanisch, D., Zien, A., Zimmer, R., Lengauer, T. Co-clustering of biological networks and gene expression data. Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2002) Bioinformatics 18 Supp. 1, 145-154 (2002)
   
• Hanisch, D., Zimmer, R. Lengauer, T. ProML - the protein markup language for specification of protein sequences, structures and families. In Silico Biology 2, 0029 (2002)
   
• Hannemann, F., Bera, A. K., Fischer, B., Lisurek, M., Teuchner, K., Bernhardt , R. Unfolding and conformational studies on bovine adrenodoxin probed by engineered intrinsic tryptophan fluorescence. Biochemistry 41, 11008-11016 (2002)
   
• Helms, V. Attraction within the Membrane - Forces behind transmembrane protein folding and supramolecular complex assembly. EMBO Rep. 3, 1133-1138 (2002)
   
• Helms, V. Electronic excitations of biomolecules studies by quantum chemistry. Curr. Opin. Struct. Biol. 12, 169-175 (2002)
   
• Hildebrandt, A. An algorithm for the efficient and reliable computation of the electrostatic contribution to the free energy of solvation using nonlocal electrodynamics. Diploma thesis, Saarland University (2002)
   
• Hindle, S. A., Rarey, M., Buning. C., Lengauer, T. Flexible docking under pharmacophore type constraints. J. Comp. Aided Mol. Des. 16, 129-149 (2002)
   
• Hollemeyer, K., Altmeyer, W., Heinzle, E. Identification and quantification of feathers, down and hair of avian and mammalian origin using MALDI-TOF- mass spectrometry. Anal. Chem., 74, 5960-5968 (2002)
   
• Hollemeyer, K., Heinzle, E., Tholey, A. Identification of oxidized methionine residues in peptides containing two methionine residues by derivatization and MALDI-TOF mass spectrometry. Proteomics 2, 1524-1531 (2002)
   
• Hutter, M. C, Helms, V. The mechanism of phosphorylation of natural nucleosides and anti-HIV analogs by nucleoside diphosphate kinase is Independent of their sugar substituents. Chembiochem, 3, 643-651 (2002)
   
• Hutter, M. C., Krebs, J., Meiler, J., Griesinger, C., Carafoli, E., Helms, V. A Structural model of the complex between phospholamban and the calcium pump of Sarcoplasmatic reticulum obtained by molecular mechanics. Chembiochem 3, 1200-1208 (2002)
   
• John, G. T., Klimant, I., Wittmann, C., Heinzle, E. Integrated optical sensing of dissolved oxygen in microtiter plates. A novel tool for microbial cultivation, Biotechnol. Bioeng. 81, 829-836 (2002)
   
• Jose, J. Towards chiral synthesis and directed evolution: cellular surface display of enzymes and enzyme inhibitors. Gemeinsame Jahrestagung der GDCH, Fachgruppe Medizinische Chemie, DPhG, Fachgruppe Pharmazeutische Chemie, Travemünde 2002, P0044 (2002)
   
• Jose, J., Bernhardt, R., Hannemann, F. Cellular surface display of dimeric Adx and whole cell P450-mediated steroid synthesis on E. coli. J. Biotechnol. 95, 257-268 (2002)
   
• Jung, A., Maier, R., Vartanian, J. P., Bocharov, G., Jung, V., Fischer, U., Meese, E., Wain-Hobson, S., Meyerhans, A., Recombination: Multiply infected spleen cells in HIV patients. Nature, 418, 414 (2002)
   
• Kämper, A., Apostolakis, J., Lengauer, T. Docking of bacterial cell-wall fragments into glycopeptide antibiotics. In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, Padua, Italy, 49 (2002)
   
• Kärkkäinen, J. Computing the threshold for q-gram filters. Algorithm Theory 2368 - SWAT 2002, 348-357 (2002)
   
• Lengauer, T., Lenhof, H.-P. (Eds.) Proceedings of the European Conference on Computational Biology (ECCB 2002). Bioinformatics 18 Suppl. 1, (2002)
   
• Lill, M. A., Helms, V. Dynamic simulations identify ultrafast proton relay in Green Fluorescent Protein. Proc. Natl. Acad. Sci. USA 99, 2778-2781 (2002)
   
• Lloyd-MacGilp S. A., Torielli, L., Bechtel, St., Tripodi, G., Gomez-Sanchez, C., Zagato, L., Bernhardt, R., Kenyon, C. J. Mutations in aldosterone synthase gene of Milan hypertensive rats: phenotypic consequences. Am. J. Physiol. Metab. 282, E608-E617 (2002)
   
• Löhbach, C., Bakowsky, U., Kneuer, C., Jahn, D., Graeter, T., Schäfers, H. J., Lehr, C. M. Wet chemical modification of PTFE implant surfaces with a specific cell adhesion molecule. ChemComm. 21, 2568-2569 (2002)
   
• Mayer, J., Meese, E. The human endogenous retrovirus family HERV-K(HML-3). Genomics 80, 331-343 (2002)
   
• Meaney. C., Florea, B. I., Ehrhardt, C., Schaefer, U. F., Lehr, C. M., Junginger, H. E., Borchard, G. Bronchial epithelial cell cultures.In: C. M. Lehr .Cell culture models of biological barrriers.. Taylor & Francis, London (2002)
   
• Meese, E., Comtesse, N. Cancer genetics and tumor antigens: Time for a Combined View? Genes, Chromosomes and Cancer 33, 107-113 (2002)
   
• Moll, A. Modellierung genregulatorischer Netzwerke. Diploma thesis, Saarland University (2002)
   
• Neumann, D., Kohlbacher, O., Lenhof, H.-P., Lehr, C.-M. Protein-sugar interactions: calculated versus experimental binding energies. Eur. J. Biochem. 269, 1518.1524 (2002)
   
• Neumann, Dirk. Computational and experimental determination of binding free energies of N-acetylglucosamine derivatives and lectins of the hevein family, Ph.D. Thesis, Saarbrücken, (2002)
   
• Noh, U., Heck, S., Giffhorn, F., Kohring, G. Phototrophic transformation of phenol to 4-hydroxy-pehenylacetate by Rhodopseudomonas palustris. Appl. Microbiol. Biotechnol. 58, 830-835 (2002)
   
• Picard, F., Barassin S., Mokhtarian, A., Hartmann, R. W. Synthesis and evaluation of 2.-substituted 4-(4.-carboxy- or 4.-carboxymethylbenzylidene)-N-acylpiperidines: highly potent and In Vivo active steroid-5.-reductase type 2 inhibitors. J. Med. Chem., 45, 3406-17 (2002)
   
• Picard, F., Schulz, T., Hartmann, R. W. 5-Phenyl substituted 1-methyl-2-pyridones and 4'- substituted biphenyl-4-carboxylic acids. Synthesis and evaluation as inhibitors of steroid-5.-reductase type 1 and 2. Bioorg. Med. Chem. 10, 437-448 (2002)
   
• Ruppert, C., Schmidt, R., Grimminger, F., Suzuki, Y., Seeger, W., Lehr, C. M., Günther, A. Chemical coupling of a monoclonal antisurfactant protein-B antibody to human urokinase for targeting surfactant-incorporating alveolar fibrin. Bioconj. Chem., 13, 804-811 (2002)
   
• Sarrazin, C., Herrmann, E., Bruch, K., Zeuzem, S., Hepatitis C virus nonstructural 5A protein and interferon resistance: a new model for testing the reliability of mutational analyses. J Virol. 7, 11079-11090 (2002)
   
• Schultheiss, E., Paar, C., Schwab, H., Jose, J. Functional esterase surface display by the autotransporter pathway in Escherichia coli. J. Mol. Catal. B. Enz. 18, 89-97 (2002)
   
• Schultheiss, E., Weiss, S., Heinzle, E., Jose, J. Functional surface display of esterase ApeE in Escherichia coli: a step towards the molecular evolution. Fourth European Graduate Student Meeting, Frankfurt/Main, Germany, P53 (2002)
   
• Schultheiss, E., Weiss, S., Heinzle, E., Jose, J. Surface Display of Functional Esterases in E. coli. Biocat2002, International Congress on Biocatalysis, Hamburg, Germany, L17 (2002)
   
• Sirava, M., Schäfer, T., Eiglsperger, M., Kaufmann, M., Kohlbacher, O., Bornberg-Bauer, E., Lenhof, H.-P. BioMiner - modeling, analysing, and visualizing biochemical pathways and networks. Proceedings of the European Conference on Compytational biology (ECCB 2002), Bioinformatics 18, Suppl. 2, 219-230 (2002)
   
• Sommer, I., Lengauer, T., Zien, A., Öhsen von, N., Zimmer, R. Confidence measures for protein fold recognition. Bioinformatics 18, 802-812 (2002)
   
• Tholey, A., Wittmann, C., Kang, M.-J., Bungert, D., Hollemeyer, K., Heinzle, E. Derivatization of small biomolecules for optimized matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom., 37, 963-973 (2002)
   
• Wagner, H., Kostka, K. H., Lehr, C. M., Schaefer U. F. Correlation between Stratum Corneum/Water-Partition Coefficient and Amounts of Flufenamic Acid Penetrated into the Stratum Corneum. J. Pharm. Sci., 91, 1915-1921 (2002)
   
• Wagner, H., Kostka, K. H., Lehr, C. M., Schäfer, U. F. Human skin penetration of flufenamic acid: Invivo/in-vitro correlation /deeper skin layers) for skin samples from the same subject. J. Invest. Dermatol. 18, 540-544 (2002)
   
• Weiss, S., John, G. T., Klimant, I., Heinzle, E. Modeling of mixing in 96-well microplates observed with fluorescence indicators. Biotechnol. Prog., 18, 821-830 (2002)
   
• Weiss, S., Schultheiss, E., Jose, J., Klimant, I., Heinzle, E. Screening of Hydrolases Displayed on the Surface of E. coli Using 96 Well Microplates with Integrated pH-Sensor. Biocat2002, International Congress on Biocatalysis, Hamburg, Germany, P011 (2002)
   
• Winden van, W. A.,Wittmann, C., Heinzle, E., Heijnen, J. J. Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol. Bioeng., 80, 477-479 (2002)
   
• Wirth, M., Kneuer, C., Lehr, C. M., Gabor, F. Lectin mediated drug delivery: Discrimination between cytoadhesion and cytoinvasion and evidence for lysosomal accumulation of wheat germ agglutinin in the Caco-2 model. J. Drug Targeting, 10(6), 439-448 (2002)
   
• Wittmann, C. Metabolic flux analysis using mass spectrometry. Adv. Biochem. Eng. Biotechnol., 74, 39-64 (2002)
   
• Wittmann, C., Hans, M., Bluemke, W. Metabolic physiology of aroma producing Kluyveromyces marxianus. Yeast, 19, 1351-1363 (2002)
   
• Wittmann, C., Hans, M., Heinzle, E. In vivo analysis of intracellular amino acid labelings by GC/MS. Anal. Biochem., 307(2), 379-82 (2002)
   
• Wittmann, C., Heinzle, E. Genealogy profiling through strain improvement using metabolic network analysis. metabolic flux genealogy of several generations of lysinge producing corynebacteria. Appl. Environ. Microbiol.68, 5843-5859 (2002)
   
• Zangen, D. Autodisplay of Enzyme Inhibitors. Ph.D. thesis, Universität des Saarlandes, Saarbrücken (2002)
   
• Zangen, D., Jose, J. Cellular surface display of protease inhibitors: selection by enzyme binding and flow cytometry. Fourth European Graduate Student Meeting, Frankfurt/Main, Germany, V60 (2002)
   
• Zien, A., Fluck, J., Zimmer, R., Lengauer, T. Microarrays: how many do you need? In: Proc. Sixth Annual Conf. on Research in Computational Molecular Biology (RECOMB2002). ACM Press, New York, 321-330 (2002)
   
• Zöllner, A., Hannemann, F., Lisurek, M., Bernhardt, R. Deletions in the loop surrounding the iron-sulfur cluster of adrenodoxin severely affect the interactions with its native redox partners adrenodoxin reductase and cytochrome P450scc (CYP11A1). J. Inorg. Biochem. 91, 644-654 (2002)
   

 
2001

• Abu-Dahab, R., Schäfer, U. F., Lehr, C. M. Lectin functionalized liposomes for pulmonary drug delivery: Effect of Nebulization on Stability and Bioadhesion. Eur. J. Pharm. Sci. 14, 37-46 (2001)
   
• Apostolakis, J., Hofmann, D., Lengauer, T. Derivation of a scoring function for crystal structure prediction. Acta Crystallographica A57, 442-450 (2001)
   
• Bartoschek, S., Buurman, G., Thauer, R.K., Geierstanger, B.H., Weyrauch, J.P., Griesinger, C., Nilges, M., Hutter, M. C., Helms, V. Re-face stereospecificity of methylenetetrahydromethanopterin dehydrogenases and methylene-tetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate. Chembiochem 2, 530-541 (2001)
   
• Bauer, C., Diesinger, I., Brass, N., Schäfers, H.-J., Steinhart, H., Iro, H., Meese, E. Translation initiation factor eIF-4G is immunogenic, overexpressed and amplified in squamous cell lung carcinoma. Cancer 92, 822-829 (2001)
   
• Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, K. Geno2pheno: a system for the interpretation of genotypic HIV drug resistance tests. IEEE Intelligent Systems 16, 35-41 (2001)
   
• Belkina, N. V., Lisurek, M., Ivanov, A. S., Bernhardt, R. Modelling of 3D-structures of cytochromes P450 11B1 and 11B2. J. Inorg. Biochem. 87, 197-207 (2001)
   
• Bonarius, H.P.J., Oezemre, A., Timmerarends, B., Skrabal, P., Tramper, J., Schmid, G., Heinzle, E. Metabolic flux analysis of continuously cultured hybridoma cells using 13CO2 mass spectrometry in combination with in combination with 13C-lactate NMR spectroscopy and metabolite balancing. Biotechnol. Bioeng. 74, 528-538 (2001)
   
• Brück, A., Abu-Dahab, R., Borchard, G., Schäfer, U. F., Lehr, C. M. Lectin-functionalized liposomes for pulmonary drug delivery: interaction with human alveolar epithelial cells, J. Drug Target. 9, 241-251 (2001)
   
• Burkhardt, S., Kärkkäinen, J.: Better filtering with gapped q-grams. In: Proc. 12th Annual Symp. on Combinatorial Pattern Matching (CPM-01). LNCS 2089, (Eds.) A. Amir, G. Landau. Springer, Berlin, 73-85 (2001)
   
• Claußen, C., Buning, C., Rarey, M., Lengauer, T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308, 377-395 (2001)
   
• Fisher, A., Friel, E. C., Bernhardt, R., Gomez-Sanchez, C., Mc Connell, J., Fraser, R., Davies, E. Effects of 18-hydroxylated steroids on corticosteroid production by human aldosterone synthase and 11.-hydroxylase. J. Clin. Endocrinol. Metab. 86, 4326-4329 (2001)
   
• Grinberg, A.V., Bernhardt, R. Contribution of a salt bridge to the thermostability of adrenodoxin determined by site-directed mutagenesis. Arch. Biochem. Biophys. 396, 25-34 (2001)
   
• Hampf, M., Ngoc Dao, N. T., Hoan, N. T., Bernhardt, R. Unequal crossing-over between aldosterone synthase and 11.-hydroxylase genes causes congenital adrenal hyperplasia. J. Clin. Endocrinol. Metab. 86, 4445-4452 (2001)
   
• Hannemann, F., Rottmann, M., Schiffler, B., Bernhardt, R. The loop region covering the iron-sulfur cluster in bovine adrenodoxin comprises a new interaction site for redox partners. J. Biol. Chem. 276, 1369-1375 (2001)
   
• Hans, M., Heinzle, E., Wittmann, C. Quantification of intracellular amino acids in batch-cultures of Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 56, 776-779 (2001)
   
• Iametti, S., Bera, A. K., Vecchio, G., Grinberg, A., Bernhardt, R., Bonomi, F. GroEL-assisted refolding of adrenodoxin during chemical cluster insertion. Eur. J. Biochem. 268, 2421-2429 (2001)
   
• John, G. T., Heinzle, E. Quantitative screening method for hydrolases in microplates using pH indicators: Determination of kinetic parameters by dynamic pH monitoring. Biotechnol. Bioeng. 72, 620-627 (2001)
   
• Jose, J. Display of functional biocatalysts on the surface of E. coli: options for the evolutive design. BioTrans 2001, Darmstadt, Germany, P59 (2001)
   
• Jose, J., Bernhardt, R., Hannemann, F. Functional display of active adrenodoxin, a .2Fe-2S. ferredoxin, on the surface of E. coli. Chembiochem. 2, 695-701 (2001)
   
• Jose, J., Bernhardt, R., Hannemann, F. Functional display of active bovine adrenodoxin on the surface of E. coli by chemical incorporation of the [2Fe-2S] cluster and whole cell P450-mediated steroid conversion. BioTrans 2001, Darmstadt, Germany, P291 (2001)
   
• Kamberaj, H., Helms, V. Monte Carlo simulation of biomolecular systems with BIOMCSIM. Comp. Phys. Comm. 141, 375-402 (2001)
   
• Kang, M.-J., Tholey, A., Heinzle, E. Application of automated matrix-assisted laser desorption/ionisation time-of-flight- mass spectrometry for the measurement of enzyme activities. Rapid Commun. Mass Spectrom. 15, 1327-1333 (2001)
   
• Kappl, R., Hüttermann J., Fetzner, S. The molybdenum-containing hydroxylases of quinoline, isoquinoline, and quinaldine. In: Molybdenum and Tungsten. Their Roles in Biological Processes. Met. Ions Biol. Syst. 39, 481-538 (2001)
   
• Kleber, A., Hartmann, R.W., Jose, J. No effect of thromboxane A2 on the attachment of the tumor cell lines MDA MB 231, DU145, and U937 to the basement membrane in an in-vitro model. J. Cancer Res. Clin. Oncol. 127, 751-754 (2001)
   
• Kneuer, C., Bakowsky, U., Olbrich, C. Safe DNA transfection with cationic solid lipid nanoparticles. New Drugs Vol. 2, 54-60 (2001)
   
• Kohlbacher, O. BALL - A framework for rapid application development in molecular modeling. In: T. Plesser, H. Hayd (Eds.), Forschung und wissenschaftliches Rechnen - GWDG Berichte: Beiträge zum Heinz-Billing-Preis 2000. Göttingen: Gesellschaft für wissenschaftliche Datenverarbeitung mbH., 13-28 (2001)
   
• Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., Lenhof, H.-P. A NMR-spectra-based scoring function for protein docking. In: Proc.5th Annual International Conference on Computational Molecular Biology (RECOMB 2001). ACM Press, New York, 169-177 (2001)
   
• Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., Lenhof, H.-P. Structure prediction of protein complexes by a NMR-based protein docking algorithm. J. Biomol. NMR 20, 15-21 (2001)
   
• Kohlbacher, Oliver. New Approaches to Protein-Docking. Ph.D. Thesis, Saarbrücken (2001)
   
• Lamprecht, A., Schäfer, U., Lehr, C. M., Size dependent bioadhesion of micro- and nanoparticulate carriers to the inflamed colonic mucosa. Pharm. Res. 18, 788-793 (2001)
   
• Lamprecht, A., Ubrich, N., Yamamoto, H., Schäfer, U., Takeuchi, H., Lehr, C. M., Maincent, P., Kawashima, Y. Design of rolipram loaded nanoparticles: comparison of two preparation methods, J. Contr. Rel. 71, 297-306 (2001)
   
• Lamprecht, A., Ubrich, N., Yamamoto, H., Schäfer, U., Takeuchi, H., Maincent, P., Kawashima, Y., Lehr, C. M. Biodegradable nanoparticles for the targeted drug delivery in treatment of inflammatory bowel disease. J. Pharmacol. Exp. Ther. 299, 775-781 (2001)
   
• Lengauer, T. (Ed.) Bioinformatics - From genomes to drugs. Series: Methods and Principles in Medicinal Chemistry, Wiley-VCH, Weinheim, Vol. 14 (2001)
   
• Lengauer, T. Bioinformatik an der Schwelle zur postgenomischen Ära. In: Was wissen wir, wenn wir das menschliche Genom kennen?. (Eds.) L. Honnefelder, P. Propping. DuMont, Köln, 56-62 (2001)
   
• Lengauer, T., Sankoff, D., Istrail, P., Pevzner, P., Waterman, M.S. (Eds.) Proceedings of the 5th Annual Conference on Research in Computational Molecular Biology (RECOMB2001). ACM Press, New York, (2001)
   
• Lill, M. A., Helms, V. Compact parameter set for fast estimation of proton transfer rates. J. Chem. Phys. 114, 1125-1132 (2001)
   
• Lill, M. A., Helms, V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD). J. Chem. Phys. 115, 7993-8005 (2001)
   
• Lill, M. A., Helms, V. Reaction rates for proton transfer over small barriers and connection to transition state theory. J. Chem. Phys. 115, 7985-7992 (2001)
   
• Lizio, R., Klenner, T., Sarlikiotis, A. W., Romeis, P., Marx, D., Nolte, T., Jahn, W., Borchard, G., Lehr, C. M. Systemic delivery of the GnRH-antagonist cetrorelix to anaesthesized and orotracheally cannulated rats by a new aerosol delivery system. Pharm. Res.18, 771-779 (2001)
   
• Olbrich, C., Bakowsky, U., Lehr, C. M., Müller R. H., Kneuer, C. Cationic solid-lipid nanoparticles (SLN) can efficiently bind and transfect plasmid DNA. J. Contr. Rel. 77, 345-355 (2001)
   
• Parschat, K., Canne, C., Kappl, R., Hüttermann, J., Fetzner, S. Xanthine dehydrogenase from Pseudomonas putida 86: Specificity, oxidation-reduction potentials of its redox-active centers, and first EPR studies. Biochim. Biophys. Acta 1544, 151-165 (2001)
   
• Reichert, W., Michel, A., Hartmann, R.W., Jose, J. Stable expression of human 5.-reductase type II in COS1 cells due to chromosomal gene integration: a novel tool for inhibitor identification. J. Steroid Biochem. Mol. Biol. 78, 275-284 (2001)
   
• Reus, K., Mayer, J., Sauter, M., Scherer, D., Müller-Lantzsch, N., Meese, E. Genomic organization of the human endogenous retrovirus HERV-K(HML-2.HOM) (ERVK6) on chromosome 7. Genomics 72, 314- 320 (2001)
   
• Reus, K., Mayer, J., Sauter, M., Zischler, H., Müller-Lantzsch, N., Meese, E. HERV-K(OLD): The ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2). J. Virol, 75, 8917-8926 (2001)
   
• Sarrazin, C., Bruckner, M., Herrmann, E., Ruster, B., Bruch, K., Roth, W. K., Zeuzem, S. Quasispecies heterogeneity of the carboxy-terminal part of the E2 gene including the PePHD and sensitivity of hepatitis C virus 1b isolates to antiviral therapy. Virology 289, 150-163 (2001)
   
• Schiffler, B., Kiefer, M., Wilken, A., Hannemann, F., Adolph, H. W., Bernhardt, R. The interaction of bovine adrenodoxin with CYP11A1 (cytochrome P450scc) and CYP11B1 (cytochrome P45011ß) acceleration of reduction and substrate conversion by site-directed mutagenesis of adrenodoxin. J. Biol. Chem. 276, 36225-36232, (2001)
   
• Solich, P., Ogrocka, E., Schaefer, U. Application of automated flow injection analysis to drug liberation studies with the Franz diffusion cell. Pharmazie, 56, 787-789 (2001)
   
• Speicher, A., Hollemeyer, K., Heinzle, E. Rapid detection of multiple chlorinated bis(bibenzyls) in bryophyte crude extracts using laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 15, 124-127 (2001)
   
• Struss, A.K., Romeike, B F.M., Munnia, A., Nastainczyk, W., Steudel, W-I., König, J., Ohgaki, H., Feiden, W., Fischer, U., Meese, E. PHF3-specific antibody responses in over 60% of patients with glioblastoma multiforme. Oncogene 12, 4107-4114 (2001)
   
• Tholey, A., Pipkorn, R., Bossemeyer, D., Kinzel, V. & Reed, J. Influence of myristoylation, phosphorylation and deamidation on the structural behaviour of the N-terminus of the catalytic subunit of cAMP-dependent protein kinase. Biochemistry 40, 225-231 (2001)
   
• Treitz, G., Maria, G., Giffhorn, F., Heinzle, E. Kinetic model discrimination via step-by-step experimental and computational procedure in the enzymatic oxidation of D-glucose. J. Biotechnol. 85, 271-287 (2001)
   
• Wagner, H., Kostka, K. H., Lehr, C. M., Schaefer, U. F. Interrelation of permeation and penetration parameters obtained from in-vitro experiments with human skin and skin equivalents, J. Contr. Rel. 75, 283-295 (2001)
   
• Wittmann, C., Heinzle, E. MALDI TOF MS for quantification of substrates and products in cultivations of lysine producing Corynebacterium glutamicum. Biotechnol. Bioeng. 72, 642-647 (2001)
   
• Wittmann, C., Heinzle, E. Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry. Metabol. Eng., 3, 173-191 (2001)
   
• Wittmann, C., Heinzle, E. Novel approach for metabolic flux analysis - application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum. Eur. J. Biochem. 268, 2441-2455 (2001)
   
• Wittmann, C., Yang, T., Kochems, I., Heinzle, E. Dynamic respiratory measurements with Corynebacterium glutamicum using membrane mass spectrometry. J. Microbiol. Biotechnol. 11, 40-49 (2001)
   
• Yoo, H. Y., Boatz, J. A., Helms, V., McCammon, J. A., Langhoff, P. W. Chromophore protonation states and the proton shuttle mechanism in Green Fluorescent Protein: Inferences drawn from ab-initio theoretical studies of chemical structures and vibrational spectra. J. Phys. Chem. 105, 2850-2857 (2001)
   
• Zien, A., Aigner, T., Zimmer R., Lengauer, T. Centralization: A biologically sensible method for the normalization of gene expression data. Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2002) Bioinformatics 17, Suppl. 1, 323-331 (2001)