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Ralf Zimmer Vis

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*2009
61EECaroline C. Friedel, Ralf Zimmer: Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 25(16): 2140-2146 (2009)
2008
60EEGergely Csaba, Fabian Birzele, Ralf Zimmer: Protein structure alignment considering phenotypic plasticity. ECCB 2008: 98-104
59 Volker Heun, Ralf Zimmer: Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) 2008: 988-991
58 Lukas Windhager, Ralf Zimmer: Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics 2008: 106-115
57 Caroline C. Friedel, Ralf Zimmer: Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics 2008: 30-43
56EECaroline C. Friedel, Jan Krumsiek, Ralf Zimmer: Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008: 3-16
55EEFlorian Erhard, Caroline C. Friedel, Ralf Zimmer: FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 9: (2008)
54EEOrland R. Gonzalez, Ralf Zimmer: Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics 24(10): 1257-1263 (2008)
53EEJan Krumsiek, Caroline C. Friedel, Ralf Zimmer: ProCope - protein complex prediction and evaluation. Bioinformatics 24(18): 2115-2116 (2008)
52EEFabian Birzele, Jan E. Gewehr, Ralf Zimmer: AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Research 36(Database-Issue): 398-401 (2008)
51EEFabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer: ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Research 36(Database-Issue): 63-68 (2008)
2007
50EECaroline C. Friedel, Ralf Zimmer: Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics 8: (2007)
49EEJan E. Gewehr, Volker Hintermair, Ralf Zimmer: AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics 23(10): 1203-1210 (2007)
48EEFabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer: Vorolign - fast structural alignment using Voronoi contacts. Bioinformatics 23(2): 205-211 (2007)
47EEKatrin Fundel, Robert Küffner, Ralf Zimmer: RelEx - Relation extraction using dependency parse trees. Bioinformatics 23(3): 365-371 (2007)
46EEJan E. Gewehr, Martin Szugat, Ralf Zimmer: BioWeka - extending the Weka framework for bioinformatics. Bioinformatics 23(5): 651-653 (2007)
2006
45EEHenning Redestig, Florian Sohler, Ralf Zimmer, Joachim Selbig: Unsupervised Decision Trees Structured by Gene Ontology (GO-UDTs) for the Interpretation of Microarray Data. GfKl 2006: 585-592
44EEChad 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. Bioinformatics 22(19): 2356-2363 (2006)
43EEJan E. Gewehr, Ralf Zimmer: SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 22(2): 181-187 (2006)
2005
42EEFlorian Sohler, Ralf Zimmer: Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI 2005: 122
41EERobert Küffner, Katrin Fundel, Ralf Zimmer: Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. ECCB/JBI 2005: 267
40EEMartin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer: Web servicing the biological office. ECCB/JBI 2005: 269
39 Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer: Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. German Conference on Bioinformatics 2005: 77-91
38EEKatrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis: A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 6(S-1): (2005)
37EEDaniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6(S-1): (2005)
36EEFabian Birzele, Jan E. Gewehr, Ralf Zimmer: QUASAR - scoring and ranking of sequence-structure alignments. Bioinformatics 21(24): 4425-4426 (2005)
2004
35 Jan E. Gewehr, Niklas von Öhsen, Ralf Zimmer: Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition. German Conference on Bioinformatics 2004: 141-148
34 Michael Amberg, Jens Wehrmann, Ralf Zimmer: Factors Influencing the Design of Mobile Services. MOBIS 2004: 199-212
33EEFlorian Sohler, Daniel Hanisch, Ralf Zimmer: New methods for joint analysis of biological networks and expression data. Bioinformatics 20(10): 1517-1521 (2004)
32EENiklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer: Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20(14): 2228-2235 (2004)
31EETorsten 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. Bioinformatics 20(2): 268-270 (2004)
2003
30 Florian Sohler, Daniel Hanisch, Ralf Zimmer: New methods for joint analysis of biological networks and expression data. German Conference on Bioinformatics 2003: 141-146
29EENiklas von Öhsen, Ingolf Sommer, Ralf Zimmer: Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing 2003: 252-263
28EEDaniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer: Playing Biology's Name Game: Identifying Protein Names in Scientific Text. Pacific Symposium on Biocomputing 2003: 403-414
27EEAlexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer: Microarrays: How Many Do You Need? Journal of Computational Biology 10(3/4): 653-667 (2003)
2002
26 Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Co-clustering of biological networks and gene expression data. ISMB 2002: 145-154
25EEAlexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer: Microarrays: how many do you need? RECOMB 2002: 321-330
24 Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer: Confidence measures for protein fold recognition. Bioinformatics 18(6): 802-812 (2002)
23EEDaniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. In Silico Biology 2: 29 (2002)
22EEMario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving fold recognition of protein threading by experimental distance constraints. In Silico Biology 2: 30 (2002)
21EEJan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer: A hypergraph-based method for unification of existing protein structure- and sequence-families. In Silico Biology 2: 31 (2002)
2001
20 Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Confidence Measures for Fold Recognition. German Conference on Bioinformatics 2001: 26-33
19 Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. German Conference on Bioinformatics 2001: 58-67
18 Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. German Conference on Bioinformatics 2001: 68-77
17 Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer: A new Method for Unification of Existing Protein Structure- and Sequence-Families. German Conference on Bioinformatics 2001: 78-84
16 Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer: Centralization: a new method for the normalization of gene expression data. ISMB (Supplement of Bioinformatics) 2001: 323-331
15EENiklas von Öhsen, Ralf Zimmer: Improving Profile-Profile Alignments via Log Average Scoring. WABI 2001: 11-26
2000
14 Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer: Analysis of Gene Expression Data with Pathway Scores. ISMB 2000: 407-417
13EEAlexander Zien, Ralf Zimmer, Thomas Lengauer: A simple iterative approach to parameter optimization. RECOMB 2000: 318-327
12 Robert Küffner, Ralf Zimmer, Thomas Lengauer: Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16(9): 825-836 (2000)
11 Thomas Lengauer, Ralf Zimmer: Protein Structure Prediction Methods for Drug Design. Briefings in Bioinformatics 1(3): 275-288 (2000)
10 Alexander Zien, Ralf Zimmer, Thomas Lengauer: A Simple Iterative Approach to Parameter Optimization. Journal of Computational Biology 7(3-4): 483-501 (2000)
1999
9 Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany AAAI 1999
8 Robert Küffner, Ralf Zimmer, Thomas Lengauer: Pathway analysis in metabolic databases via differetial metabolic display (DMD). German Conference on Bioinformatics 1999: 141-147
7EEChristian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Application of Parameter Optimization to Molecular Comparison Problems. Pacific Symposium on Biocomputing 1999: 482-493
1998
6 Ralf Zimmer, Marko Wöhler, Ralf Thiele: New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics 14(3): 295-308 (1998)
1997
5 Marko Wöhler, Ralf Thiele, Ralf Zimmer: New scoring Schemes for Protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics 1997: 111-120
4EERalf Zimmer, Thomas Lengauer: Fast and numerically stable parametric alignment of biosequences. RECOMB 1997: 344-353
1996
3 Ralf Zimmer, Ralf Thiele: Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. German Conference on Bioinformatics 1996: 78-83
2 Ralf Zimmer, Ralf Thiele: Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. German Conference on Bioinformatics - Selected Papers 1996: 137-146
1995
1 Ralf Thiele, Ralf Zimmer, Thomas Lengauer: Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. ISMB 1995: 384-392

Coauthor Index

1Thomas Aigner [16] [39]
2Mario Albrecht [18] [22]
3Michael Amberg [34]
4Iris Antes [31]
5Joannis Apostolakis [38]
6Rico Basekow [31]
7Fabian Birzele [36] [48] [51] [52] [60]
8Peer Bork [9] [31]
9Douglas L. Brutlag [9]
10Christian Buning [31]
11Maik Christensen [31]
12Holger Claussen [31]
13Torsten Crass [31]
14Gergely Csaba [48] [60]
15Chad A. Davis [44]
16Christian Ebeling [31]
17Florian Erhard [55]
18Peter Ernst [31]
19Juliane Fluck [25] [27] [28] [37]
20Jan Freudenberg [17] [21]
21Caroline C. Friedel [44] [50] [53] [55] [56] [57] [61]
22Katrin Fundel [37] [38] [39] [40] [41] [44] [47]
23Valérie Gailus-Durner [31]
24Fabian Gerick [44]
25Jan E. Gewehr [35] [36] [43] [46] [48] [49] [52]
26Janice I. Glasgow [9]
27Karl-Heinz Glatting [31]
28Rolf Gohla [31]
29Orland R. Gonzalez [54]
30Frank Gößling [31]
31Korbinian Grote [31]
32Daniel Güttler [38] [40]
33Daniel Hanisch [17] [18] [19] [21] [22] [23] [26] [28] [30] [33] [37]
34Karsten R. Heidtke [31]
35Alexander Herrmann [31]
36Volker Heun [59]
37Volker Hintermair [44] [49]
38O. Kießlich [31]
39Sven Kolibal [31]
40Jan O. Korbel [31]
41Jan Krumsiek [53] [56]
42Robert Küffner [8] [12] [14] [39] [41] [44] [47] [51]
43Christian Lemmen [7]
44Thomas Lengauer [1] [4] [7] [8] [9] [10] [11] [12] [13] [14] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [31] [32]
45Ines Liebich [31]
46Mark van der Linden [31]
47Hannes Luz [31]
48Franziska Meier [51]
49Kathrin Meissner [31]
50Christian von Mering [31]
51Heinz-Theodor Mevissen [28] [31] [37]
52Hans-Werner Mewes [9] [31]
53Holger Michael [31]
54Martin Mokrejs [31]
55Tobias Müller [31]
56Sean O'Keeffe [31]
57Florian Oefinger [51]
58Niklas von Öhsen [15] [20] [24] [29] [32] [35]
59Heike Pospisil [31]
60Christian Potthast [51]
61Matthias Rarey [31]
62Henning Redestig [45]
63Jens G. Reich [31]
64Ralf Schneider [31]
65Reinhard Schneider [9]
66Dietmar Schomburg [31]
67Steffen Schulze-Kremer [31]
68Knut Schwarzer [31]
69Joachim Selbig [45]
70Florian Sohler [30] [33] [40] [42] [45]
71Ingolf Sommer [20] [24] [29] [31] [32]
72Stephan Springstubbe [31]
73Sándor Suhai [31]
74Martin Szugat [40] [46]
75Ralf Thiele [1] [2] [3] [5] [6]
76Gnanasekaran Thoppae [31]
77Martin Vingron [31]
78Jens Warfsmann [31]
79Jens Wehrmann [34]
80Thomas Werner [31]
81Daniel Wetzler [31]
82Lukas Windhager [58]
83Edgar Wingender [31]
84Marko Wöhler [5] [6]
85Alexander Zien [7] [10] [13] [14] [16] [20] [24] [25] [26] [27]

Colors in the list of coauthors

Copyright © Tue Nov 3 08:52:44 2009 by Michael Ley (ley@uni-trier.de)