Ralf Zimmer

	2009
63		Caroline C. Friedel, Ralf Zimmer: Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 25(16): 2140-2146 (2009)
	2008
62		Gergely Csaba, Fabian Birzele, Ralf Zimmer: Protein structure alignment considering phenotypic plasticity. ECCB 2008: 98-104
61		Volker Heun, Ralf Zimmer: Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) 2008: 988-991
60		Lukas Windhager, Ralf Zimmer: Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics 2008: 106-115
59		Caroline C. Friedel, Ralf Zimmer: Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics 2008: 30-43
58		Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer: Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008: 3-16
57		Florian Erhard, Caroline C. Friedel, Ralf Zimmer: FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 9: (2008)
56		Orland R. Gonzalez, Ralf Zimmer: Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics 24(10): 1257-1263 (2008)
55		Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer: ProCope - protein complex prediction and evaluation. Bioinformatics 24(18): 2115-2116 (2008)
54		Fabian 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)
53		Fabian 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
52		Caroline C. Friedel, Ralf Zimmer: Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics 8: (2007)
51		Jan E. Gewehr, Volker Hintermair, Ralf Zimmer: AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics 23(10): 1203-1210 (2007)
50		Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer: Vorolign - fast structural alignment using Voronoi contacts. Bioinformatics 23(2): 205-211 (2007)
49		Katrin Fundel, Robert Küffner, Ralf Zimmer: RelEx - Relation extraction using dependency parse trees. Bioinformatics 23(3): 365-371 (2007)
48		Jan E. Gewehr, Martin Szugat, Ralf Zimmer: BioWeka - extending the Weka framework for bioinformatics. Bioinformatics 23(5): 651-653 (2007)
	2006
47		Henning 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
46		Katrin Fundel, Ralf Zimmer: Gene and protein nomenclature in public databases. BMC Bioinformatics 7: 372 (2006)
45		Caroline C. Friedel, Ralf Zimmer: Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 7: 519 (2006)
44		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. Bioinformatics 22(19): 2356-2363 (2006)
43		Jan E. Gewehr, Ralf Zimmer: SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 22(2): 181-187 (2006)
	2005
42		Florian Sohler, Ralf Zimmer: Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI 2005: 122
41		Robert 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
40		Martin 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
38		Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis: A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 6(S-1): (2005)
37		Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6(S-1): (2005)
36		Fabian 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
33		Florian Sohler, Daniel Hanisch, Ralf Zimmer: New methods for joint analysis of biological networks and expression data. Bioinformatics 20(10): 1517-1521 (2004)
32		Niklas 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)
31		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. 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
29		Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer: Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing 2003: 252-263
28		Daniel 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
27		Alexander 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
25		Alexander 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)
23		Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. In Silico Biology 2: 29 (2002)
22		Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving fold recognition of protein threading by experimental distance constraints. In Silico Biology 2: 30 (2002)
21		Jan 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
15		Niklas 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
13		Alexander 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
7		Christian 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
4		Ralf 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

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

Colors in the list of coauthors