Lehr- und Forschungseinheit Bioinformatik
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PublikationenPublications

2017
Papers
Thomas Bonfert, Caroline C. Friedel, Prediction of Poly(A) Sites by Poly(A) Read Mapping, PLOS ONE, vol. 12, no. 1, pp. 1-32, 2017.
Matthias Barann, Ralf Zimmer, Fabian Birzele, Manananggal - A Novel Viewer For Alternative Splicing Events, BMC Bioinformatics, vol. Accepted, 2017.
2016
Papers
Evi Berchtold, Gergely Csaba, Ralf Zimmer, Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data, PLoS ONE, vol. 11, no. 10, 2016.
Vinicius Henrique Silva, Luciana Correia Almeida Regitano, Ludwig Geistlinger, Fábio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natália Silva Morosini, Ralf Zimmer, Luiz Lehmann Coutinho, Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle, PLOS ONE, vol. 11, no. 6, pp. e0157711, 2016.
Patricia Schöppner, Gergely Csaba, T Braun, M Daake, B Richter, Oliver F Lange, Martin Zacharias, Ralf Zimmer, Martin Haslbeck, Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins, Journal of Molecular Biology, vol. 428, no. 8, pp. 1544-57, 2016.
Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer, Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis, BMC Bioinformatics, vol. 17, pp. 45, 2016.
Jian-Nan Zhang, Uwe Michel, Christof Lenz, Caroline C. Friedel, Sarah Köster, Zara d’Hedouville, Lars Tönges, Henning Urlaub, Mathias Bähr, Paul Lingor, Jan C. Koch, Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration, Scientific Reports, vol. 6, pp. 37050, 2016.
Robert Pesch, Ralf Zimmer, Cross-Species Conservation of Context-Specific Networks, BMC Systems Biology, vol. 10, no. 76, 2016.
Theses
Marco Lombardi, Implementation and Evaluation of Algorithms for Approximate Tandem Repeats, Master Thesis, LFE Bioinformatik, 2016.
Benjamin Albrecht, Computing Hybridization Networks Using Agreement Forests, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
Ludwig Geistlinger, Network-based analysis of gene expression data, PhD Thesis, LMU München, 2016.
Thomas Bonfert, Context-based RNA-seq mapping, PhD Thesis, LMU München, 2016.
Robert Pesch, Cross-Species Network and Transcript Transfer, PhD Thesis, Ludwig-Maximilians-Universität München, 2016.
2015
Papers
Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner, Addressing false discoveries in network inference, Bioinformatics, vol. 31, no. 17, pp. 2836-43, 2015.
Benjamin Albrecht, Computing all hybridization networks for multiple binary phylogenetic input trees, BMC Bioinformatics, vol. 16, no. 236, pp. 439-441, 2015.
Andreas Osterman, Thorsten Stellberger, Anna Gebhardt, Marisa Kurz, Caroline C. Friedel, Peter Uetz, Hans Nitschko, Armin Baiker, Maria G. Vizoso-Pinto, The Hepatitis E virus intraviral interactome, Scientific reports, vol. 5, pp. 13872, 2015.
Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C. Friedel, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler, RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway., Nature communications, vol. 6, pp. 7367, 2015.
Florian Erhard, Ralf Zimmer, Count ratio model reveals bias affecting NGS fold changes, Nucleic Acids Research, pp. pii: gkv696., 2015.
Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus, Thomas Bonfert, Florian Erhard, Anne Dueck, Norbert Eichner, Caroline C. Friedel, Gunter Meister, Ralf Zimmer, Bettina Warscheid, Heiko Hermeking, p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses., Molecular & cellular proteomics : MCP, 2015.
Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer, Alternative splicing in next generation sequencing data of Saccharomyces Cerevisiae, PLoS ONE, 2015.
Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel, ContextMap 2: fast and accurate context-based RNA-seq mapping., BMC bioinformatics, vol. 16, pp. 122, 2015.
Andrzej J. Rutkowski, Florian Erhard, Anne L’Hernault, Thomas Bonfert, Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou, Ralf Zimmer, Caroline C. Friedel, Lars Dölken, Wide-spread disruption of host transcription termination in HSV-1 infection, Nature Communications, vol. 6, no. 7126, 2015.
Theses
Anna-Kathrin Kopetzki, On Closest String Problems for Different Distances and Norms, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Katharina Schmid, Efficient Construction of de Bruijn Graphs Using Suffix Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2015.
Julia Sophia Gerke, Integrated analysis of gene expression data and clinical data, Master Thesis, LFE Bioinformatik / LMU München, 2015.
Vinicius H. Silva, Metabolic pathways and meat tenderness: from CNVs to gene expression in Nelore cattle breed, Master Thesis, Escola Superior de Agricultura Luiz de Queiroz (ESALQ) / Universidade de São Paulo (USP), 2015.
2014
Papers
Tatyana Goldberg, Maximilian Hecht, Tobias Hamp, Timothy Karl, Guy Yachdav, Nadeem Ahmed, Uwe Altermann, Philipp Angerer, Sonja Ansorge, Kinga Balasz, Michael Bernhofer, Alexander Betz, Laura Cizmadija, Kieu Trinh Do, Julia Gerke, Robert Greil, Vadim Joerdens, Maximilian Hastreiter, Katharina Hembach, Max Herzog, Maria Kalemanov, Michael Kluge, Alice Meier, Hassan Nasir, Ulrich Neumaier, Verena Prade, Jonas Reeb, Aleksandr Sorokoumov, Ilira Troshani, Susann Vorberg, Sonja Waldraff, Jonas Zierer, Henrik Nielsen, Burkhard Rost, LocTree3 prediction of localization., Nucleic acids research, vol. 42, pp. W350-5, 2014.
Florian Erhard, Jürgen Haas, Diana Lieber, Georg Malterer, Lukasz Jaskiewicz, Mihaela Zavolan, Lars Dölken, Ralf Zimmer, Widespread context-dependency of microRNA-mediated regulation., Genome research, 2014.
Robert Küffner, N Zach, R Norel, Johann Hawe, D Schoenfeld, G Stolovitsky, M L Leitner, et al, Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression, Nature Biotechnology, no. Nov 2, 2014.
Caroline C. Friedel, Treatment of Noise and Artifacts in Affymetrix Arrays, Microarray Image and Data Analysis: Theory and Practice (Luis Rueda, ed.), CRC Press, pp. 251-276, 2014.
Robert Pesch, Ralf Zimmer, To be, or not to be: konservierte eukaryotische Regulationsnetzwerke?, BIOspektrum, vol. 20, no. 5, pp. 514-516, 2014.
Benjamin Albrecht, Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests, arXiv:1408.3044, 2014.
Lukas Windhager, Jonas Zierer, Robert Küffner, Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets, PLoS One, vol. 9, no. 2, pp. e84596, 2014.
Theses
Matthias Danner, Implementierung und Evaluierung einer fehlertoleranten Textsuche basierend auf Suffix-Arrays, Bachelor Thesis, LFE Bioinformatik / LMU München, 2014.
Elisabeth Frank, Evaluation of transcript reconstruction methods for newly transcribed RNA measurements, Bachelor Thesis, LMU München, 2014.
Yvonne Awaloff, Reconstruction of microbial transcripts from RNA-seq experiments, Bachelor Thesis, LMU München, 2014.
Julia Söllner, Evaluation of RNA-seq mapping methods for newly transcribed RNA measurements, Bachelor Thesis, LMU München, 2014.
Laura Schiller, Efficient computation of hybridization networks, Master Thesis, LFE Bioinformatik / LMU München, 2014.
Evelyn Kirner, Detektion von zirkulären RNAs in Sequenzierdaten, Bachelor Thesis, LMU München, 2014.
Florian Erhard, Algorithmic Methods for Systems Biology of Herpes-viral microRNAs, PhD Thesis, LMU München, 2014.
Caroline C. Friedel, Bioinformatics methods for the biological interpretation of high-throughput experiments, Habilitation, Ludwig-Maximilians-Universität München, 2014.
2013
Papers
Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel, Mining RNA-Seq Data for Infections and Contaminations, PloS one, vol. 8, pp. e73071, 2013.
Ludwig Geistlinger, Gergely Csaba, Simon Dirmeier, Robert Küffner, Ralf Zimmer, A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae, Nucleic Acids Research, vol. 41, no. 18, pp. 8452-8463, 2013.
Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimić H, Babić M, Miklić K, Malić S, Verweij MC, Baiker A, Gonzalez O, von Brunn A, Ralf Zimmer, Früh K, Verjans GM, Jonjić S, Jürgen Haas, Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection, J Virol. 2013, vol. 87, no. 12, pp. 6943-54, 2013.
Herbert B. Schiller, Michaela-Rosemarie Hermann, Julien Polleux, Timothée Vignaud, Sara Zanivan, Caroline C. Friedel, Zhiqi Sun, Aurelia Raducanu, Kay-E Gottschalk, Manuel Théry, Matthias Mann, Reinhard Fässler, β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments, Nature cell biology, vol. 15, pp. 625-36, 2013.
Mayuko Kurome, Ludwig Geistlinger, Barbara Keßler, Valeri Zakhartchenko, Nikolai Klymiuk, Annegret Wünsch, Anne Richter, Andrea Bähr, Katrin Krähe, Katinka Burkhardt, Krzysztof Flisikowski, Tatiana Flisikowska, Claudia Merkl, Martina Landmann, Marina Durkovic, Alexander Tschukes, Simone Kraner, Dirk Schindelhauer, Tobias Petri, Alexander Kind, Hiroshi Nagashima, Angelika Schnieke, Ralf Zimmer, Eckhard Wolf, Factors Influencing the Efficiency of Generating Genetically Engineered Pigs by Nuclear Transfer: Multi-Factorial Analysis of a Large Data Set, BMC Biotechnology, vol. 13, no. 43, 2013.
Sorg D, Danowski K, Korenkova V, Rusnakova V, Robert Küffner, Ralf Zimmer, Meyer HH, Kliem H, Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens, Animal, vol. 7, no. 5, pp. 799-805, 2013.
Florian Erhard, Lars Dölken, Ralf Zimmer, RIP-chip enrichment analysis, Bioinformatics, vol. 29, no. 1, September 2012, Basel, Switzerland, pp. 77–83, 2013.
Kaspar Burger, Bastian Mühl, Markus Kellner, Michaela Rohrmoser, Anita Gruber-Eber, Lukas Windhager, Caroline C. Friedel, Lars Dölken, Dirk Eick, 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response, RNA biology, vol. 10, 2013.
K Danowski, JJ Gross, K Gellrich, T Petri, HA Van Dorland, RM Bruckmaier, HD Reichenbach, R Zimmer, HHD Meyer, FJ Schwarz, H Kliem, Metabolic status and oestrous cycle in dairy cows, International Journal of Livestock Production, vol. 4, no. 9, pp. 135–147, 2013.
Florian Erhard, Lars Dölken, Lukasz Jaskiewicz, Ralf Zimmer, PARma: identification of microRNA target sites in AGO-PAR-CLIP data., Genome biology, vol. 14, pp. R79, 2013.
Schrynemackers M, Robert Küffner, Geurts P, On protocols and measures for the validation of supervised methods for the inference of biological networks, Front Genet., vol. 4, pp. 262, 2013.
Robert Maier, Ralf Zimmer, Robert Küffner, A Turing test for artificial expression data, Bioinformatics, vol. 29, no. 20, pp. 2603-2609, 2013.
Caroline C. Friedel, Computational analysis of virus-host interactomes, Methods in molecular biology, vol. 1064, pp. 115-30, 2013.
Harth-Hertle ML, Scholz BA, Florian Erhard, Glaser LV, Dölken L, Ralf Zimmer, Bettina Kempkes, Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9, PLoS Pathogens, vol. 9, no. 9, pp. e1003638, 2013.
Roland H. Friedel, Caroline C. Friedel, Thomas Bonfert, Roland Rad, Philippe Soriano, Clonal expansion of transposon insertions identifies candidate cancer genes in a PiggyBac mutagenesis screen, PLoS ONE, vol. 8, no. 8, pp. e72338, 2013.
Mirko Trilling, Nicolas Bellora, Andrzej J. Rutkowski, Miranda de Graaf, Paul Dickinson, Kevin Robertson, Olivia Prazeres da Costa, Peter Ghazal, Caroline C. Friedel, M. Mar Alba, Lars Dölken, Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis, Nucleic Acids Research, 2013.
Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump, Orland Gonzalez, Caroline C. Friedel, Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou, Ralf Zimmer, Peter Ghazal, Jürgen Haas, A systematic analysis of host factors reveals a Med23-interferon-lambda regulatory axis against Herpes simplex virus Type 1 replication, PLoS Pathogens, vol. 9, no. 8, pp. e1003514, 2013.
Bernd Rädle, Andrzej Rutkoswki, Zsolt Ruzsics, Caroline C. Friedel, Ulrich H Koszinowski, Lars Dölken, Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture, J. Vis. Exp., vol. 78, pp. e50195, 2013.
Robert Pesch, Ralf Zimmer, Complementing the Eukaryotic Protein Interactome, PLOS One, vol. 8, no. 6, pp. e66635, 2013.
Ronny Kramer, Simone Wolf, Tobias Petri, Dirk von Soosten, Sven Dänicke, Eva-Maria Weber, Ralf Zimmer, Juergen Rehage, Gerhard Jahreis, A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation, Lipids in Health and Disease, vol. 12, no. 96, 2013.
Theses
Judith Boldt, Entwicklung eines Validierungs-Programms von Real-Time PCRs in der GVO-Analytik, Bachelor Thesis, LMU München, 2013.
Lars von den Driesch, Evolutionary conservation of PAR-CLIP microRNA target sites, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
Alexander Grün, Interactive Modeling of Complex Hypothesis Using Ontologies, Bachelor Thesis, LFE Bioinformatik / LMU München, 2013.
Gergely Csaba, Context Based Bioinformatics, PhD Thesis, LMU München, 2013.
Lukas Windhager, Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, PhD Thesis, LMU München, 2013.
2012
Papers
Celine Scornavacca, Simone Linz, Benjamin Albrecht, A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees, Journal of Computational Biology, vol. 19, no. 11, pp. 1227-1242, 2012.
Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner, Rigorous assessment of gene set enrichment tests, Bioinformatics, vol. bts164v1-bts164, pp. 7, 2012.
Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer, Inferring Gene Regulatory Networks by ANOVA, Bioinformatics, vol. 28, no. 10, pp. 1376-1382, 2012.
Lukas Windhager, Thomas Bonfert, Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L’Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel, Ralf Zimmer, Dirk Eick, Caroline C. Friedel, Lars Dölken, Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution., Genome research, vol. 22, pp. 2031-42, 2012.
Florian Erhard, Ralf Zimmer, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Journal of Proteomics, vol. 75, no. 11, pp. 3230-9, 2012.
Milan Spasic, Caroline C. Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin, Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm, PLoS Genet, vol. 8, no. 1, pp. e1002433, 2012.
Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky, Wisdom of crowds for robust gene network inference., Nature methods, vol. 9, pp. 796-804, 2012.
Lisa Marcinowski, Michael Lidschreiber, Lukas Windhager, Martina Rieder, Jens B. Bosse, Bernd Rädle, Thomas Bonfert, Ildiko Györy, Miranda de Graaf, Olivia Prazeres da Costa, Philip Rosenstiel, Caroline C. Friedel, Ralf Zimmer, Zsolt Ruzsics, Lars Dölken, Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection, PLoS Pathog, vol. 8, no. 9, pp. e1002908, 2012.
Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Florian Erhard, Benkartek C, Babic M, Ralf Zimmer, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Lars Dölken, Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathogens, vol. 8, no. 2, pp. e1002510, 2012.
Robert Lindner, Caroline C. Friedel, A comprehensive evaluation of alignment algorithms in the context of RNA-Seq, PLoS ONE, vol. 7, no. 12, pp. e52403, 2012.
Robert Pesch, Matthias Böck, Ralf Zimmer, ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes, Proceedings of the German Conference on Bioinformatics (GCB), vol. 26, pp. 69-81, 2012.
Tobias Stögbauer, Lukas Windhager, Ralf Zimmer, Joachim O. Rädler, Experiment and Mathematical Modeling of Gene Expression Dynamics in a Cell-Free System, Integrative Biology, vol. 4 (5), pp. 494 - 501, 2012.
Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel, A context-based approach to identify the most likely mapping for RNA-seq experiments, BMC Bioinformatics, vol. 13(Suppl 6), pp. S9, 2012.
Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C. Friedel, Detection and correction of probe-level artefacts on microarrays, BMC Bioinformatics, vol. 13, pp. 114, 2012.
Benjamin Albrecht, Volker Heun, Space Efficient Modifications to Structator - a Fast Index-Based Search Tool for RNA Sequence-Structure Patterns, Proceedings of the 11th International Symposium on Experimental Algorithms (SEA 2012) (Ralf Klasing, ed.), Springer Verlag, vol. 7276, Bordeaux, France, June 7-9, 2012, pp. 27-38, 2012.
Theses
Lucia Puchbauer, Analysis of High-Throughput Data in Oncology, Master Thesis, LFE Bioinformatik / LMU München, 2012.
Johann Hawe, Prediction of disease progression in patients with Amyotrophic Lateral Sclerosis, Bachelor Thesis, Bioinformatics, LMU München, 2012.
Haroon Naeem, Activity of microRNAs and transcription factors in Gene Regulatory Networks, PhD Thesis, LMU München, 2012.
Evi Berchtold, RELEXplain - Relation Networks Explaining Biological Processes, Master Thesis, LFE Bioinformatik / LMU München, 2012.
2011
Papers
Orland Gonzalez, Ralf Zimmer, Contextual analysis of RNAi-based functional screens using interaction networks, Bioinformatics, vol. 27, pp. 2707-2713, 2011.
Naeem H, Küffner R, Zimmer R., MIRTFnet: analysis of miRNA regulated transcription factors, PLoS One, pp. 6(8):e22519, 2011.
Dintner Sebastian, Anna Staroń, Evi Berchtold, Tobias Petri, Thorsten Mascher, Susanne Gebhard, Co-evolution of ABC-transporters and two-component regulatory systems as resistance modules against antimicrobial peptides in Firmicutes bacteria, Journal of Bacteriology, vol. 193, no. 15, pp. 3851–3862, 2011.
Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola Mulder, Ralf Zimmer, From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems, Bioinformatics, vol. 27, no. 13, pp. i366-i373, 2011.
Zhen Wang, Guohui Ding, Ludwig Geistlinger, Hong Li, Lei Liu, Rong Zeng, Yoshio Tateno, Yixue Li, Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes, Molecular Biology and Evolution, vol. 28, no. 3, pp. 1131-40, 2011.
Susanne Pfefferle, Julia Schöpf, Manfred Kögl, Caroline C. Friedel, Marcel A. Müller, Javier Carbajo-Lozoya, Thorsten Stellberger, Ekatarina von Dall’Armi, Petra Herzog, Stefan Kallies, Daniela Niemeyer, Vanessa Ditt, Thomas Kuri, Roland Züst, Ksenia Pumpor, Rolf Hilgenfeld, Frank Schwarz, Ralf Zimmer, Imke Steffen, Friedemann Weber, Volker Thiel, Georg Herrler, Heinz-Jürgen Thiel, Christel Schwegmann-Weßels, Stefan Pöhlmann, Jürgen Haas, Christian Drosten, Albrecht von Brunn, The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors, PLoS Pathog, vol. 7, no. 10, pp. e1002331, 2011.
Herbert B. Schiller, Caroline C. Friedel, Cyril Boulegue, Reinhard Fässler, Quantitative proteomics of the integrin adhesome reveals a myosin II-dependent recruitment of LIM domain proteins, EMBO Reports, vol. 12, no. 3, pp. 259-66, 2011.
Tobias Petri, Robert Küffner, Ralf Zimmer, Experiment Specific Expression Patterns, RECOMB 2011, Research in Computational Molecular Biology (Vineet Bafna, S. Cenk Sahinalp, eds.), Springer, vol. 15, pp. 339-354, 2011.
Florian Erhard, Ralf Zimmer, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, Detecting outlier peptides in quantitative high-throughput mass spectrometry data, September 2011, Weihenstephan, Germany, 2011.
Benjamin Albrecht, Celine Scornavacca, Alberto Cenci, Daniel H Huson, Fast computation of minimum hybridization networks, Bioinformatics, vol. 28, no. 2, pp. 191-197, 2011.
Caroline C. Friedel, Jürgen Haas, Virus-host interactomes and global models of virus-infected cells, Trends in Microbiology, vol. 19, no. 10, pp. 501-8, 2011.
Johannes Fischer, Volker Heun, Space-Efficient Preprocessing Schemes for Range Minimum Queries on Static Arrays, SIAM Journal on Computing, vol. 40, no. 2, pp. 465-492, 2011.
Theses
Vadim Jördens, Optimization of Homology-based Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Michael Kluge, miRNA regulation mechanisms of Herpes viruses, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Uwe Altermann, Analysis of Expression Data of Tissue Mixtures, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Philipp Angerer, Model Based Data Viewing and Analysis, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Michael Bernhofer, Analysis of Virus Host Interaction Networks, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Jonas Zierer, Transcript Quantification Biases in Next Generation Sequencing Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
Andreas Kolberg, Automatische Klassifizierung von Alternativen Splicing-Events in Proteinstrukturen, Bachelor Thesis, LFE Bioinformatik, LMU München, 2011.
2010
Papers
Carola Marzi, Eva Albrecht, Pirro G. Hysi, Vasiliki Lagou, Melanie Waldenberger, Anke Tönjes, Inga Prokopenko, Katharina Heim, Hannah Blackburn, Janina S. Ried, Marcus E. Kleber, Massimo Mangino, Barbara Thorand, Annette Peters, Christopher J. Hammond, Harald Grallert, Bernhard O. Boehm, Peter Kovacs, Ludwig Geistlinger, Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger, Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A, PLoS Genetics, vol. 6, no. 11, pp. e1001213, 2010.
Benjamin Albrecht, Philip Effinger, Markus Held, Michael Kaufmann, An Automatic Layout Algorithm for BPEL Processes, SoftVis ’10: Proceedings of the 5th ACM Symposium on Software visualization, ACM, New York, NY, USA, 2010.
Gergely Csaba, Ralf Zimmer, Vorescore - fold recognition improved by rescoring of protein structure models, Bioinformatics, vol. 26, no. 18, pp. i482-i488, 2010.
Florian Erhard, Ralf Zimmer, Classification of ncRNAs using position and size information in deep sequencing data, Bioinformatics, vol. 26, no. 18, pp. i426-i432, 2010.
Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer, HALO - A Java framework for precise transcript half-life determination, Bioinformatics, vol. 26, no. 9, pp. 1264-1266, 2010.
Lars Dölken, Georg Malterer, Florian Erhard, Sheila Kothe, Caroline C. Friedel, Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer, Ralf Zimmer, Ulrich H Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas, Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays, Cell Host & Microbe, vol. 7, no. 4, pp. 324-334, 2010.
Johannes Fischer, Volker Heun, Finding Range Minima in the Middle: Approximations and Applications, Mathematics in Computer Science, vol. 3, no. 1, pp. 17-30, 2010.
Johannes Fischer, Volker Heun, Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), College Publications, vol. 12, September 13-15, 2008, Nagoya, Japan, pp. 239-252, 2010.
R Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer, Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization, PLoS One, vol. 5, pp. e12807, 2010.
Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer, miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature, BMC Bioinformatics, vol. 11, pp. 135, 2010.
Wolfgang Fischer, Lukas Windhager, Stefanie Rohrer, Matthias Zeiller, Arno Karnholz, Reinhard Hoffmann, Ralf Zimmer, Rainer Haas, Strain-specific genes of Helicobacter pylori: Genome evolution driven by a novel type IV secretion system and genomic island transfer, Nucleic Acids Research, vol. 38, no. 18, pp. 6089-101, 2010.
Caroline C. Friedel, Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 2010.
Lukas Windhager, Florian Erhard, Ralf Zimmer, Fuzzy modeling, Modeling in Systems Biology: The Petri Net Approach (Ina Koch, Wolfgang Reisig, Falk Schreiber, eds.), Springer, 2010.
Florian Erhard, Caroline C. Friedel, Ralf Zimmer, FERN - Stochastic Simulation and Evaluation of Reaction Networks, Systems Biology for Signaling Networks (Sangdun Choi, ed.), Springer, vol. 1, Part 4, pp. 751-775, 2010.
Orland Gonzalez, Tanja Oberwinkler, Locedie Mansueto, Friedhelm Pfeifer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt, Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis, PLoS Computational Biology, vol. 6, no. 6, pp. e1000799, 2010.
Benjamin Albrecht, Philip Effinger, Markus Held, Michael Kaufmann, Stephan Kottler, Visualization of Complex BPEL Models, Proc. of the 17th International Symposium on Graph Drawing (GD ’09), 2010.
Theses
Markus Meier, Visualisierung von Repeats im Genom, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Evi Berchtold, Quality Check and Differential Expression Using Newly Synthesized RNA, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Florian Goebels, Network Oriented Transfer of Experimental Data Between Organisms, Diploma Thesis, LFE Bioinformatik, LMU München, 2010.
Bernd Streppel, Representation of Structure Variations of Protein Families by Partial Order Graphs, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
Ludwig Geistlinger, Gene Graph Enrichment Analysis (GGEA): Mapping of Gene Expression Data onto Networks of Biochemical Processes, Diploma Thesis, LFE Bioinformatik, LMU München, 2010.
Sebastian Ullherr, Prediction of Transcript Half-Lives, Bachelor Thesis, LFE Bioinformatik, LMU München, 2010.
2009
Papers
Caroline C. Friedel, Lars Dölken, Metabolic tagging and purification of nascent RNA: Implications for transcriptomics, Molecular BioSystems, vol. 5, no. 11, pp. 1271-8, 2009.
Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski, Ralf Zimmer, Conserved principles of mammalian transcriptional regulation revealed by RNA half-life, Nucleic Acids Research, vol. 37, no. 17, pp. e115, 2009.
Even Fossum, Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas, Evolutionarily conserved herpesviral protein interaction networks., PLoS Pathog, vol. 5, no. 9, pp. e1000570, 2009.
Simon W. Ginzinger, Marko Skocibusic, Volker Heun, CheckShift Improved: Fast Chemical Shift Reference Correction with High Accuracy, Journal of Biomolecular NMR, vol. 44, no. 4, pp. 207-211, 2009.
Caroline C. Friedel, Ralf Zimmer, Identifying the topology of protein complexes from affinity purification assays, Bioinformatics, vol. 25, no. 16, pp. 2140-2146, 2009.
Simon W. Ginzinger, Murray Coles, SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database, Journal of Biomolecular NMR, vol. 43, no. 3, pp. 179-185, 2009.
AG Moll, MT Lindenmeyer, M Kretzler, PJ Nelson, Ralf Zimmer, CD Cohen, Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays, PLoS ONE, vol. 4, no. 3, pp. e4702, 2009.
Gergely Csaba, Fabian Birzele, Ralf Zimmer, Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis, BMC Structural Biology, vol. 9, no. 23, 2009.
Orland Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt, Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, R Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer, Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen, Informatik-Spektrum, vol. 32, no. 4, pp. 310-319, 2009.
Philippe Audebaud, Luca Chiarabini, New Development in Extracting Tail Recursive Programs from Proofs, Pre-Proceedings of the 19th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR’09), Coimbra, Portugal, September 9-11, 2009, 2009.
Luca Chiarabini, Automatic Synthesis of an Efficient Algorithm for the Similarity of Strings Problem, Proceedings of the 4th Workshop on Automated Formal Methods (AFM’09) (H. Saidi, N. Shankar, eds.), Grenoble, France, June 27, 2009, pp. 23-30, 2009.
O. Gonzalez, S. Gronau, F. Pfeiffer, E. Mendoza, Ralf Zimmer, D. Oesterhelt, Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum, PloS Computational Biology, vol. 5, no. 4, pp. e1000332, 2009.
Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer, Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Journal of Computational Biology, vol. 16, no. 8, pp. 1-17, 2009.
Nino Shervashidze, SVN Vishwanathan, Tobias Petri, Kurt Mehlhorn, Karsten Borgwardt, Efficient Graphlet Kernels for Large Graph Comparison, 12th International Conference on Artificial Intelligence and Statistics (AISTATS), Society for Artificial Intelligence and Statistics, Clearwater Beach, Fl, USA, April, 16-18, 2009, 2009.
Theses
Luca Chiarabini, Program Development by Proof Transformation, PhD Thesis, LMU München, 2009.
Johannes Bräuer, Optimization of 3D Protein Structure Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Mark Heron, Network Oriented Analysis of CLA Expression Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Yanxiang Zhou, Small RNA Annotation and Analysis in Deep Sequencing Data, Bachelor Thesis, LFE Bioinformatik, LMU München, 2009.
Jeremias Weihmann, Genome-Rearrangements: Sortieren mit erweiterten Transreversals, Diploma Thesis, LFE Bioinformatik / LMU München, 2009.
Stefan Heinisch, Integration of Textmining Priors into Structural Inference of Bayesian Networks, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Maximilian Miller, miRNA-Target-Networks, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Nikolas Gross, Prediction of Protein Secondary Structure, Bachelor Thesis, LFE Bioinformatik / LMU München, 2009.
Caroline C. Friedel, Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, PhD Thesis, LMU München, 2009.
Fabian Birzele, Alternative Splicing and Protein Structure Evolution, PhD Thesis, LMU München, 2009.
Orland Gonzalez, Reconstruction, Modeling and Analysis of Haloarcheal Metabolic Networks, PhD Thesis, LMU München, 2009.
2008
Papers
Christian Gieger, Ludwig Geistlinger, Elisabeth Altmaier, Martin Hrabé-de-Angelis, Florian Kronenberg, Thomas Meitinger, Hans-Werner Mewes, H.-Erich Wichmann, Klaus M. Weinberger, Jerzy Adamski, Thomas Illig, Karsten Suhre, Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum, PLoS Genetics, vol. 4, no. 11, pp. e1000282, 2008.
Lars Dölken, Zsolt Ruzsics, Bernd Rädle, Caroline C. Friedel, Ralf Zimmer, Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H Koszinowski, High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay, RNA, vol. 14, no. 9, pp. 1959–1972, 2008.
Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer, ProCope–protein complex prediction and evaluation, Bioinformatics, vol. 24, no. 18, pp. 2115–2116, 2008.
Gergely Csaba, Fabian Birzele, Ralf Zimmer, Protein structure alignment considering phenotypic plasticity, Bioinformatics, vol. 24, pp. 98–104, 2008.
Fabian Birzele, Gergely Csaba, Ralf Zimmer, Alternative splicing and protein structure evolution, Nucleic Acids Res., vol. 36, pp. 550–558, 2008.
Fabian Birzele, Jan Erik Gewehr, Ralf Zimmer, AutoPSI: a database for automatic structural classification of protein sequences and structures, Nucleic Acids Res., vol. 36, pp. 398–401, 2008.
Fabian Birzele, R 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., vol. 36, pp. D63–68, 2008.
Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Katrin Fundel, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L, Overview of BioCreative II gene normalization., Genome Biology, vol. 9, no. Supplement 2, pp. S3, 2008.
Michaela Falb, Kerstin Müller, Lisa Königsmaier, Tanja Oberwinkler, Patrick Horn, Susanne von Gronau, Orland Gonzalez, Friedhelm Pfeiffer, Erich Bornberg-Bauer, Dieter Oesterhelt, Metabolism of halophilic archaea, Extremophiles, vol. 12, no. 2, pp. 177-196, 2008.
Katrin Fundel, R Küffner, T. Aigner, Ralf Zimmer, Normalization and gene p-value estimation: issues in microarray data processing, Bioinform Biol Insights, vol. 2, pp. 291-305, 2008.
Luca Chiarabini, Program Development by Proof Transformation: Recent Evolutions, 15th International Conferences on Logic for Programming, Artificial Intelligence and Reasoning (LPAR’08), Doha, Qatar, November 22-27, 2008, 2008.
Luca Chiarabini, Extraction of Efficient Programs from Proofs: The Case of Structural Induction over Natural Numbers, Local Proceedings of the Fourth Conference on Computability in Europe: Logic and Theory of Algorithms (CiE’08) (A. Beckmann, C. Dimitracopoulos, B. Löwe, eds.), Athens, Greece, June 15-20, 2008, pp. 64-76, 2008.
Caroline C. Friedel, Ralf Zimmer, Identifying the topology of protein complexes from affinity purification assays, Proceedings of the German Conference on Bioinformatics (GCB 2008), GI, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 30-43, 2008.
Orland Gonzalez, Ralf Zimmer, Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes, Bioinformatics, vol. 24, no. 10, pp. 1257-63, 2008.
Orland Gonzalez, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza, Ralf Zimmer, D. Oesterhelt, Reconstruction, modeling & analysis of Halobacterium salinarum R-1metabolism, Mol Biosyst, vol. 4, no. 2, pp. 148-59, 2008.
Katrin Fundel, Jochen Haag, Pia M. Gebhard, Ralf Zimmer, Thomas Aigner, Normalization strategies for mRNA expression data in cartilage research, Osteoarthritis Cartilage, vol. 16, pp. 947-955, 2008.
Jörn Marialke, Simon Tietze, Joannis Apostolakis, Similarity based docking, J. Chem. Inf. Model., vol. 48, no. 1, pp. 186–196, 2008.
Joannis Apostolakis, Oliver Sacher, Robert Körner, Johann Gasteiger, Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database, J. Chem. Inf. Model., vol. 48, no. 6, pp. 1190–1198, 2008.
Robert Körner, Joannis Apostolakis, Determination of Reaction Mappings and Reaction Center Information: The Imaginary Transition State Energy approach, J. Chem. Inf. Model., vol. 48, no. 6, pp. 1181–1189, 2008.
R Küffner, Tatjana Schilling, Ralf Zimmer, Ludger Klein-Hitpass, Franz Jakob, Norbert Schütze, Microarray analyses of transdifferentiated mesenchymal stem cells, Journal of Cellular Biochemistry, vol. 103, no. 2, pp. 413-433, 2008.
Lukas Windhager, Ralf Zimmer, Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic, German Conference on Bioinformatics, Gesellschaft für Informatik, vol. P-136, September 9-12, 2008, Dresden, Germany, pp. 106-115, 2008.
Robert Pesch, Artem Lysenko, Matthew Hindle, Keywan Hassani-Pak, Ralf Thiele, Christopher J. Rawlings, Jacob Köhler, Jan Taubert, Graph-based sequence annotation using a data integration approach, Journal of Integrative Bioinformatics, vol. 5, no. 2, 2008.
Volker Heun, Analysis of a Modification of Gusfield’s Recursive Algorithm for Reconstructing Ultrametric Trees, Information Processing Letters, vol. 108, no. 4, pp. 222-225, 2008.
Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer, Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast, Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008 (Sorin Istrail, Pavel Pevzner, Michael Waterman, eds.), Springer, vol. 4955, Singapore, March 30 - April 2, 2008, pp. 3-16, 2008.
Johannes Fischer, Volker Heun, Horst Martin Stühler, Practical Entropy-Bounded Schemes for O(1)-Range Minimum Queries, Proceedings of the 2008 Data Compression Conference (DCC’08) (J.A. Storer, M.W. Marcellin, eds.), IEEE Computer Society, Snowbird, Utah, U.S.A., March 25-27, 2008, pp. 272-281, 2008.
Johannes Fischer, Volker Heun, Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing, Local Proceedings of the 19th International Workshop on Combinatorial Algorithms (IWOCA’08) (Mirka Miller, Koichi Wada, eds.), Nagoya, Japan, September 13-15, 2008, pp. 239-252, 2008.
Florian Erhard, Caroline C. Friedel, Ralf Zimmer, FERN - a Java framework for stochastic simulation and evaluation of reaction networks, BMC Bioinformatics, vol. 9, no. 1, pp. 356, 2008.
Theses
Sebastian Pölsterl, Comparison of Alternative Splicing in Higher Organisms, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Thomas Mair, Analysis of Alternative Splicing of Proteins, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Annabelle Teresa Klarl, Konstruktion und Anwendung von Affixarrays, Bachelor Thesis, LFE Bioinformatik, LMU München, 2008.
Simon Berger, Protonation State and Enzyme Substrate Interaction, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Stefan Brandmaier, Strukturelle Analyse von alternativem Splicing, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Florian Erhard, Petri Net Based System for Spatio-Temporal Simulation of Gene Regulation, Diploma Thesis, LFE Bioinformatik/LMU München, 2008.
Theresa Niederberger, Regelbasierte Extraktion von Proteinwechselwirkungen, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2008.
Marko Skocibusic, Improving CheckShift, Diploma Thesis, LFE Bioinformatik, LMU München, 2008.
Simon W. Ginzinger, Bioinformatics Methods for NMR Chemical Shift Data, PhD Thesis, LMU München, 2008.
2007
Papers
Simon W. Ginzinger, Fabian Gerick, Murray Coles, Volker Heun, CheckShift: Automatic Correction of Inconsistent Chemical Shift Referencing, Journal of Biomolecular NMR, vol. 39, no. 3, pp. 223-227, 2007.
Jan Erik Gewehr, Volker Hintermair, Ralf Zimmer, AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings, Bioinformatics, vol. 23, no. 10, pp. 1203-1210, 2007.
Fabian Birzele, Jan Erik Gewehr, Gergely Csaba, Ralf Zimmer, Vorolign - Fast Structural Alignment using Voronoi Contacts, Bioinformatics, vol. 23, no. 2, pp. e205-e211, 2007.
Alexander Zien, Pia M. Gebhard, Katrin Fundel, Thomas Aigner, Phenotyping of chondrocytes in vivo and in vitro using cDNA array technology, Clin Orthop Relat Res, vol. 460, pp. 226-33, 2007.
Jan Erik Gewehr, Martin Szugat, Ralf Zimmer, BioWeka–extending the Weka framework for bioinformatics, Bioinformatics, vol. 23, no. 5, pp. 651-653, 2007.
Z. Fan, S. Soder, S. Oehler, Katrin Fundel, Thomas Aigner, Activation of interleukin-1 signaling cascades in normal and osteoarthritic articular cartilage, Am J Pathol, vol. 171, no. 3, pp. 938-946, 2007.
Thomas Aigner, Jochen Haag, Ralf Zimmer, Functional genomics, evo-devo and systems biology: a chance to overcome complexity?, Curr Opin Rheumatol, vol. 19, no. 5, pp. 463-470, 2007.
Joannis Apostolakis, Jörn Marialke, Robert Körner, Simon Tietze, Predicting activated conformations of substrates in enzyme binding sites, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007.
Simon Tietze, Jörn Marialke, Robert Körner, Joannis Apostolakis, Graph-Based Molecular Alignment (GMA), Journal of Chemical Information and Modelling, vol. 47, no. 2, pp. 591-601, 2007.
Simon Tietze, Joannis Apostolakis, GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes, Journal of Chemical Information and Modelling, vol. 47, no. 4, pp. 1657–1672, 2007.
Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kämper, Thomas Lengauer, Gerhard Wenz, Joannis Apostolakis, Improved Cyclodextrin-Based Receptors for Camptothecin by Inverse Virtual Screening, Chemistry 2007, vol. 13, no. 24, pp. 6801-6809, 2007.
Markus Böhl, Simon Tietze, Andrea Sokoll, Sineej Madathil, Frank Pfennig, Joannis Apostolakis, Karim Fahmy, Herwig O. Gutzeit, Flavonoids Affect Actin Functions in Cytoplasm and Nucleus, Biophysical Journal, vol. 93, no. 8, pp. 2767-2780, 2007.
Andreas Steffen, Maximilian Karasz, Carolin Thiele, Thomas Lengauer, Andreas Kämper, Gerhard Wenz, Joannis Apostolakis, Combined Similarity and QSPR Virtual Screening for Guest Molecules of β-Cyclodextrin, New Journal of Chemistry, vol. 31, pp. 1941 - 1949, 2007.
Stefan Zahler, Simon Tietze, Frank Totzke, Michael Kubbutat, Laurent Meijer, Angelika M. Vollmar, Joannis Apostolakis, Inverse in silico screening of 5/6/67 substituted Halogenoindirubins reveals PDK1 as target, Chem. Biol., vol. 14, no. 11, pp. 1207-1214, 2007.
Andreas Steffen, Joannis Apostolakis, On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes, Chem Cent J., vol. 1, no. 29, 2007.
Katrin Fundel, Ralf Zimmer, Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation, Second BioCreative Challenge Evaluation Workshop, 2007.
Katrin Fundel, R Küffner, Ralf Zimmer, RelEx - Relation extraction using dependency parse trees, Bioinformatics, vol. 23, no. 3, pp. 365-371, 2007.
Simon W. Ginzinger, Volker Heun, SimShiftDB: Chemical-Shift-Based Homology Modeling, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria., 2007.
Simon W. Ginzinger, Thomas Gräupl, Volker Heun, SimShiftDB: Chemical-Shift-Based Homology Modeling, Proceedings of the First International Conference on Bioinformatics Research and Development (BIRD’07) (Sepp Hochreiter, Roland Wagner, eds.), Springer, vol. 4414, Berlin, Germany, March 12-14, pp. 357-370, 2007.
Caroline C. Friedel, Ralf Zimmer, Influence of degree correlations on network structure and stability in protein-protein interaction networks, BMC Bioinformatics, vol. 8, pp. 297, 2007.
Johannes Fischer, Volker Heun, A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array, Proceedings of the International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE’07) (Bo Chen, Mike Paterson, Guochuan Zhang, eds.), Springer-Verlag, vol. 4614, Hangzhou, China, April 7-9, 2007, pp. 459-470, 2007.
Paolo Ferragina, Johannes Fischer, Suffix Arrays on Words, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07) (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 328-339, 2007.
Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Caroline C. Friedel, Ralf Zimmer, Rhonda Roberts, Jürgen Haas, Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS ONE, vol. 2, no. 5, pp. e459, 2007.
K.M. Borgwardt, Tobias Petri, SVN Vishwanathan, H.P. Kriegel, An efficient sampling scheme for comparison of large graphs, Mining and Learning with Graphs, Electronic Proceedings, no. 1, 2007.
Amihood Amir, Johannes Fischer, Moshe Lewenstein, Two-Dimensional Range Minimum Queries, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM’07), (Bin Ma, Kaizhong Zhang, eds.), Springer-Verlag, vol. 4580, London, Ontario, July 9-11, 2007, pp. 286-294, 2007.
Theses
Gergely Csaba, Phenotypic Plasticity as a Measure for Protein Structural Similarity, Master Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Sebastian Dümcke, Optimization of Sequence-Structure Alignments using the Vorolign-Scoring Function, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Horst Martin Stühler, Practical Performance of Preprocessing Schemes for Range Minimum Queries, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Johannes Fischer, Data Structures for Efficient String Algorithms, PhD Thesis, LMU München, 2007.
Jan Erik Gewehr, New Methods for the Prediction and Classification of Protein Domains, PhD Thesis, Ludwig-Maximilians-Universität München, 2007.
Volker Hintermair, Comparative Analysis of Bos Taurus and Homo Sapiens DNA Microarrays, Master Thesis, LMU München, 2007.
Katrin Fundel, Text Mining and Gene Expression Analysis - Towards Combined Interpretation of High Throughput Data, PhD Thesis, LMU München, 2007.
Andreas Grimm, 3D tomographic and single-particle reconstruction using level set methods, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Anton Moll, Splice-isoform analysis using data from standard human gene DNA chips, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Lukas Windhager, Vergleichende Genomanalyse eines neu sequenzierten H.pylori Stamms, Master Thesis, LFE Bioinformatik, LMU München, 2007.
Matthias Siebert, Voronoi contact patterns for protein function prediction, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Florian Oefinger, A Database for Alternative Splicing in the Context of Protein Structures,, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alexander Pöschl, Browsing the protein space, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Robert Körner, Analyse biochemischer Reaktionen an Hand von imaginären Übergangszuständen, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Frank Wallrapp, Empirical Scoring Functions for Protein Structure Analysis, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alex Jarasch, Similarity-Based Analysis of Medium- and High Throughput Screening Data, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2007.
Alois Huber, OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems, Diploma Thesis, LFE Bioinformatik, LMU München, 2007.
Tobias Petri, Novel Graph Kernels for Biological Network Comparison, Diploma Thesis, Database and Information Systems/LMU München, 2007.
2006
Papers
Caroline C. Friedel, Ralf Zimmer, Inferring topology from clustering coefficients in protein-protein interaction networks, BMC Bioinformatics, vol. 7, pp. 519, 2006.
Caroline C. Friedel, Ralf Zimmer, Toward the complete interactome, Nat Biotechnol, vol. 24, no. 6, pp. 614-615, 2006.
Jan Erik Gewehr, Ralf Zimmer, SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles, Bioinformatics, vol. 22, no. 2, pp. 181-187, 2006.
Orland Gonzalez, Christoph Küper, Kirsten Jung, Prospero Naval, Eduardo Mendoza, Parameter estimation using Simulated Annealing for S-system models of biochemical networks, Bioinformatics, vol. 23, no. 4, pp. 480-486, 2006.
Peter Uetz, Yu-An Dong, Christine Zeretzke, C. Atzler, Armin Baiker, B. Berger, Seesandra V. Rajagopala, M. Roupelieva, Dietlinde Rose, Even Fossum, Jürgen Haas, Herpesviral protein networks and their interaction with the human proteome, Science, vol. 311, no. 5758, pp. 239-42, 2006.
Martin Szugat, Wikimanie, Entwicklermagazin, vol. 2006, no. 1, pp. 96-99, 2006.
Martin Szugat, Web Servicing the Office, XML and Web Services Magazin, vol. 2006, no. 1, pp. 150-152, 2006.
Joachim Saas, Jochen Haag, D. Rueger, S. Chubinskaya, Florian Sohler, Ralf Zimmer, Eckart Bartnik, Thomas Aigner, IL-1beta, but not BMP-7 leads to a dramatic change in the gene expression pattern of human adult articular chondrocytes–portraying the gene expression pattern in two donors, Cytokine, vol. 36, no. 1-2, pp. 90-99, 2006.
H. Redestig, Florian Sohler, Ralf Zimmer, J. Selbig, Unsupervised Decision Trees Based on Gene Ontology Terms for the Interpretation of Gene Expression Data, Advances in Data Analysis. Proc. 30th Annual Conference of the German Classification Society (GfKl) (R. Decker, H.-J. Lenz, eds.), Springer-Verlag, Heidelberg-Berlin, 2007, pp. 385-594, 2006.
Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Colored Petri Net Modeling and Simulation of Signal Transduction Pathways, Metabolic Engineering, vol. 8, no. 2, pp. 112-122, 2006.
Thomas Aigner, Katrin Fundel, Joachim Saas, Pia M. Gebhard, Jochen Haag, Tilo Weiss, Alexander Zien, Franz Obermayer, Ralf Zimmer, Eckart Bartnik, Large-Scale Gene Expression Profiling of Osteoarthritic Cartilage Degeneration, Arthritis&Rheumatism, vol. 54, no. 11, pp. 3533-3544, 2006.
Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer, Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies, Journal of Chemical Information and Modelling, vol. 46, no. 2, pp. 903–911, 2006.
Gene and protein nomenclature in public databases, BMC Bioinformatics, vol. 7, pp. 372, 2006.
R Küffner, T. Duchrow, Katrin Fundel, Ralf Zimmer, Characterization of Protein Interactions, German Conference on Bioinformatics (GCB) (Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, Andreas Zell, eds.), Gesellschaft für Informatik, vol. P-83, Tübingen, Germany, September 19-22, 2006, pp. 64-73, 2006.
Thomas Aigner, Pia M Gebhard‌, R Küffner, Hongwei Zhang‌, K Wayne Marshall, cDNA arrays in degenerative arthritis research, Future Rheumatology, vol. 11, pp. 101-109, 2006.
Simon W. Ginzinger, Johannes Fischer, SimShift: Identifying structural similarities from NMR chemical shifts, Bioinformatics, vol. 22, no. 4, pp. 460-465, 2006.
Johannes Fischer, Volker Heun, Stefan Kramer, Optimal String Mining Under Frequency Constraints, Proceedings of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD’06) (J. Fürnkranz, T. Scheffer, M. Spiliopoulou, eds.), Springer-Verlag, vol. 4213, Berlin, Germany, September 18-22, 2006, pp. 139-150, 2006.
Johannes Fischer, Volker Heun, Theoretical and Practical Improvements on the RMQ-Problem with Applications to LCA and LCE, Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM’06) (Moshe Lewenstein, Gabriel Valiente, eds.), Springer-Verlag, vol. 4009, Barcelona, Spain, July 5-7, 2006, pp. 36-48, 2006.
Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, R Küffner, Ralf Zimmer, Reliable gene signatures for microarray classification: assessment of stability and performance, Bioinformatics, vol. 22, no. 19, pp. 2356-2363, 2006.
Books
Martin Szugat, Jan Erik Gewehr, Cordula Lochmann, Social Software, entwickler.press, 2006.
Theses
Gergely Csaba, Analysis of Protein Sequence-Structure Alignments, Bachelor Thesis, LMU München, 2006.
Jonathan Hoser, Ein Scheduling System für netzwerkorientierte Bioinformatik Arbeitsabläufe, Bachelor Thesis, LMU München, 2006.
Maximilian Karasz, A Fragment-Based Approach to Virtual Screening, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Jörn Marialke, Similarity Based Methods for the Prediction of Protein Ligand Complexes, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Simon Tietze, Prediction of Specificity in Protein-Ligand Interactions Using Structure Based Virtual Screening, Diploma Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Florian Sohler, Contextual Analysis of Gene Expression Data, PhD Thesis, LMU München, 2006.
Fabian Gerick, Identification and Correction of Errors in NMR-Chemical Shift Data, Master Thesis, LFE Bioinformatik, LMU München, 2006.
Chad A. Davis, Feature Selection Methods in Bioinformatics, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2006.
Julia Sellmeier, Analysis of Available Bioinformatic Tools for Exploration of Microarray Data using Gene Ontology and Design of a Bioinformatic Tool with a Graphical User Interface for Interactive Exploration of Gene Networks Predicted from Microarray Data, Diploma Thesis, LFE Bioinformatik, LMU München, 2006.
Sebastian Bauer, Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte, Bachelor Thesis, LFE Bioinformatik, LMU München, 2006.
Daniel Güttler, LiMB - Ein interaktiver Browser zur Analyse biomedizinischer Texte mit Hilfe von Textmining, Diploma Thesis, LMU München, 2006.
2005
Papers
Fabian Birzele, Jan Erik Gewehr, Ralf Zimmer, QUASAR–scoring and ranking of sequence-structure alignments, Bioinformatics, vol. 21, no. 24, pp. 4425–4426, 2005.
Johannes Fischer, Volker Heun, Stefan Kramer, Fast Frequent String Mining Using Suffix Arrays, TUM-I0512, Institut für Informatik der Technischen Universität München, no. TUM-I0512, 2005.
Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis, A simple approach for protein name identification: prospects and limits, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S15, 2005.
Katrin Fundel, Daniel Hanisch, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck, ProMiner: rule-based protein and gene entity recognition, BMC Bioinformatics, vol. 6, no. (Suppl.1), pp. S14, 2005.
Florian Sohler, Jan Erik Gewehr, Inference of Developmental Transcription Factor Activities in Drosophila Melanogaster (Extended abstract of oral presentation), Proceedings of the Moscow Conference on Computational Molecular Biology (MCCMB), 2005.
Katrin Fundel, R Küffner, Thomas Aigner, Ralf Zimmer, Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments, German Conference on Bioinformatics (GCB) 2005 (A. Torda, S. Kurtz, Matthias Rarey, eds.), GI, vol. P-71, pp. 77-91, 2005.
Florian Sohler, Ralf Zimmer, Identifying active transcription factors and kinases from expression data, Bioinformatics, vol. 21, no. Suppl 2, pp. 115-122, 2005.
M. Gebauer, Joachim Saas, Florian Sohler, Jochen Haag, S. Soder, M. Pieper, Eckart Bartnik, J. Beninga, Ralf Zimmer, Thomas Aigner, Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1beta, Osteoarthritis Cartilage, vol. 13, no. 8, pp. 697-708, 2005.
Thomas Aigner, Joachim Saas, Alexander Zien, Ralf Zimmer, Pia M. Gebhard, Thomas Knorr, Analysis of Differential Gene Expression in Healthy and Osteoarthritic Cartilage and Isolated Chondrocytes by Microarray Analysis, Methods in Molecular Medicine, vol. 100, pp. 109-128, 2005.
Thomas Aigner, L. McKenna, Alexander Zien, Z. Fan, Pia M. Gebhard, Ralf Zimmer, Gene expression profiling of serum- and interleukin-1beta-stimulated primary human adult articular chondrocytes–a molecular analysis based on chondrocytes isolated from one donor, Cytokine, vol. 31, no. 3, pp. 227-240, 2005.
Joannis Apostolakis, Robert Körner, Jörn Marialke, Embedded subgraph isomorphism and its applications in cheminformatics and metabolomics, 1st German Conference in Chemoinformatics, 2005.
Martin Szugat, Daniel Güttler, Florian Sohler, Ralf Zimmer, Web Servicing the Biological Office, Bioinformatics, vol. 21, no. (Suppl. 2), pp. 268-269, 2005.
A Facius, C Englbrecht, Fabian Birzele, A Groscurth, S Benjamin, S Wanka, HW Mewes, PRIME: a graphical interface for integrating genomic/proteomic databases, Proteomics, vol. 5, no. 1, pp. 76-80, 2005.
R Küffner, Katrin Fundel, Ralf Zimmer, Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts, Bioinformatics, vol. 21, no. Suppl 2, pp. 259-267, 2005.
Caroline C. Friedel, Katharina H.V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, Igor V. Tetko, Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage, Bioinfomatics, vol. 21, no. 8, pp. 1383-1388, 2005.
Simon W. Ginzinger, Johannes Fischer, SimShift: Identifying Structural Similarities from NMR Chemical Shifts, European Conference on Computational Biology (ECCB05), 2005.
Johannes Fischer, Volker Heun, Stefan Kramer, Fast Frequent String Mining Using Suffix Arrays, Proceedings of the 5th IEEE International Conference on Data Mining (ICDM’05), IEEE Computer Society, Houston, TX, USA, November 27-30, 2005, pp. 609-612, 2005.
Johannes Fischer, Simon W. Ginzinger, A 2-Approximation Algorithm for Sorting by Prefix Reversals, Proceedings of the 13th Annual European Symposium on Algorithms (ESA’05) (Gerth Stølting Brodal, Stefano Leonardi, eds.), Springer-Verlag, vol. 3669, Mallorca, Spain, October 3-6, 2005, pp. 415-425,, 2005.
Theses
Stephan Vogt, Topic Maps, Bachelor Thesis, LMU München, 2005.
Alexander Kohn, Quantitative Analyse von Protein-Massenspektren, Diploma Thesis, LFE Bioinformatik, LMU München, 2005.
Martin Szugat, BioWeka: Extending the Weka framework for Bioinformatics, Bachelor Thesis, LMU München, 2005.
Lukas Windhager, Inference of Regulatory Networks Using Physical Models, Bachelor Thesis, LFE Bioinformatik, LMU München, 2005.
Fabian Gerick, Ein programmierbarer Web Service zur Charakterisierung biologischer Objekte, Bachelor Thesis, LMU München, 2005.
Niklas Von Öhsen, Profile-Profile alignment for remote homology and domain detection of proteins, PhD Thesis, Ludwig-Maximilians-Universität München, 2005.
Caroline C. Friedel, On Abstaining Classifiers, Master Thesis, TU München, 2005.
2004
Papers
Daniel Hanisch, Florian Sohler, Ralf Zimmer, ToPNet - an application for interactive analysis of expression data and biological networks, Bioinformatics, vol. 20, no. 9, pp. 1470-1471, 2004.
Niklas Von Öhsen, Ingolf Sommer, Ralf Zimmer, Arby: automatic protein structure prediction using profile-profile alignment and confidence measures, Bioinformatics, vol. 20, no. 14, pp. 2228-35, 2004.
Niklas Von Öhsen, Joannis Apostolakis, Ralf Zimmer, Dopro: Automatic Protein Domain Structure Prediction using a Stochastic Model for Analyzing Homology Search Results, CAFASP 2004, pp. extended abstract, 2004.
Peter Uetz, Seesandra V. Rajagopala, Yu-An Dong, Jürgen Haas, From ORFeomes to protein interaction maps in viruses, Genome Res, vol. 14, no. 10B, pp. 2029-2033, 2004.
Florian Sohler, Daniel Hanisch, Ralf Zimmer, New methods for joint analysis of biological networks and expression data, Bioinformatics, vol. 20, no. 10, pp. 1517-1521, 2004.
Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Knowledge representation model for systems-level analysis of signal transduction networks, Genome Inform Ser Workshop Genome Inform, vol. 15, no. 2, pp. 234-243, 2004.
Jan T. Kim, Jan Erik Gewehr, Thomas Martinetz, Binding Matrix: A Novel Approach for Binding Site Recognition, Journal of Bioinformatics and Computational Biology, vol. 2, no. 2, pp. 289-307, 2004.
Jan Erik Gewehr, Niklas Von Öhsen, Ralf Zimmer, Combining Secondary Structure Element Alignment and Profile Alignment for Fold Recognition, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 141-148, 2004.
T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claussen, C. Ebeling, P. Ernst, K. Heidtke, A. Herrmann, S. O’Keeffe, O. Kiesslich, S. Kolibal, J. O. Korbel, T. Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, H. T. Mevissen, HW Mewes, H. Michael, M. Mokrejs, T. Muller, H. Pospisil, M. Rarey, J. G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, I. Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender, Ralf Zimmer, The Helmholtz Network for Bioinformatics: an integrative web portal forbioinformatics resources, Bioinformatics, vol. 20, no. 2, pp. 268-70, 2004.
Thomas Aigner, E. Bartnik, F. Sohler, Ralf Zimmer, Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses, Clin Orthop Relat Res, no. 427 Suppl, pp. 138-143, 2004.
Christoph Best, Ralf Zimmer, Joannis Apostolakis, Probabilistic methods for predicting protein functions in protein-protein interaction networks, German Conference on Bioinformatics, GCB 2004 (Robert Giegerich, Jens Stoye, eds.), Gesellschaft für Informatik, vol. P-53, Bielefeld, Germany, October 4-6, 2004, pp. 159-168, 2004.
Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck, ProMiner: Organism-specific protein name detection using approximate string matching, BioCreative Challenge Evaluation Workshop, 2004.
Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis, Exact versus approximate string matching for protein name identification, BioCreative Challenge Evaluation Workshop, 2004.
Theses
Volker Hintermair, Characterisation and Visualisation of Protein Families based on Multicriterial Clustering, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Andreas Spitzmüller, JRDP - Ein Java Framework für Rekursive Dynamische Programmierung, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Thomas Obkircher, Eine erweiterbare Bioinformatik Umgebung zur kriterienbasierten Protein Identifizierung, Bachelor Thesis, LFE Praktische Informatik und Bioinformatik / LMU München, 2004.
Dorothee Liebich, Packungsprobleme bei Proteinen, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2004.
Daniel Hanisch, New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks, PhD Thesis, Ludwig-Maximilians-Universität München, 2004.
Patents
Ralf Zimmer, R Küffner, Alexander Zien, Method for Evaluation of Gene Expression and DNA Chip Data using Metabolic/Regulatory Pathways and Statistical Significance Measures with Applications to Drug Target Finding, GMD Forschungszentrum Informationstechnik GmbH, no. PCT Patent application, European patent office 12.11.1999, 2004.
Ralf Zimmer, D. Hoffmann, Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA), no. PCT Patent application, European patent office 10.08.2001, 2004.
2003
Papers
Niklas Von Öhsen, Ingolf Sommer, Ralf Zimmer, Profile-profile alignment: a powerful tool for protein structure prediction, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 252-63, 2003.
Thomas Martinetz, Jan Erik Gewehr, Jan T. Kim, Statistical Learning for Detecting Protein-DNA Binding Sites, Proc. of the International Joint Conference on Neural Networks (IJCNN) (D. C. Wunsch II, M. Hasselmo, K. Venayagamoorthy, eds.), IEEE Press, pp. 2940-2945, 2003.
Jan T. Kim, Jan Erik Gewehr, Thomas Martinetz, Binding Matrix: A Novel Approach for Binding Site Recognition, Bioinformatics 2003, Bioinformatics, pp. Poster, 2003.
Jan Erik Gewehr, Jan T. Kim, Thomas Martinetz, On the Correspondence between Scoring Matrices and Binding Site Sequence Distributions, ISMB 2003, Brisbane, pp. Poster, 2003.
Thomas Aigner, Ralf Zimmer, The promise and limitations of DNA microarray analysis: comment on the editorial by Firestein and Pisetsky, Arthritis Rheum, vol. 48, no. 3, pp. 860; author reply 862, 2003.
Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer, Microarrays: How Many Do You Need?, Journal of Computational Biology, vol. 10, no. 3-4, pp. 653-667, 2003.
Florian Sohler, Daniel Hanisch, Ralf Zimmer, New methods for joint analysis of biological networks and expression data, Proceedings of the German Conference on Bioinformatics, GCB 2003 (W. Mewes, D. Frishman, V. Heun, S. Kramer, eds.), belleville Verlag, München, Neuherberg and Garching, Germany, October 12-14, 2003, pp. 141-146, 2003.
Thomas Aigner, Alexander Zien, Daniel Hanisch, Ralf Zimmer, J. Bone, Gene expression in chondrocytes assessed with use of microarrays, Joint Surg Am, vol. 85-A, no. Suppl 2, pp. 117-123, 2003.
D. Hofmann, Joannis Apostolakis, Crystal structure prediction with data mining, J. Mol. Struct., vol. 647, no. 1, pp. 17-39, 2003.
Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer, Playing biology’s name game: identifying protein names in scientific text, Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003) (Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein, eds.), Lihue, Hawaii, USA, January 3-7, 2003, pp. 403-414, 2003.
Volker Heun, Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Computational Molecular Biology (S. Istrail, P. Pevzner, R. Shamir, eds.), North Holland, vol. 12, 2003.
Volker Heun, Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices, Discrete Applied Mathematics, vol. 127, no. 1, pp. 163-177, 2003.
Books
Volker Heun, Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen, Vieweg Verlag, 2003.
Werner Mewes, Dmitrij Frishman, Volker Heun, Stefan Kramer, Proceedings of the German Conference on Bioinformatics, GCB 2003 (Neuherberg and Garching, Germany, October 12-14, 2003), belleville Verlag München, 2003.
Theses
William Travis Holton, Evaluation of mapping consistency between public gene and protein databases, Bachelor Thesis, Ludwig-Maximilians-Universität München, 2003.
Caroline C. Friedel, Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems, Bachelor Thesis, LMU München, 2003.
Cornelia Donner, Erkennung von Gennamen in wissenschaftlichen Texten - automatische Generierung von Synonymlisten und Präprozessierung der Texte, Bachelor Thesis, LMU München, 2003.
Alexander Zien, Computational Methods for Gene Expression Data Analysis, PhD Thesis, Friedrich-Wilhelms-Universität Bonn, 2003.
Jan Erik Gewehr, The Binding Matrix - A Statistical Learning Approach to Protein-DNA Binding Site Prediction, Diploma Thesis, University of Lübeck, 2003.
2002
Papers
Alexander Zien, Juliane Fluck, Thomas Lengauer, Ralf Zimmer, Microarrays: How many do you need?, Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002 (E Myers, et al, eds.), ACM Press, New York, Washington, DC, USA, April 18-21, 2002, pp. 321-330, 2002.
Ingolf Sommer, Alexander Zien, Niklas Von Öhsen, Ralf Zimmer, Thomas Lengauer, Confidence measures for protein fold recognition, Bioinformatics, vol. 18, no. 6, pp. 802-812, 2002.
Thomas Martinetz, Jan Erik Gewehr, Jan T. Kim, A Statistical Learning Approach to Predicting Protein-DNA-Binding Sites, European Conference on Computational Biology (ECCB) 2002, pp. Poster, 2002.
Daniel Hanisch, Ralf Zimmer, Thomas Lengauer, ProML - the protein markup language for specification of protein sequences, structures and families, In Silico Biol, vol. 2, no. 3, pp. 313-24, 2002.
J. Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer, A hypergraph-based method for unification of existing protein structure-and sequence-families, In Silico Biol, vol. 2, no. 3, pp. 339-349, 2002.
Joannis Apostolakis, D. Güttler, Florian Sohler, Ralf Zimmer, Prediction of gene functions from biological interactions, RECOMB 2002 (M. Vingron, ed.), vol. Poster, 2002.
Joannis Apostolakis, D. Güttler, Florian Sohler, Ralf Zimmer, Biological context and the analysis of gene expression data, ECCB 2002 (H.-P. Lenhof, ed.), vol. Poster, 2002.
Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer, Improving fold recognition of protein threading by experimental distance constraints, In Silico Biol, vol. 2, no. 3, pp. 325-337, 2002.
Thomas Aigner, E. Bartnik, Alexander Zien, Ralf Zimmer, Functional genomics of osteoarthritis, Pharmacogenomics, vol. 3, no. 5, pp. 635-50, 2002.
Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer, Co-clustering of biological networks and gene expression data, Bioinformatics, vol. 18, no. 90001, pp. S145-S154, 2002.
Philippe Ferrara, Joannis Apostolakis, Amedeo Caflisch, Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins: Structure, Function, and Bioinformatics, vol. 46, no. 1, pp. 24-33, 2002.
2001
Papers
Ralf Zimmer, Thomas Lengauer, Protein Structure Prediction, Bioinformatics - From Genomes to Drugs (Thomas Lengauer, ed.), Wiley-VCH, pp. 237-313, 2001.
Niklas Von Öhsen, Ralf Zimmer, Improving profile-profile alignments via log average scoring, Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 2001) (O. Gascuel, B.M.E. Moret, eds.), Springer-Verlag, vol. 2149, Århus, Denmark, August 28-31, 2001, pp. 11-26, 2001.
Ingolf Sommer, Niklas Von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer, Confidence Measures for fold recognition, German Conference on Bioinformatics (E. Wingender, ed.), pp. 26-33, 2001.
D. Hoffmann, V. Schnaible, S. Wefing, Mario Albrecht, Daniel Hanisch, Fast solution of Protein-3D-structures, Coupling of Biological and Electronic Systems, Proceedings of the 2nd caesarium (Karl-Heinz Hoffmann, ed.), Springer-Verlag, pp. 59-78, 2001.
Daniel Hanisch, Ralf Zimmer, Thomas Lengauer, ProML - The protein markup language for specification of protein sequences, structures and families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 58-67, 2001.
Daniel Hanisch, Ralf Zimmer, Thomas Lengauer, Evaluation of structure prediction models using the ProML specification language, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
J. Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer, A new method for unification of existing protein structure- and sequence-families, German Conference on Bioinformatics (GCB 2001) (E. Wingender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 78-84, 2001.
Mario Albrecht, Ralf Zimmer, Protein structure prediction by threading with experimental constraints, Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), vol. Poster, 2001.
Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer, Improving fold recognition of protein threading by experimental distance constraints, German Conference on Bioinformatics (GCB 2001) (E. Windender, R. Hofestädt, I. Liebich, eds.), Braunschweig, Germany, October 7-10, 2001, pp. 68-77, 2001.
Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer, Centralization: a new method for the normalization of gene expression data, Bioinformatics, vol. 17, no. Suppl.1, pp. S323-S331, 2001.
Joannis Apostolakis, D. Hofmann, Thomas Lengauer, Using simple learning machines to derive a new potential for molecular modelling, in Rational Approaches to Drug Design, Proc. of 13th Eur. Symp. on QSAR, Prous Science, pp. 125-134, 2001.
D. Hofmann, Joannis Apostolakis, Thomas Lengauer, Derivation of a scoring function for crystal structure prediction, Acta Crystallogr A., vol. 57, no. Pt4, pp. 442-50, 2001.
Patents
Ralf Zimmer, Frei programmierbares, universelles Parallel-rechnersystem zur Durchführung von allgemeinen Berechnungen, GMD - Forschungszentrum Informationstechnik GmbH, Sankt Augustin, no. PCT Patent application, European patent office 15.04.1998, 2001.

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