HUSAR Bioinformatics Lab
Deutsches Krebsforschungszentrum Department of Molecular Biophysics
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HUSAR Publications
 

  • The transcriptome of the colonial marine hydroid Hydractinia echinata.,
    J. Soza-Ried, A. Hotz-Wagenblatt, K.H. Glatting, C. del Val, K. Fellenberg, H.R. Bode, U. Frank, J.D. Hoheisel, and M. Frohme.
    FEBS J., 277(1):197-209, 2010.

  • PromoterSweep: a tool for identification of transcription factor binding sites.,
    C. del Val, O. Pelz, K.H. Glatting, E. Barta, and A. Hotz-Wagenblatt.
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)., Suhai Festschrift Issue, 2009.

  • TissueDistributionDBs: a repository of organism-specific tissue-distribution profiles.,
    S. Kogenaru, C. del Val, A. Hotz-Wagenblatt, and K.H. Glatting.
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)., Suhai Festschrift Issue, 2009.

  • Profile analysis and prediction of tissue-specific CpG island methylation classes..,
    C. Previti, O. Harari, I. Zwir, and C. del Val.
    BMC Bioinformatics., 21(10), 2009.

  • QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.,
    J.U. Appelt, F.A. Giordano, M. Ecker, I. Roeder, A. Hotz-Wagenblatt, G. Opelz, W.J. Zeller, H. Allgayer, S. Fruehauf, and S. Laufs.
    Gene Therapy., 16(7):885-893, 2009.

  • Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress.,
    S. Dittami, D. Scornet, J.-L. Petit, B. Segurens, C. Da Silva, E. Corre, M. Dondrup, K.H. Glatting, R. Koenig, L. Sterck, P. Rouze, Y. Van de Peer, J.M. Cock, C. Boyen, and T. Tonon.
    Genome Biology., 10(66), 2009.

  • Automatic detection of exonic splicing enhancers (ESEs) using SVMs.,
    B. Mersch, A. Gepperth, S. Suhai, and A. Hotz-Wagenblatt.
    BMC Bioinformatics., 10(9), 2008.

  • New miRNAs cloned from neuroblastoma.,
    E.A. Afanasyeva, A. Hotz-Wagenblatt, K. H. Glatting, and F. Westermann.
    BMC Genomics, 9(9), 2008.

  • Functions, structure, and read-through alternative splicing of feline APOBEC3 genes.,
    C. Münk, T. Beck, J. Zielonka, A. Hotz-Wagenblatt, S. Chareza, M. Battenberg, J. Thielebein, K. Cichutek, I. G. Bravo, S. J. O'Brien, M. Löchelt, and N. Yuhki.
    Genome Biol, 9:R48, 2008.

  • Off-target effects of siRNA specific for GFP.,
    C. Tschuch, A. Schulz, A. Pscherer, W. Werft, A. Benner, A. Hotz-Wagenblatt, L. S. Barrionuevo, P. Lichter, and D. Mertens.
    BMC Mol Biol, 9:60, 2008.

  • SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.,
    Britta Mersch, Noa Sela, Gil Ast, Sandor Suhai, and Agnes Hotz-Wagenblatt.
    BMC Genetics, 8(1), 2007.

  • Evolutionary Optimization of Sequence Kernels for Detection of Bacterial Gene Starts,
    Britta Mersch, Tobias Glasmachers, Peter Meinicke, and Christian Igel.
    International Journal of Neural Systems, 17(5):369-381, 2007.

  • Mining and Predicting CpG islands,
    Christopher Previti, Oscar Harari, and Coral del Val.
    In Fuzzy Systems Conference, FUZZ-IEEE 2007, pages 1-6, 2007.

  • Comparative analysis of transposed elements' insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome,
    Noa Sela, Britta Mersch, Nurit Gal-Mark, Galit Lev-Maor, Agnes Hotz-Wagenblatt, and Gil Ast.
    Genome Biology, 8, 2007.

  • ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ.,
    del Val C., Ernst P., Falkenhahn M., Fladerer C., Glatting KH., Suhai S., and Hotz-Wagenblatt A.
    Nucleic Acids Research, 2007.

  • Gradient-based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection,
    C. Igel, T. Glasmachers, B. Mersch, N. Pfeifer, and P. Meinicke.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(2):216-26, 2007.

  • Induced and repressed genes after irradiation sensitizing by pentoxyphylline.,
    Waldeck W., Strunz AM., Müller G., Hotz-Wagenblatt A., Wijenne J., Langowski J., Didinger B., Debus J., and Braun K.
    International Journal of Cancer, 120(6):1198-207, 2007.

  • New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors.,
    Giordano FA, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, and Laufs S.
    Methods Inf Med., 46(5):542-7, 2007.

  • CAFTAN: a tool for fast mapping, and quality assessment of cDNAs,
    C. del Val, VY. Kuryshev, KH. Glatting, P. Ernst, A. Hotz-Wagenblatt, A. Poustka, S. Suhai, and S. Wiemann.
    BMC Bioinformatics, 7:473+, 2006.

  • Evolutionary Optimization of Sequence Kernels for Detection of Bacterial Gene Starts,
    B. Mersch, T. Glasmachers, P. Meinicke, and C. Igel.
    In International Conference on Artificial Neural Networks (ICANN 2006), Kollias et al., editors, number 4132 in LNCS, pages 827-836. Springer-Verlag, 2006.

  • CpGcluster: a distance-based algorithm for CpG-island detection,
    M. Hackenberg, C. Previti, P. Luque-Escamilla, P. Carpena, J. Martinez-Aroza, and JL. Oliver.
    BMC Bioinformatics, 7:446, 2006.

  • Lentiviral vector integration sites in human NOD/SCID repopulating cells,
    S. Laufs, G. Guenechea, A. Gonzalez-Murillo, K. Z. Nagy, M. L. Lozano, C. del Val, S. Jonnakuty, A. Hotz-Wagenblatt, W. J. Zeller, J. A. Bueren, and S. Fruehauf.
    J. Gene Med., 8:1197-1207, 2006.

  • Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur in gene groups with specific molecular functions,
    F. A. Giordano, B. Fehse, A. Hotz-Wagenblatt, S. Jonnakuty, C. del Val, J.-U. Appelt, K. Z. Nagy, K. Kuehlcke, S. Naundorf, A. R. Zander, W. J. Zeller, A. D. Ho, S. Fruehauf, and S. Laufs.
    Bone Marrow Transplantation, 38:229-235, 2006.

  • The LIFEdb database in 2006,
    A. Mehrle, H. Rosenfelder, I. Schupp, C. del Val, D. Arlt, F. Hahne, S. Bechtel, J. Simpson, O. Hofmann, W. Hide, KH. Glatting, W. Huber, R. Pepperkok, A. Poustka, and S. Wiemann.
    Nucleic Acids Research, 34:D415-18, 2006.

  • Genomic analysis of Xenopus organizer function,
    AL. Hufton, A. Vinayagam, S. Suhai, and JC. Baker.
    BMC Developmental Biology, 6:27, 2006.

  • GOPET: A tool for automated predictions of gene ontology terms,
    A. Vinayagam, C. Del Val, F. Schubert, R. Eils, KH. Glatting, S. Suhai, and R. König.
    BMC Bioinformatics, 7:161, 2006.

  • Interdependent regulation of insulin receptor kinase activity by ADP and hydrogen peroxide,
    T. L. Schmitt, A. Hotz-Wagenblatt, H. Klein, and W. Dröge.
    J. Biol. Chem., 280:3795-3801, 2005.

  • GOPET: a tool for automatic Gene Ontology term prediction,
    A. Vinayagam, C. del Val, F. Schubert, R. Eils, KH. Glatting, S. Suhai, and R. König.
    In Proceedings of the Automatic Function Prediction SIG-meeting at the 13th International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 24, pages 37-38, Detroit, MI, USA, 2005.

  • Global gene expression profiling and cluster analysis in Xenopus laevis,
    D. Baldessari, Y. Shin, O. Krebs, R. König, T. Koide, A. Vinayagam, U. Fenger, M. Mochii, C. Terasaka, A. Kitayama, D. Peiffer, N. Ueno, R. Eils, KW. Cho, and C. Niehrs.
    Mech Dev., 122(3):441-75, 2005.

  • Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels,
    J. Derbinski, J. Gabler, B. Brors, S. Tierling, S. Jonnakuty, M. Hergenhahn, L. Peltonen, J. Walter, and B. Kyewski.
    J Exp Med., 202(1):33-45, 2005.

  • The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources,
    T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claußen, C. Ebeling, P. Ernst, V. Gailus-Durner, K.-H. Glatting, R. Gohla, F. Gößling, K. Grote, K. Heidtke, A. Herrmann, S. O´Keeffe, O. Kießlich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H.-T. Mevissen, H.-W. Mewes, H. Michael, M. Mokrejs, T. Müller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender, and R. Zimmer.
    Bioinformatics, 20(2):268-270, 2004.

  • High-throughput protein analysis integrating bioinformatics and experimental assays,
    C. del Val, A. Mehrle, M. Falkenhahn, M. Seiler, K.-H. Glatting, A. Poustka, S. Suhai, and S. Wiemann.
    Nucleic Acids Research, 32(2):742-748, 2004.

  • Applying Support Vector Machines for Gene ontology based gene function prediction,
    A. Vinayagam, R. König, J. Moormann, F. Schubert, R. Eils, K.-H. Glatting, and S. Suhai.
    BMC Bioinformatics, 5:116-129, 2004.

  • Insertion of retroviral vectors in NOD/SCID repopulating human peripheral blood progenitor cells occurs preferentially in the vicinity of transcription start regions and in introns,
    S. Laufs, K. Z. Nagy, F. A. Giordano, A. Hotz-Wagenblatt, W. J. Zeller, and S. Fruehau.
    Mol. Therapy, 10:874-881, 2004.

  • LIFE-DB: A database for storing the results of functional experiments, recombining data from various data sources, and serving as a sampletracking system,
    D. Bannasch, A. Mehrle, K.-H. Glatting, R. Pepperkok, A. Poustka, and S. Wiemann.
    Nucleic Acid Research, 32:D505-D508, 2004.

  • cDNA2Genome: a tool for mapping and annotating cDNAs,
    C. del Val, K.-H. Glatting, and S. Suhai.
    BMC Bioinformatics, 4:39-46, 2003.

  • ESTAnnotator: a tool for high throughput EST annotation,
    A. Hotz-Wagenblatt, T. Hankeln, P. Ernst, K.-H. Glatting, E.R. Schmidt, and S. Suhai.
    Nucleic Acids Research, 31(13):3716-3719, 2003.

  • DDBASE2.0: updated domain database with improved identification of structural domains,
    A. Vinayagam, J. Shi, G. Pugalenthi, B. Meenakshi, T. L. Blundell, and R. Sowdhamini.
    Bioinformatics, 19:1760-1764, 2003.

  • A task framework for the Web interface W2H,
    P. Ernst, K.-H. Glatting, and S. Suhai.
    Bioinformatics, 19:278-282, 2003.

  • PATH: a task for the inference of phylogenies,
    C. del Val, P. Ernst, R. Bräuning, K.-H. Glatting, and S. Suhai.
    Bioinformatics, 18:646-647, 2002.

  • Relationships and distinctions in iron-regulatory networks responding to interrelated signals,
    M. Mückenthaler, A. Richter, N. Gunkel, M. Polycarpou-Schwarz, S. Hentze, M. Falkenhahn, W. Stremmel, W. Ansorge, and M. W. Hentze.
    Blood, 101:3690-3698, 2002.

  • Redox-mediated functional and structural changes in insulin receptor kinase,
    A. Hotz-Wagenblatt and W. Dröge.
    Methods Enzymology, 348:288-296, 2002.

  • Bioinformatik - Lichtblick am Ende des Datentunnels?,
    R. Bräuning, M. van der Linden, B. Pardon, and S. Suhai.
    Biospektrum, 1:72-75, 2001.

  • Distributed application management in bioinformatics,
    M. Senger, P. Ernst, and K.-H. Glatting.
    In Genomics and Proteomics: Functional and Computational Aspects, S. Suhai, editor, pages 215-229. Kluwer Academic/Plenum Publishers, New York, 2000.

  • Inhibition of the insulin receptor kinase phosphorylation by nitric oxide: functional and structural aspects,
    E. Schmid, A. Hotz-Wagenblatt, and W. Dröge.
    Antioxid. Redox Signal, 1:45-53, 1999.

  • Phosphorylation of the insulin receptor kinase by phosphocreatine in combination with hydrogen peroxide: the structural basis of redox priming,
    E. Schmid, A. Hotz-Wagenblatt, V. Hacj, and W. Dröge.
    FASEB J., 13:1491-1500, 1999.

  • W2H: WWW interface to the GCG sequence analysis package,
    M. Senger, T. Flores, K.-H. Glatting, P. Ernst, A. Hotz-Wagenblatt, and S. Suhai.
    Bioinformatics, 14:452-457, 1998.
    project page: http://www.w2h.dkfz-heidelberg.de.
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