Ralf Zimmer - RankMe

98 papers A 4B 5C 2Misc 3Journal 58Unranked 24

Year	Rank	Type	Title / Venue / Authors
2022	—	`conf`	Collecting SARS-CoV-2 Encoded miRNAs via Text Mining. IWBBIO (1) Alexandra Schubö, Armin Hadziahmetovic, Markus Joppich, Ralf Zimmer
2022	—	`conf`	Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium. IWBBIO (2) Karel Sedlár, Ralf Zimmer
2021	J	`jnl`	Toward a gold standard for benchmarking gene set enrichment analysis. Briefings Bioinform. Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
2020	J	`jnl`	CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinform. Vinícius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana C. A. Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger
2019	J	`jnl`	Comparison of six breast cancer classifiers using qPCR. Bioinform. Evi Berchtold, Martina Vetter, Melanie Gündert, Gergely Csaba, Christine Fathke, Susanne E. Ulbrich, Christoph Thomssen, Ralf Zimmer, Eva J. Kantelhardt
2019	J	`jnl`	YESdb: integrative analysis of environmental stress in yeast. Database J. Biol. Databases Curation Evi Berchtold, Gergely Csaba, Ralf Zimmer
2017	—	`ch.`	Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge. 50 Jahre Universitäts-Informatik in München Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
2017	J	`jnl`	Bioinformatics advances biology and medicine by turning big data troves into knowledge. Inform. Spektrum Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost
2017	J	`jnl`	Manananggal - a novel viewer for alternative splicing events. BMC Bioinform. Matthias Barann, Ralf Zimmer, Fabian Birzele
2017	J	`jnl`	RelExplain - integrating data and networks to explain biological processes. Bioinform. Evi Berchtold, Gergely Csaba, Ralf Zimmer
2016	J	`jnl`	Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinform. Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
2016	J	`jnl`	Cross-species Conservation of context-specific networks. BMC Syst. Biol. Robert Pesch, Ralf Zimmer
2016	—	`ch.`	Fuzzy Modeling. Modeling in Systems Biology, The Petri Net Approach Lukas Windhager, Florian Erhard, Ralf Zimmer
2015	J	`jnl`	Addressing false discoveries in network inference. Bioinform. Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner
2015	J	`jnl`	ContextMap 2: fast and accurate context-based RNA-seq mapping. BMC Bioinform. Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel
2013	J	`jnl`	A Turing test for artificial expression data. Bioinform. Robert Maier, Ralf Zimmer, Robert Küffner
2013	J	`jnl`	RIP-chip enrichment analysis. Bioinform. Florian Erhard, Lars Dölken, Ralf Zimmer
2012	J	`jnl`	A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinform. Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel
2012	—	`conf`	ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. GCB Robert Pesch, Matthias Böck, Ralf Zimmer
2012	J	`jnl`	Detection and correction of probe-level artefacts on microarrays. BMC Bioinform. Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C. Friedel
2012	J	`jnl`	Inferring gene regulatory networks by ANOVA. Bioinform. Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer
2012	J	`jnl`	Rigorous assessment of gene set enrichment tests. Bioinform. Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner
2011	J	`jnl`	Contextual analysis of RNAi-based functional screens using interaction networks. Bioinform. Orland R. Gonzalez, Ralf Zimmer
2011	B	`conf`	Experiment Specific Expression Patterns. RECOMB Tobias Petri, Robert Küffner, Ralf Zimmer
2011	J	`jnl`	Experiment Specific Expression Patterns. J. Comput. Biol. Tobias Petri, Robert Küffner, Ralf Zimmer
2011	J	`jnl`	From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinform. Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola J. Mulder, Ralf Zimmer
2010	J	`jnl`	Characterization of Growth and Metabolism of the Haloalkaliphile PLoS Comput. Biol. Orland R. Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt
2010	J	`jnl`	Classification of ncRNAs using position and size information in deep sequencing data. Bioinform. Florian Erhard, Ralf Zimmer
2010	J	`jnl`	HALO - a Java framework for precise transcript half-life determination. Bioinform. Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer
2010	J	`jnl`	Vorescore - fold recognition improved by rescoring of protein structure models. Bioinform. Gergely Csaba, Ralf Zimmer
2010	J	`jnl`	miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinform. Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer
2009	J	`jnl`	Algorithmische Systembiologie mit Petrinetzen - Von qualitativen zu quantitativen Systemmodellen. Inform. Spektrum Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, Robert Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer
2009	J	`jnl`	Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. J. Comput. Biol. Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
2009	J	`jnl`	Identifying the topology of protein complexes from affinity purification assays. Bioinform. Caroline C. Friedel, Ralf Zimmer
2009	J	`jnl`	Systems Analysis of Bioenergetics and Growth of the Extreme Halophile PLoS Comput. Biol. Orland R. Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt
2008	J	`jnl`	Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinform. Orland R. Gonzalez, Ralf Zimmer
2008	J	`jnl`	AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res. Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
2008	B	`conf`	Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
2008	J	`jnl`	FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinform. Florian Erhard, Caroline C. Friedel, Ralf Zimmer
2008	—	`conf`	Identifying the Topology of Protein Complexes from Affinity Purification Assays. German Conference on Bioinformatics Caroline C. Friedel, Ralf Zimmer
2008	—	`conf`	Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics Lukas Windhager, Ralf Zimmer
2008	J	`jnl`	ProCope - protein complex prediction and evaluation. Bioinform. Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer
2008	J	`jnl`	ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res. Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer
2008	C	`conf`	Protein structure alignment considering phenotypic plasticity. ECCB Gergely Csaba, Fabian Birzele, Ralf Zimmer
2008	—	`conf`	Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. GI Jahrestagung (2) Volker Heun, Ralf Zimmer
2007	J	`jnl`	AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinform. Jan E. Gewehr, Volker Hintermair, Ralf Zimmer
2007	J	`jnl`	BioWeka - extending the Weka framework for bioinformatics. Bioinform. Jan E. Gewehr, Martin Szugat, Ralf Zimmer
2007	J	`jnl`	Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinform. Caroline C. Friedel, Ralf Zimmer
2007	J	`jnl`	RelEx - Relation extraction using dependency parse trees. Bioinform. Katrin Fundel, Robert Küffner, Ralf Zimmer
2007	J	`jnl`	Vorolign - fast structural alignment using Voronoi contacts. Bioinform. Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer
2006	—	`conf`	Characterization of Protein Interactions. German Conference on Bioinformatics Robert Küffner, Timo Duchrow, Katrin Fundel, Ralf Zimmer
2006	J	`jnl`	Gene and protein nomenclature in public databases. BMC Bioinform. Katrin Fundel, Ralf Zimmer
2006	J	`jnl`	Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinform. Caroline C. Friedel, Ralf Zimmer
2006	J	`jnl`	Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinform. Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer
2006	J	`jnl`	SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinform. Jan E. Gewehr, Ralf Zimmer
2006	—	`conf`	Unsupervised Decision Trees Structured by Gene Ontology (GO-UDTs) for the Interpretation of Microarray Data. GfKl Henning Redestig, Florian Sohler, Ralf Zimmer, Joachim Selbig
2005	J	`jnl`	A simple approach for protein name identification: prospects and limits. BMC Bioinform. Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis
2005	—	`conf`	Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. German Conference on Bioinformatics Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer
2005	—	`conf`	Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. ECCB/JBI Robert Küffner, Katrin Fundel, Ralf Zimmer
2005	—	`conf`	Identifying active transcription factors and kinases from expression data using pathway queries. ECCB/JBI Florian Sohler, Ralf Zimmer
2005	J	`jnl`	ProMiner: rule-based protein and gene entity recognition. BMC Bioinform. Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck
2005	J	`jnl`	QUASAR - scoring and ranking of sequence-structure alignments. Bioinform. Fabian Birzele, Jan E. Gewehr, Ralf Zimmer
2005	—	`conf`	Web servicing the biological office. ECCB/JBI Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer
2004	J	`jnl`	Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinform. Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, Thomas Lengauer
2004	—	`conf`	Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition. German Conference on Bioinformatics Jan E. Gewehr, Niklas von Öhsen, Ralf Zimmer
2004	—	`conf`	Factors Influencing the Design of Mobile Services. MOBIS Michael Amberg, Jens Wehrmann, Ralf Zimmer
2004	J	`jnl`	New methods for joint analysis of biological networks and expression data. Bioinform. Florian Sohler, Daniel Hanisch, Ralf Zimmer
2004	J	`jnl`	The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinform. 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
2003	J	`jnl`	Microarrays: How Many Do You Need? J. Comput. Biol. Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
2003	—	`conf`	New methods for joint analysis of biological networks and expression data. German Conference on Bioinformatics Florian Sohler, Daniel Hanisch, Ralf Zimmer
2003	Misc	`conf`	Playing Biology's Name Game: Identifying Protein Names in Scientific Text. Pacific Symposium on Biocomputing Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer
2003	Misc	`conf`	Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. Pacific Symposium on Biocomputing Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer
2002	J	`jnl`	A hypergraph-based method for unification of existing protein structure- and sequence-families. Silico Biol. Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer
2002	A	`conf`	Co-clustering of biological networks and gene expression data. ISMB Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer
2002	J	`jnl`	Confidence measures for protein fold recognition. Bioinform. Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer
2002	J	`jnl`	Improving fold recognition of protein threading by experimental distance constraints. Silico Biol. Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
2002	B	`conf`	Microarrays: how many do you need? RECOMB Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer
2002	J	`jnl`	ProML - the Protein Markup Language for specification of protein sequences, structures and families. Silico Biol. Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
2001	—	`conf`	A new Method for Unification of Existing Protein Structure- and Sequence-Families. German Conference on Bioinformatics Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer
2001	—	`conf`	Centralization: a new method for the normalization of gene expression data. ISMB (Supplement of Bioinformatics) Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer
2001	—	`conf`	Confidence Measures for Fold Recognition. German Conference on Bioinformatics Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
2001	—	`conf`	Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. German Conference on Bioinformatics Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
2001	C	`conf`	Improving Profile-Profile Alignments via Log Average Scoring. WABI Niklas von Öhsen, Ralf Zimmer
2001	—	`conf`	ProML - the Protein Markup Language for specification of protein sequences, structures and families. German Conference on Bioinformatics Daniel Hanisch, Ralf Zimmer, Thomas Lengauer
2000	J	`jnl`	A Simple Iterative Approach to Parameter Optimization. J. Comput. Biol. Alexander Zien, Ralf Zimmer, Thomas Lengauer
2000	B	`conf`	A simple iterative approach to parameter optimization. RECOMB Alexander Zien, Ralf Zimmer, Thomas Lengauer
2000	A	`conf`	Analysis of Gene Expression Data with Pathway Scores. ISMB Alexander Zien, Robert Küffner, Ralf Zimmer, Thomas Lengauer
2000	J	`jnl`	Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinform. Robert Küffner, Ralf Zimmer, Thomas Lengauer
2000	J	`jnl`	Protein Structure Prediction Methods for Drug Design. Briefings Bioinform. Thomas Lengauer, Ralf Zimmer
1999	Misc	`conf`	Application of Parameter Optimization to Molecular Comparison Problems. Pacific Symposium on Biocomputing Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer
1999	—	`conf`	Pathway analysis in metabolic databases via differetial metabolic display (DMD). German Conference on Bioinformatics Robert Küffner, Ralf Zimmer, Thomas Lengauer
1999	A	`ed.`	Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany ISMB Thomas Lengauer, Reinhard Schneider, Peer Bork, Douglas L. Brutlag, Janice I. Glasgow, Hans-Werner Mewes, Ralf Zimmer
1998	J	`jnl`	New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinform. Ralf Zimmer, Marko Wöhler, Ralf Thiele
1997	B	`conf`	Fast and numerically stable parametric alignment of biosequences. RECOMB Ralf Zimmer, Thomas Lengauer
1997	—	`conf`	New scoring Schemes for Protein fold recognition based on Voronoi contacts. German Conference on Bioinformatics Marko Wöhler, Ralf Thiele, Ralf Zimmer
1996	—	`conf`	Fast Protein Fold Recognition and Accurate Sequence to Structure Alignment. German Conference on Bioinformatics Ralf Zimmer, Ralf Thiele
1996	—	`conf`	Fast Protein Fold Recognition and Accurate Sequence-Structure Alignment. German Conference on Bioinformatics - Selected Papers Ralf Zimmer, Ralf Thiele
1995	A	`conf`	Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. ISMB Ralf Thiele, Ralf Zimmer, Thomas Lengauer