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Ralf Zimmer: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Florian Sohler, Ralf Zimmer
    Identifying active transcription factors and kinases from expression data using pathway queries. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:122- [Conf]
  2. Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer
    Web servicing the biological office. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:269- [Conf]
  3. Robert Küffner, Katrin Fundel, Ralf Zimmer
    Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:267- [Conf]
  4. Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
    Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:68-77 [Conf]
  5. Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer
    A new Method for Unification of Existing Protein Structure- and Sequence-Families. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:78-84 [Conf]
  6. Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer
    Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2005, pp:77-91 [Conf]
  7. Jan E. Gewehr, Niklas von Öhsen, Ralf Zimmer
    Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2004, pp:141-148 [Conf]
  8. Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
    ProML - the Protein Markup Language for specification of protein sequences, structures and families. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:58-67 [Conf]
  9. Robert Küffner, Ralf Zimmer, Thomas Lengauer
    Pathway analysis in metabolic databases via differetial metabolic display (DMD). [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1999, pp:141-147 [Conf]
  10. Marko Wöhler, Ralf Thiele, Ralf Zimmer
    New scoring Schemes for Protein fold recognition based on Voronoi contacts. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1997, pp:111-120 [Conf]
  11. Ralf Zimmer, Ralf Thiele
    Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics - Selected Papers, 1996, pp:137-146 [Conf]
  12. Ralf Zimmer, Ralf Thiele
    Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1996, pp:78-83 [Conf]
  13. Florian Sohler, Daniel Hanisch, Ralf Zimmer
    New methods for joint analysis of biological networks and expression data. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2003, pp:141-146 [Conf]
  14. Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
    Confidence Measures for Fold Recognition. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:26-33 [Conf]
  15. Michael Amberg, Jens Wehrmann, Ralf Zimmer
    Factors Influencing the Design of Mobile Services. [Citation Graph (0, 0)][DBLP]
    MOBIS, 2004, pp:199-212 [Conf]
  16. Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer
    Co-clustering of biological networks and gene expression data. [Citation Graph (0, 0)][DBLP]
    ISMB, 2002, pp:145-154 [Conf]
  17. Ralf Thiele, Ralf Zimmer, Thomas Lengauer
    Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. [Citation Graph (0, 0)][DBLP]
    ISMB, 1995, pp:384-392 [Conf]
  18. Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer
    Centralization: a new method for the normalization of gene expression data. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2001, pp:323-331 [Conf]
  19. Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer
    Analysis of Gene Expression Data with Pathway Scores. [Citation Graph (0, 0)][DBLP]
    ISMB, 2000, pp:407-417 [Conf]
  20. Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer
    Playing Biology's Name Game: Identifying Protein Names in Scientific Text. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 2003, pp:403-414 [Conf]
  21. Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer
    Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 2003, pp:252-263 [Conf]
  22. Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
    Application of Parameter Optimization to Molecular Comparison Problems. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 1999, pp:482-493 [Conf]
  23. Alexander Zien, Ralf Zimmer, Thomas Lengauer
    A simple iterative approach to parameter optimization. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2000, pp:318-327 [Conf]
  24. Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
    Microarrays: how many do you need? [Citation Graph (0, 0)][DBLP]
    RECOMB, 2002, pp:321-330 [Conf]
  25. Ralf Zimmer, Thomas Lengauer
    Fast and numerically stable parametric alignment of biosequences. [Citation Graph (0, 0)][DBLP]
    RECOMB, 1997, pp:344-353 [Conf]
  26. Niklas von Öhsen, Ralf Zimmer
    Improving Profile-Profile Alignments via Log Average Scoring. [Citation Graph (0, 0)][DBLP]
    WABI, 2001, pp:11-26 [Conf]
  27. Thomas Lengauer, Ralf Zimmer
    Protein Structure Prediction Methods for Drug Design. [Citation Graph (0, 0)][DBLP]
    Briefings in Bioinformatics, 2000, v:1, n:3, pp:275-288 [Journal]
  28. Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
    QUASAR - scoring and ranking of sequence-structure alignments. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:24, pp:4425-4426 [Journal]
  29. Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer
    The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:2, pp:268-270 [Journal]
  30. Jan E. Gewehr, Ralf Zimmer
    SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:2, pp:181-187 [Journal]
  31. Robert Küffner, Ralf Zimmer, Thomas Lengauer
    Pathway analysis in metabolic databases via differential metabolic display (DMD). [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2000, v:16, n:9, pp:825-836 [Journal]
  32. Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer
    Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:14, pp:2228-2235 [Journal]
  33. Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer
    Confidence measures for protein fold recognition. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:6, pp:802-812 [Journal]
  34. Florian Sohler, Daniel Hanisch, Ralf Zimmer
    New methods for joint analysis of biological networks and expression data. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:10, pp:1517-1521 [Journal]
  35. Ralf Zimmer, Marko Wöhler, Ralf Thiele
    New scoring schemes for protein fold recognition based on Voronoi contacts. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:3, pp:295-308 [Journal]
  36. Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer
    Reliable gene signatures for microarray classification: assessment of stability and performance. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:19, pp:2356-2363 [Journal]
  37. Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer
    Vorolign - fast structural alignment using Voronoi contacts. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:2, pp:205-211 [Journal]
  38. Jan E. Gewehr, Martin Szugat, Ralf Zimmer
    BioWeka - extending the Weka framework for bioinformatics. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:5, pp:651-653 [Journal]
  39. Katrin Fundel, Robert Küffner, Ralf Zimmer
    RelEx - Relation extraction using dependency parse trees. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:3, pp:365-371 [Journal]
  40. Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
    Improving fold recognition of protein threading by experimental distance constraints. [Citation Graph (0, 0)][DBLP]
    In Silico Biology, 2002, v:2, n:, pp:30- [Journal]
  41. Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer
    A hypergraph-based method for unification of existing protein structure- and sequence-families. [Citation Graph (0, 0)][DBLP]
    In Silico Biology, 2002, v:2, n:, pp:31- [Journal]
  42. Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
    ProML - the Protein Markup Language for specification of protein sequences, structures and families. [Citation Graph (0, 0)][DBLP]
    In Silico Biology, 2002, v:2, n:, pp:29- [Journal]
  43. Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
    Microarrays: How Many Do You Need? [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2003, v:10, n:3/4, pp:653-667 [Journal]
  44. Alexander Zien, Ralf Zimmer, Thomas Lengauer
    A Simple Iterative Approach to Parameter Optimization. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2000, v:7, n:3-4, pp:483-501 [Journal]
  45. Jan E. Gewehr, Volker Hintermair, Ralf Zimmer
    AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:10, pp:1203-1210 [Journal]

  46. Protein structure alignment considering phenotypic plasticity. [Citation Graph (, )][DBLP]


  47. Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. [Citation Graph (, )][DBLP]


  48. Identifying the Topology of Protein Complexes from Affinity Purification Assays. [Citation Graph (, )][DBLP]


  49. Characterization of Protein Interactions. [Citation Graph (, )][DBLP]


  50. Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. [Citation Graph (, )][DBLP]


  51. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. [Citation Graph (, )][DBLP]


  52. Unsupervised Decision Trees Structured by Gene Ontology (GO-UDTs) for the Interpretation of Microarray Data. [Citation Graph (, )][DBLP]


  53. Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. [Citation Graph (, )][DBLP]


  54. ProCope - protein complex prediction and evaluation. [Citation Graph (, )][DBLP]


  55. Identifying the topology of protein complexes from affinity purification assays. [Citation Graph (, )][DBLP]


  56. HALO - a Java framework for precise transcript half-life determination. [Citation Graph (, )][DBLP]


  57. Influence of degree correlations on network structure and stability in protein-protein interaction networks. [Citation Graph (, )][DBLP]


  58. FERN - a Java framework for stochastic simulation and evaluation of reaction networks. [Citation Graph (, )][DBLP]


  59. ProMiner: rule-based protein and gene entity recognition. [Citation Graph (, )][DBLP]


  60. A simple approach for protein name identification: prospects and limits. [Citation Graph (, )][DBLP]


  61. Gene and protein nomenclature in public databases. [Citation Graph (, )][DBLP]


  62. Inferring topology from clustering coefficients in protein-protein interaction networks. [Citation Graph (, )][DBLP]


  63. miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. [Citation Graph (, )][DBLP]


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