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Ralf Zimmer
Person information
- affiliation: Ludwig Maximilian University of Munich, Germany
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2020 – today
- 2022
- [c37]Karel Sedlár
, Ralf Zimmer
:
Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium. IWBBIO (2) 2022: 45-56 - [c36]Alexandra Schubö
, Armin Hadziahmetovic
, Markus Joppich
, Ralf Zimmer
:
Collecting SARS-CoV-2 Encoded miRNAs via Text Mining. IWBBIO (1) 2022: 429-441 - 2021
- [j58]Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos
, Lucas Schiffer
, Nitesh Turaga, Charity W. Law, Sean R. Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer
, Levi Waldron
:
Toward a gold standard for benchmarking gene set enrichment analysis. Briefings Bioinform. 22(1): 545-556 (2021) - 2020
- [j57]Vinícius da Silva
, Marcel Ramos
, Martien Groenen
, Richard Crooijmans, Anna Johansson
, Luciana C. A. Regitano
, Luiz Coutinho, Ralf Zimmer
, Levi Waldron
, Ludwig Geistlinger
:
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinform. 36(3): 972-973 (2020)
2010 – 2019
- 2019
- [j56]Evi Berchtold
, Gergely Csaba, Ralf Zimmer
:
YESdb: integrative analysis of environmental stress in yeast. Database J. Biol. Databases Curation 2019: baz023 (2019) - [j55]Evi Berchtold
, Martina Vetter, Melanie Gündert, Gergely Csaba, Christine Fathke, Susanne E. Ulbrich, Christoph Thomssen, Ralf Zimmer
, Eva J. Kantelhardt:
Comparison of six breast cancer classifiers using qPCR. Bioinform. 35(18): 3412-3420 (2019) - 2017
- [j54]Evi Berchtold
, Gergely Csaba, Ralf Zimmer
:
RelExplain - integrating data and networks to explain biological processes. Bioinform. 33(12): 1837-1844 (2017) - [j53]Matthias Barann
, Ralf Zimmer
, Fabian Birzele:
Manananggal - a novel viewer for alternative splicing events. BMC Bioinform. 18(1): 120:1-120:13 (2017) - [j52]Julien Gagneur
, Caroline C. Friedel
, Volker Heun, Ralf Zimmer
, Burkhard Rost
:
Bioinformatics advances biology and medicine by turning big data troves into knowledge. Inform. Spektrum 40(2): 153-160 (2017) - [p2]Julien Gagneur, Caroline C. Friedel
, Volker Heun, Ralf Zimmer, Burkhard Rost:
Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge. 50 Jahre Universitäts-Informatik in München 2017: 33-45 - 2016
- [j51]Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
:
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinform. 17: 45 (2016) - [j50]Robert Pesch
, Ralf Zimmer
:
Cross-species Conservation of context-specific networks. BMC Syst. Biol. 10: 76 (2016) - [p1]Lukas Windhager, Florian Erhard, Ralf Zimmer:
Fuzzy Modeling. Modeling in Systems Biology, The Petri Net Approach 2016: 179-205 - 2015
- [j49]Tobias Petri, Stefan Altmann
, Ludwig Geistlinger, Ralf Zimmer
, Robert Küffner:
Addressing false discoveries in network inference. Bioinform. 31(17): 2836-2843 (2015) - [j48]Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer
, Caroline C. Friedel
:
ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinform. 16: 122:1-122:15 (2015) - 2013
- [j47]Florian Erhard, Lars Dölken, Ralf Zimmer
:
RIP-chip enrichment analysis. Bioinform. 29(1): 77-83 (2013) - [j46]Robert Maier, Ralf Zimmer
, Robert Küffner:
A Turing test for artificial expression data. Bioinform. 29(20): 2603-2609 (2013) - 2012
- [j45]Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer
:
Inferring gene regulatory networks by ANOVA. Bioinform. 28(10): 1376-1382 (2012) - [j44]Haroon Naeem
, Ralf Zimmer
, Pegah Tavakkolkhah, Robert Küffner:
Rigorous assessment of gene set enrichment tests. Bioinform. 28(11): 1480-1486 (2012) - [j43]Tobias Petri, Evi Berchtold
, Ralf Zimmer
, Caroline C. Friedel
:
Detection and correction of probe-level artefacts on microarrays. BMC Bioinform. 13: 114 (2012) - [j42]Thomas Bonfert, Gergely Csaba, Ralf Zimmer
, Caroline C. Friedel
:
A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinform. 13(S-6): S9 (2012) - [c35]Robert Pesch, Matthias Böck, Ralf Zimmer
:
ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. GCB 2012: 69-81 - 2011
- [j41]Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder
, Ralf Zimmer
:
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinform. 27(13): 366-373 (2011) - [j40]Orland R. Gonzalez, Ralf Zimmer
:
Contextual analysis of RNAi-based functional screens using interaction networks. Bioinform. 27(19): 2707-2713 (2011) - [j39]Tobias Petri, Robert Küffner, Ralf Zimmer
:
Experiment Specific Expression Patterns. J. Comput. Biol. 18(11): 1423-1435 (2011) - [c34]Tobias Petri, Robert Küffner, Ralf Zimmer
:
Experiment Specific Expression Patterns. RECOMB 2011: 339-354 - 2010
- [j38]Caroline C. Friedel
, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer
:
HALO - a Java framework for precise transcript half-life determination. Bioinform. 26(9): 1264-1266 (2010) - [j37]Gergely Csaba, Ralf Zimmer
:
Vorescore - fold recognition improved by rescoring of protein structure models. Bioinform. 26(18) (2010) - [j36]Florian Erhard, Ralf Zimmer
:
Classification of ncRNAs using position and size information in deep sequencing data. Bioinform. 26(18) (2010) - [j35]Haroon Naeem
, Robert Küffner, Gergely Csaba, Ralf Zimmer
:
miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinform. 11: 135 (2010) - [j34]Orland R. Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeiffer
, Eduardo Mendoza, Ralf Zimmer
, Dieter Oesterhelt:
Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis. PLoS Comput. Biol. 6(6) (2010)
2000 – 2009
- 2009
- [j33]Caroline C. Friedel
, Ralf Zimmer
:
Identifying the topology of protein complexes from affinity purification assays. Bioinform. 25(16): 2140-2146 (2009) - [j32]Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel
, Robert Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer
:
Algorithmische Systembiologie mit Petrinetzen - Von qualitativen zu quantitativen Systemmodellen. Inform. Spektrum 32(4): 310-319 (2009) - [j31]Caroline C. Friedel
, Jan Krumsiek, Ralf Zimmer
:
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. J. Comput. Biol. 16(8): 971-987 (2009) - [j30]Orland R. Gonzalez, Susanne Gronau, Friedhelm Pfeiffer
, Eduardo Mendoza, Ralf Zimmer
, Dieter Oesterhelt:
Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum. PLoS Comput. Biol. 5(4) (2009) - 2008
- [j29]Orland R. Gonzalez, Ralf Zimmer
:
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinform. 24(10): 1257-1263 (2008) - [j28]Jan Krumsiek, Caroline C. Friedel
, Ralf Zimmer
:
ProCope - protein complex prediction and evaluation. Bioinform. 24(18): 2115-2116 (2008) - [j27]Florian Erhard, Caroline C. Friedel
, Ralf Zimmer
:
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinform. 9 (2008) - [j26]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 Res. 36(Database-Issue): 63-68 (2008) - [j25]Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
:
AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res. 36(Database-Issue): 398-401 (2008) - [c33]Gergely Csaba, Fabian Birzele, Ralf Zimmer
:
Protein structure alignment considering phenotypic plasticity. ECCB 2008: 98-104 - [c32]Caroline C. Friedel, Ralf Zimmer:
Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics 2008: 30-43 - [c31]Lukas Windhager, Ralf Zimmer:
Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics 2008: 106-115 - [c30]Volker Heun, Ralf Zimmer:
Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) 2008: 988-991 - [c29]Caroline C. Friedel
, Jan Krumsiek, Ralf Zimmer
:
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008: 3-16 - 2007
- [j24]Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer
:
Vorolign - fast structural alignment using Voronoi contacts. Bioinform. 23(2): 205-211 (2007) - [j23]Katrin Fundel, Robert Küffner, Ralf Zimmer
:
RelEx - Relation extraction using dependency parse trees. Bioinform. 23(3): 365-371 (2007) - [j22]Jan E. Gewehr, Martin Szugat, Ralf Zimmer
:
BioWeka - extending the Weka framework for bioinformatics. Bioinform. 23(5): 651-653 (2007) - [j21]Jan E. Gewehr, Volker Hintermair, Ralf Zimmer
:
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinform. 23(10): 1203-1210 (2007) - [j20]Caroline C. Friedel
, Ralf Zimmer
:
Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinform. 8 (2007) - 2006
- [j19]Jan E. Gewehr, Ralf Zimmer
:
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinform. 22(2): 181-187 (2006) - [j18]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. Bioinform. 22(19): 2356-2363 (2006) - [j17]Katrin Fundel, Ralf Zimmer
:
Gene and protein nomenclature in public databases. BMC Bioinform. 7: 372 (2006) - [j16]Caroline C. Friedel
, Ralf Zimmer
:
Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinform. 7: 519 (2006) - [c28]Robert Küffner, Timo Duchrow, Katrin Fundel, Ralf Zimmer:
Characterization of Protein Interactions. German Conference on Bioinformatics 2006: 64-73 - [c27]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 - 2005
- [j15]Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
:
QUASAR - scoring and ranking of sequence-structure alignments. Bioinform. 21(24): 4425-4426 (2005) - [j14]Katrin Fundel, Daniel Güttler, Ralf Zimmer
, Joannis Apostolakis:
A simple approach for protein name identification: prospects and limits. BMC Bioinform. 6(S-1) (2005) - [j13]Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer
, Juliane Fluck
:
ProMiner: rule-based protein and gene entity recognition. BMC Bioinform. 6(S-1) (2005) - [c26]Florian Sohler
, Ralf Zimmer
:
Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI 2005: 122 - [c25]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 - [c24]Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler
, Ralf Zimmer
:
Web servicing the biological office. ECCB/JBI 2005: 269 - [c23]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 - 2004
- [j12]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. Bioinform. 20(2): 268-270 (2004) - [j11]Florian Sohler
, Daniel Hanisch, Ralf Zimmer
:
New methods for joint analysis of biological networks and expression data. Bioinform. 20(10): 1517-1521 (2004) - [j10]Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer
, Thomas Lengauer:
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinform. 20(14): 2228-2235 (2004) - [c22]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 - [c21]Michael Amberg, Jens Wehrmann, Ralf Zimmer:
Factors Influencing the Design of Mobile Services. MOBIS 2004: 199-212 - 2003
- [j9]Alexander Zien, Juliane Fluck
, Ralf Zimmer
, Thomas Lengauer:
Microarrays: How Many Do You Need? J. Comput. Biol. 10(3/4): 653-667 (2003) - [c20]Florian Sohler, Daniel Hanisch, Ralf Zimmer:
New methods for joint analysis of biological networks and expression data. German Conference on Bioinformatics 2003: 141-146 - [c19]Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer:
Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing 2003: 252-263 - [c18]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 - 2002
- [j8]Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer
, Thomas Lengauer:
Confidence measures for protein fold recognition. Bioinform. 18(6): 802-812 (2002) - [j7]Daniel Hanisch, Ralf Zimmer, Thomas Lengauer:
ProML - the Protein Markup Language for specification of protein sequences, structures and families. Silico Biol. 2(3): 313-324 (2002) - [j6]Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer:
Improving fold recognition of protein threading by experimental distance constraints. Silico Biol. 2(3): 325-337 (2002) - [j5]Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer:
A hypergraph-based method for unification of existing protein structure- and sequence-families. Silico Biol. 2(3): 339-349 (2002) - [c17]Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer:
Co-clustering of biological networks and gene expression data. ISMB 2002: 145-154 - [c16]Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer:
Microarrays: how many do you need? RECOMB 2002: 321-330 - 2001
- [c15]Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer:
Confidence Measures for Fold Recognition. German Conference on Bioinformatics 2001: 26-33 - [c14]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 - [c13]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 - [c12]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 - [c11]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 - [c10]Niklas von Öhsen, Ralf Zimmer
:
Improving Profile-Profile Alignments via Log Average Scoring. WABI 2001: 11-26 - 2000
- [j4]Thomas Lengauer, Ralf Zimmer
:
Protein Structure Prediction Methods for Drug Design. Briefings Bioinform. 1(3): 275-288 (2000) - [j3]Robert Küffner, Ralf Zimmer, Thomas Lengauer:
Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinform. 16(9): 825-836 (2000) - [j2]Alexander Zien, Ralf Zimmer
, Thomas Lengauer:
A Simple Iterative Approach to Parameter Optimization. J. Comput. Biol. 7(3-4): 483-501 (2000) - [c9]Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer:
Analysis of Gene Expression Data with Pathway Scores. ISMB 2000: 407-417 - [c8]Alexander Zien, Ralf Zimmer, Thomas Lengauer:
A simple iterative approach to parameter optimization. RECOMB 2000: 318-327
1990 – 1999
- 1999
- [c7]Robert Küffner, Ralf Zimmer, Thomas Lengauer:
Pathway analysis in metabolic databases via differetial metabolic display (DMD). German Conference on Bioinformatics 1999: 141-147 - [c6]Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer:
Application of Parameter Optimization to Molecular Comparison Problems. Pacific Symposium on Biocomputing 1999: 482-493 - [e1]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, ISBN 1-57735-083-9 [contents] - 1998
- [j1]Ralf Zimmer
, Marko Wöhler, Ralf Thiele:
New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinform. 14(3): 295-308 (1998) - 1997
- [c5]Marko Wöhler, Ralf Thiele, Ralf Zimmer:
New scoring Schemes for Protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics 1997: 111-120 - [c4]Ralf Zimmer
, Thomas Lengauer:
Fast and numerically stable parametric alignment of biosequences. RECOMB 1997: 344-353 - 1996
- [c3]Ralf Zimmer, Ralf Thiele:
Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. German Conference on Bioinformatics 1996: 78-83 - [c2]Ralf Zimmer, Ralf Thiele:
Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. German Conference on Bioinformatics - Selected Papers 1996: 137-146 - 1995
- [c1]Ralf Thiele, Ralf Zimmer, Thomas Lengauer:
Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. ISMB 1995: 384-392 - 1990
- [b1]Ralf Martin Zimmer:
Zur Pragmatik eines operationalisierten λ-Kalküls als Basis für interaktive Reduktionssysteme. University of Kiel, Germany, Oldenbourg 1990, ISBN 978-3-486-21956-2, pp. 1-382
Coauthor Index
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