LFE

Lehre

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Intern

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Forschungs-
projekte


ExpressionLab@LMU

NetworkLab@LMU

Proteinstrukturen

Protein Interaktionen

Textmining

Algorithmische Bioinformatik


Publikationen

Publikationen seit September 2001

[2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009]

2009

Papers:

Gonzalez, O., S. Gronau, F. Pfeiffer, E. Mendoza, Zimmer, R., and Oesterhelt, D. Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum PloS Computational Biology, 2009, accepted.

Birzele, F., Hoffmann, E., Csaba, G. and Zimmer, R. Alternative Splicing of Protein Repeats submitted

Dong, Y.-A., Koegl, M., Stelzl, U., Baiker, A., Friedel, C.C., Rose, D., Lutter, P., von Brunn, A., Schwarz, F., Kasmapour, B., Wanker, E., Koszinowski, U., Zimmer, R., Uetz, P., Fossum, E. and Haas, J. Herpesviral proteins preferentially target highly connected human host proteins. submitted.

Even Fossum, Caroline C. Friedel, Silpa Suthram, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Sourav Bandyopadhyay, Dietlinde Rose, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas. Comparative interactomics point to evolutionary conserved herpesviral protein-protein interaction networks. submitted.

Küffner, R., Birzele, F., Zimmer, R. PASS: Reliable detection of alternative splicing with microarrays submitted

Gergely Csaba, Fabian Birzele, Ralf Zimmer. Systematic Comparison of SCOP and CATH: A new Gold Standard for Protein Structure Analysis. submitted.


Theses:

Orland Gonzalez, Reconstruction, Modeling & Analysis of Haloarcheal Metabolic Networks, PhD Thesis, January 2009.

Fabian Birzele, Alternative Splicing and Protein Structure Evolution, PhD Thesis, January 2009.

Caroline Friedel, Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life, PhD Thesis, February 2009.

2008

Papers:

Volker Heun. Analysis of a Modification of Gusfield's Recursive Algorithm for Reconstructing Ultrametric Trees. Information Processing Letters, Vol. 108, No. 4, 222-225, 2008. [DOI 10.1016/j.ipl.2008.05.008]

Johannes Fischer, Volker Heun. Range Median of Minima Queries, Super-Cartesian Trees, and Text Indexing. Proceedings of the 19th International Workshop on Combinatorial Algorithms, (IWOCA'08), Nagoya, Japan, September 13-15, 239-252.

Gergely Csaba, Fabian Birzele, Ralf Zimmer. Protein Structure Alignment considering Phenotypic Plasticity. Proceedings of the Seventh European Conference on Computational Biology, 22-26 September 2008, Cagliari, Italy (ECCB'08), Supplement of Bioinformatics, Vol.24, No.16, i98-i104, 2008. [DOI 10.1093/bioinformatics/btn271]

Caroline C. Friedel, Ralf Zimmer. Identifying the topology of protein complexes from affinity purification assays. Proceedings of the German Conference on Bioinformatics, GCB 2008, September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, Vol. P-136, 30-43, GI, Gesellschaft für Informatik, 2008.

Lukas Windhager, Ralf Zimmer. Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. Proceedings of the German Conference on Bioinformatics, GCB 2008, September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, Vol. P-136, 106-115, GI, Gesellschaft für Informatik, 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, accepted. [DOI 10.1261/rna.1136108]

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer. ProCope - Protein Complex Prediction and Evaluation. Bioinformatics 2008 24: 2115-2116. [DOI 10.1093/bioinformatics/btn376]

Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - A Java Framework for Stochastic Simulation and Evaluation of Reaction Networks. BMC Bioinformatics, 2008, 9:356 [DOI 10.1186/1471-2105-9-356]

Orland Gonzalez, Ralf Zimmer. Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics, 24(10):1257-1263

J. Apostolakis, O. Sacher, R. Körner, J. Gasteiger. Automatic Determination of Reaction Mappings and Reaction Center Information II: Validation on a Biochemical Reaction Database. J Chem Inf Model, 48 (6), 1190-1198, 2008.

R. Körner, J. Apostolakis. Determination of Reaction Mappings and Reaction Center Information: The Imaginary Transition State Energy approach. J Chem Inf Model, 48 (6), 1181-1189, 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), Snowbird, Utah, U.S.A., March 25-27, 272-281, IEEE Computer Society Press, 2008. [DOI 10.1109/DCC.2008.45]

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008, LNBI 4955, pp. 3-16. © Springer-Verlag Berlin Heidelberg 2008 [Draft].

Katrin Fundel, Alexander Zien, Jochen Haag, Pia M. Gebhard, Ralf Zimmer, Thomas Aigner. Normalization Strategies for mRNA Expression Data in Cartilage Research. Osteoarthritis and Cartilage, Volume 16, Issue 8, 947-955 [Feb 5; Epub ahead of print]

Fabian Birzele, Gergely Csaba, Ralf Zimmer. Alternative Splicing and Protein Structure Evolution. Nucleic Acids Research Vol. 36:2, 550-558, 2008 (Article)

Jörn Marialke, Simon Tietze, Joannis Apostolakis. Similarity based docking. Journal of Chemical Information and Modelling, 48(1), 186-196, 2008. [Epub 2007-11-29] [DOI 10.1021/ci700124r]

Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, Ralf Zimmer. ProSAS: A database for analyzing alternative splicing in the context of protein structure. Nucleic Acids Research, 2008, 36, D63-D68 Abstract

Fabian Birzele*, Jan E. Gewehr*, Ralf Zimmer. AutoPSI: A database for automatic structural classification of protein sequences and structures. Nucleic Acids Research, 36: D398-D401 Abstract
*authors contributed equally

Schilling, T., R. Küffner, L. Klein-Hitpass, R. Zimmer, F. Jakob, N. Schütze. Microarray analyses of transdifferentiated mesenchymal stem cells. J Cell Biochem, Vol. 03, Issue 2, 413-433, 2008. [Epub 2007-07-03] [DOI 10.1002/jcb.21415]


Theses:

Simon W. Ginzinger: Bioinformatics Methods for NMR Chemical Shift Data, PhD Thesis, February 2008.

Marko Skocibusic: Imroving CheckShift, Diploma Thesis, June 2008.

Florian Erhard: Petri net based system for spatio-temporal simulation of gene regulation, Diploma Thesis, July 2008.

Theresa Niederberger: Regelbasierte Extraktion von Proteinwechselwirkungen, Diploma Thesis, July 2008.

Annabelle Klarl: Konstruktion und Anwendung von Affixarrays, Bachelor Thesis, August 2008.

Simon Berger: Protonation State and Enzyme Substrate Interaction, Diploma Thesis, August 2008.

Stefan Brandmaier: Strukturelle Analyse von alternativem Splicing, Diploma Thesis, August 2008.

Thomas Mair: Analysis of Alternative Splicing of Proteins, Bachelor Thesis, September 2008.

Sebastian Pölsterl: Comparison of Alternative Splicing in Higher Organisms, Bachelor Thesis, Oktober 2008.

2007

Papers:

Andreas Steffen, Joannis Apostolakis. On the ease of predicting thermodynamic properties of beta cyclodextrin inclusion complexes. Chem Cent J. 2007 Nov 15; 1:29. [Epub 2007-11-15]

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. 2007 Nov;14(11):1207-14

KM Borgwardt, T Petri, SVN Vishwanathan, HP Kriegel. An Efficient Sampling Scheme For Comparison of Large Graphs. Mining and Learning with Graphs, MLG 2007, Electronic Proceedings, Firence, Italy, August 1-3, 2007, (video lecture | PDF)

Fan Z, Söder S, Oehler S, Fundel K, Aigner T. Activation of interleukin-1 signaling cascades in normal and osteoarthritic articular cartilage. Am J Pathol, 171(3):938-46, Sep 2007. [Epub 2007-07-19]

Zien A, Gebhard PM, Fundel K, Aigner T. Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology. Clin Orthop Relat Res. 460:226-233, July 2007 [Epub 2007-02-22]

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, No. 11, 1941-1949.

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, 223-227. [DOI 10.1007/s10858-007-9191-5]

Caroline C. Friedel, Ralf Zimmer. Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics, Vol. 8, No. 297. [DOI: 10.1186/1471-2105-8-297]

Thomas Aigner, Jochen Haag, Ralf Zimmer. Functional Genomics, Evo-Devo and Systems Biology - A Chance to Overcome Complexity? Current Opinion in Rheumatology, Vol. 19, No 5, 463-470,

Böhl M, Tietze S.,Sokoll A., Madathil S., Pfennig F., Apostolakis J., Fahmy K., Gutzeit H.O. Flavonoids affect actin functions in cytoplasm and nucleus, Biophysical Journal, Vol. 93, 2767-2780.

Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kaemper, Thomas Lengauer, Gerhard Wenz, Joannis Apostolakis. Improved cyclodextrin based receptors for camptothecin by inverse virtual screening. Chemistry: A European Journal, Vol. 13, Issue 24, 6801-6809.

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, 1657-1672.

Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Caroline C. Friedel, Ralf Zimmer, Rhonda Roberts, Ralph Baric, Jürgen Haas. Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome. PLoS ONE 2007, 2:e459.

Paolo Ferragina, Johannes Fischer. Suffix Arrays on Words. Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), London, Ontario, July 9-11, Lecture Notes in Computer Science 4580, 328-339, Springer. [DOI 10.1007/978-3-540-73437-6_33]

Amihood Amir, Johannes Fischer, Moshe Lewenstein. Two-Dimensional Range Minimum Queries. Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), London, Ontario, July 9-11, Lecture Notes in Computer Science 4580, 286-294, Springer. [DOI 10.1007/978-3-540-73437-6_29]

Katrin Fundel, Ralf Zimmer. Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation. Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, 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), Hangzhou, China, April 7-9, Lecture Notes in Computer Science 4614, 459-470, Springer, 2007. [DOI 10.1007/978-3-540-74450-4_41]

Jan E. Gewehr, Volker Hintermair, Ralf Zimmer. AutoSCOP: Automated Prediction of SCOP Classifications using Unique Pattern-Class Mappings. Bioinformatics, Vol. 23, No. 10, 1203-1210.

Jan E. Gewehr*, Martin Szugat*, Ralf Zimmer. BioWeka - Extending the Weka Framework for Bioinformatics. Bioinformatics, Vol. 23, No. 5, 2007, 651-653. (HTML)
*authors contributed equally

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), Berlin, Germany, March 12-14, Lecture Notes in Bioinformatics 4414, 357-370, Springer, 2007. [DOI 10.1007/978-3-540-71233-6_28]

Jörn Marialke, Robert Körner, Simon Tietze, Joannis Apostolakis. Graph based molecular alignment. Journal of Chemical Information and Modelling, 2007, 47(2):591-601.

Katrin Fundel, Robert Küffner, Ralf Zimmer. RelEx - relation extraction using dependency parse trees. Bioinformatics 2007 23(3):365-371; doi:10.1093/bioinformatics/btl616 (HTML).

Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer. Vorolign - Fast Structural Alignment using Voronoi Contacts, Bioinformatics, Vol. 23, No. 2, 2007, e205-e211 (Journal Article).


Abstracts, Posters:

Joannis Apostolakis, Jörn Marialke, Robert Körner, Simon Tietze. Predicting activated conformations of substrates in enzyme binding sites. PLoS Track talk in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria.

Caroline C. Friedel, Ralf Zimmer. Inferring topology from clustering coefficients in protein-protein interaction networks. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria.

Simon W. Ginzinger, Volker Heun. SimShiftDB: Chemical-Shift-Based Homology Modeling. PLoS Track talk and Poster at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria.


Theses:

Alois Huber: OBMASS: Entwicklung eines linearen Algorithmus zur Berechnung des Bounded Maximum Average Scoring Subsequence Problems, Diploma Thesis, Janaury 2007.

Frank Wallrapp: Empirical Scoring Functions for Protein Structure Analysis, Diploma Thesis, February 2007.

Alex Jarasch: Similarity-Based Analysis of Medium- and High Throughput Screening Data, Diploma Thesis, February 2007.

Robert Körner: Analyse biochemischer Reaktionen an Hand von imaginären Übergangszuständen, Diploma Thesis, March 2007.

Alexander Pöschl: Browsing the protein space, Diploma Thesis, May 2007

Matthias Siebert: Voronoi contact patterns for protein function prediction, Diploma Thesis, June 2007.

Florian Oefinger: A Database for Alternative Splicing in the Context of Protein Structures, Diploma Thesis, June 2007.

Anton Moll: Splice-isoform analysis using data from standard human gene DNA chips, Diploma Thesis, July 2007.

Lukas Windhager: Vergleichende Genomanalyse eines neu sequenzierten H.pylori Stamms, Master Thesis, July 2007.

Andreas Grimm: 3D tomographic and single-particle reconstruction using level set methods, Diploma Thesis, August 2007.

Katrin Fundel: Text Mining and Gene Expression Analysis - Towards Combined Interpretation of High Throughput Data, PhD Thesis, September 2007.

Volker Hintermair: Comparative Analysis of Bos taurus and Homo sapiens DNA Microarrays, Master Thesis, September 2007.

Johannes Fischer: Data Structures for Efficient String Algorithms, PhD Thesis, October 2007.

Jan Erik Gewehr: New Methods for the Prediction and Classification of Protein Domains, PhD Thesis, October 2007.

Martin Stühler: Practical Performance of Preprocessing Schemes for Range Minimum Queries, Diploma Thesis, October 2007.

Sebastian Dümcke: Optimization of Sequence-Structure Alignments using the Vorolign-Scoring Function, Bachelor Thesis, November 2007.

Gergely Csaba: Phenotypic Plasticity as a Measure for Protein Structural Similarity, Master Thesis, November 2007.

2006

Papers:

Aigner, T., Gebhard, P.M., Küffner, R., Zhang, H., Marshall, W. cDNA arrays in degenerative arthritis research. Future Rheumatology 1(1): 101-9

Küffner, R., Duchrow, T., Fundel, K.,Zimmer, R. Characterization of Protein Interactions GCB2006, Tübingen, GI Lecture Notes in Informatics.

Caroline C. Friedel, Ralf Zimmer. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 2006, 7:519.

Fabian Birzele, Stefan Kramer. A New Representation for Protein Secondary Structure Prediction based on Frequent Patterns. Bioinformatics vol. 22, No. 21, 2628-2634, 2006 (HTML).

Katrin Fundel, Ralf Zimmer. Gene and protein nomenclature in public databases. BMC Bioinformatics 2006, 7:372 (HTML)

Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer. Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics Vol. 22, No. 19, 2356-2363, 2006. (HTML)

Thomas Aigner, Katrin Fundel, Joachim Saas, Pia M. Gebhard, Jochen Haag, Tilo Weiss, Alexander Zien, Franz Obermayr, Ralf Zimmer, Eckart Bartnik. Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Osteoarthritic Cartilage Degeneration. Arthritis and Rheumatism, 2006 Oct 30;54(11):3533-3544

Johannes Fischer, Volker Heun, Stefan Kramer. Optimal String Mining under Frequency Constraints. Proc. of the 10th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'06), Lecture Notes in Computer Science 4213, 139-150, Springer-Verlag, 2006. [DOI 10.1007/11871637_17]

Johannes Fischer, Volker Heun. Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE. Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM'06), Lecture Notes in Computer Science 4009, 36-48, Springer-Verlag, 2006. [DOI 10.1007/11780441_5]

Caroline C. Friedel, Ralf Zimmer. Toward the complete interactome. Nature Biotechnology 24, 614 - 615.

Jan E. Gewehr, Ralf Zimmer. SSEP-Domain: Protein Domain Prediction by Alignment of Secondary Structure Elements and Profiles. Bioinformatics, Vol. 22, No. 2, 2006, 181-187. (HTML)

Andreas Kaemper, 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, 2006, 46(2), 903-911.

Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying Structural Similarities from NMR Chemical Shifts. Bioinformatics, Vol. 22, No. 4, 460-465, 2006. [DOI 10.1093/bioinformatics/bti805]

Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Sunwon Park. Colored Petri Net Modeling and Simulation of Signal Transduction Pathways. Metabolic Engineering, 2006 Mar;8(2):112-22.

Uetz, P., Y.A. Dong, C. Zeretzke, C. Atzler, A. Baiker, B. Berger, S.V. Rajagopala, M. Roupelieva, D. Rose, E. Fossum, J. Haas. Herpesviral protein networks and their interaction with the human proteome. Science. 2006 Jan 13;311(5758):239-42.


Theses:

Daniel Güttler: LiMB - Ein interaktiver Browser fr die Analyse biomedizinischer Texte mit Hilfe von Textmining. Diploma Thesis, April 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 Micro\-array Data. Diploma Thesis, May 2006.

Sebastian Bauer: Vergleich und Visualisierung von Algorithmen zur Konstruktion von Suffix-Arrays anhand sehr langer Texte. Bachelor's Thesis, May 2006.

Chad Davis: Feature Selection Methods in Bioinformatics. Bachelor's Thesis, June 2006.

Fabian Gerick: Identification and Correction of Errors in NMR-Chemical Shift Data. Master Thesis, June 2006.

Florian Sohler: Contextual Analysis of Gene Expression Data. PhD Thesis, July 2006.

Simon Tietze: Prediction of Specificity in Protein-Ligand Interactions Using Structure Based Virtual Screening. Diploma Thesis, August 2006.

Jörn Marialke: Similarity Based Methods for the Prediction of Protein Ligand Complexes. Diploma Thesis, November 2006.

Maximilian Karasz: A Fragment-Based Approach to Virtual Screening. Diploma Theisis, December 2006.

Jonathan Hoser: Ein Scheduling System für netzwerkstrukturierte Bioinformatik Arbeitsabläufe. Bachelor's Thesis, December 2006.

Gergely Csaba: Analysis of Protein Sequence-Structure Alignments. Bachelor's Thesis, December 2006

2005

Papers:

Aigner, T., L. McKenna, A. Zien, Z. Fan, P. M. Gebhard, R. 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 31(3): 227-40, 2005.

Fabian Birzele*, Jan E. Gewehr*, Ralf Zimmer. QUASAR - Scoring and Ranking of Sequence-Structure Alignments. Bioinformatics, Vol. 21, No. 24, 2005, 4425-4426. (HTML)
*authors contributed equally

Facius, A., C, Englbrecht, F. Birzele, A. Groscurth, S. Benjamin, S. Wanka, W. Mewes. PRIME: a graphical interface for integrating genomic/proteomic databases. Proteomics. 2005 Jan;5(1):76-80.

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), Lecture Notes in Computer Science 3669, 415-425, Springer-Verlag, 2005. (PDF) [DOI 10.1007/11561071]

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), 619-612, IEEE Computer Society, 2005. (Technical Report PS) [DOI 10.1109/ICDM.2005.62]

Caroline C. Friedel¹, Katharina H.V. Jahn¹, Selina Sommer¹, Stephen Rudd, Hans W. Mewes, Igor V. Tetko. Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinfomatics, 21(8):1383-1388.
¹authors contributed equally.

Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis. A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 2005, 6(Suppl 1):S15 (24 May 2005)

Katrin Fundel, Robert Küffner, Thomas Aigner, Ralf Zimmer. Data Processing Effects on the Interpretation of Microarray Gene Expression Experiments. A. Torda, S. Kurtz, Matthias Rarey (eds.): German Conference on Bioinformatics (GCB) 2005.
GI Lecture Notes in Informatics; P-71: 77-91 (PDF)

M. Gebauer, J. Saas, F. Sohler, J. Haag, S. Söder, M. Pieper, E. Bartnik, J. Beninga, R. Zimmer, T. Aigner. Comparison of the Chondrosarcoma Cell Line SW1353 with Primary Human Adult Articular Chondrocytes Regarding their Gene Expression Profile and their Reactivity to IL-1β. Osteoarthritis and Cartilage. 2005; 13(8), 697-708.

Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, Juliane Fluck. ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005, 6(Suppl 1):S14 (24 May 2005)

Robert Küffner, Katrin Fundel, Ralf Zimmer. Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics. 2005; 21(Suppl.2):ii259-ii267

Dong-Yup Lee, Ralf Zimmer, Sang-Yup Lee, Sunwon Park. Colored Petri Net Modeling and Simulation of Signal Transduction Pathways. Metabolic Engineering, [Epub 2005-12-22].

Florian Sohler, Jan E. 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.

Florian Sohler, Ralf Zimmer: Identifying active transcription factors and kinases from expression data using Pathway Queries. Bioinformatics. 2005; 21(Suppl. 2):ii115-ii122.

M. Szugat, D. Güttler, K. Fundel, F. Sohler, R. Zimmer. Web Servicing the Biological Office. Bioinformatics. 2005; 21(Suppl. 2):ii268-ii269.

Aigner, T., J. Saas, A. Zien, R. Zimmer, P. M. Gebhard, T. Knorr. Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis. Methods Mol Med 100: 109-28, 2005.


Abstracts, Posters:

M. Bundschus, S. Paradies, M. Siebert, F. Birzele, K. Fundel, R. Küffner, R. Zimmer. Disease-relevant gene clusters derived by joint literature and gene expression analysis. German Conference on Bioinformatics (GCB) 2005.

C. Davis, F. Gerick, V. Hintermair, C.C. Friedel, K. Fundel, R. Küffner, R. Zimmer. SAMPL: Sampling and Model-Selection PipeLine - Systematically Combining Stable Gene Selection and Classification. German Conference on Bioinformatics (GCB) 2005.

Jan E. Gewehr, Ralf Zimmer. SSEP-Domain: Protein Domain Prediction by Alignment of Secondary Structure Elements and Profiles. European Conference on Computational Biology (ECCB) 2005, Madrid, Spain.

Simon W. Ginzinger, Johannes Fischer. SimShift: Identifying Structural Similarities from NMR Chemical Shifts. European Conference on Computational Biology (ECCB) 2005.

T. Niederberger, M. Piskarev, F. Sohler, R. Zimmer. Identification of significantly regulated pathways using ToPNet. German Conference on Bioinformatics (GCB) 2005.

Florian Sohler. Generating Contexts for Expression Data using Pathway Queries. In Principles and Practice of Semantic Web Reasoning; Fages, Francois; Soliman, Sylvain (Eds.); Lecture Notes in Computer Science, Vol. 3703:160-162; 2005, ISBN: 3-540-28793-0.


Theses:

Fabian Gerick: Ein programmierbarer Web Service zur Charakterisierung biologischer Objekte Bachelor's Thesis, February 2005.

Alexander Kohn: Quantitative Analyse von Protein-Massenspektren. Diploma Thesis, October 2005.

Martin Szugat. BioWeka: Extending the Weka framework for Bioinformatics. Bachelor's Thesis, October 2005.

Lukas Windhager. Inference of Regulatory Networks Using Physical Models. Bachelor's Thesis, September 2005.

von Oehsen, N. Profile-Profile alignment for remote homology and domain detection of proteins. PhD Thesis, Computer Science, Ludwig-Maximilians-Universität München, 2005.

Stephan Vogt. Topic Maps. Bachelor's Thesis, December 2005.


2004

Papers:

Thomas Aigner, Eckart Bartnik, Florian Sohler, Ralf Zimmer. Functional Genomics of Osteoarthritis: On the Way to Evaluate Disease Hypotheses. Clin Orthop. 2004 Oct; 1(427S):S138-S143.

Christoph Best, Ralf Zimmer, Joannis Apostolakis. Probabilistic methods for predicting protein functions in protein-protein interaction networks. In: R. Giegerich and Jens Stoye (eds.): German Conference on Bioinformatics (GCB) 2004, GI Lecture Notes in Informatics P-53, 2004. (PDF)

Crass, T., I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, H. Claussen, C. Ebeling, P. Ernst, V. Gailus-Durner, K. H. Glatting, R. Gohla, F. Gossling, K. Grote, 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, H. W. 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, R. Zimmer. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics 20(2): 268-70, 2004.

Johannes Fischer, Luc De Raedt: Towards Optimizing Conjunctive Inductive Queries. Proceedings of the Eighth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD'04), Lecture Notes in Computer Science 3056, 625-637, Springer-Verlag, 2004. (PDF)

Fundel, K., D. Guettler, R. Zimmer, J. Apostolakis. Exact versus approximate string matching for protein name identification. BioCreative Challenge Evaluation Workshop, Granada, Spain, 2004.

Jan E. Gewehr, Niklas von Oehsen, Ralf Zimmer. Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition. In: R. Giegerich and Jens Stoye (eds.): German Conference on Bioinformatics (GCB) 2004, GI Lecture Notes in Informatics P-53, 141-148,2004.

Hanisch, D., K. Fundel, H.-T. Mevissen, R. Zimmer, J. Fluck. ProMiner: Organism-specific protein name detection using approximate string matching. BioCreative Challenge Evaluation Workshop, Granada, Spain, 2004.

Daniel Hanisch, Florian Sohler, Ralf Zimmer. ToPNet - an application for interactive analysis of expression data and biological networks. Bioinformatics. 2004 Jun 12;20(9):1470-1.

Jan T. Kim, Jan E. Gewehr, Thomas Martinetz. Binding Matrix: A Novel Approach for Binding Site Recognition. Journal of Bioinformatics and Computational Biology, Vol. 2, No. 2 (2004) 289-307.

Lee, D. Y., R. Zimmer, S. Y. Lee, D. Hanisch, S. Park. Knowledge representation model for systems-level analysis of signal transduction networks. Genome Inform Ser Workshop Genome Inform 15(2): 234-43, 2004.

Florian Sohler, Daniel Hanisch, Ralf Zimmer. New methods for joint analysis of biological networks and expression data. Bioinformatics. 2004 Jul 1;20(10):1517-21.

von Oehsen, N., I. Sommer, R. Zimmer, T. Lengauer. Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20(14): 2228-35, 2004.


Patents:

Hoffmann, D., R. Zimmer. Fluorescent Energy for Elucidating the 3D Structure of Biological Macromolecules (FETMA), 2004, Appl-No.: PCT Patent application, European patent office 10.08.2001, Patent-No.: PCT/EP 99/01008 (Feb 10, 1999), US 6,713,256 B1 (Mar 30, 2004)

Zimmer, R., R. Kffner, A. 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, 2004, Appl-No.: PCT Patent application, European patent office 12.11.1999, Patent-No.: PCT/EP 00/11171


Abstracts, Posters:

Jan E. Gewehr, Alessandro Macri, Ralf Zimmer. Secondary Structure Elements and Profiles. CASP6,Abstracts Book. CASP 6 Meeting, Gaeta, Italy, 2004.

Sabine Trochim, Florian Sohler, Daniel Hanisch, Ralf Zimmer. Validation of Biological Hypotheses Using Joint Analysis of Biological Networks And Expression Data. Poster at the 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2004, Glasgow, Scotland.

Katrin Fundel, Daniel Güttler, Ralf Zimmer, Joannis Apostolakis. A simple approach for protein name identification. Poster at the 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) 2004, Glasgow, Scotland.


Theses:

Hanisch, D. New Analysis Methods for Gene Expression Data via Construction and Incorporation of Biological Networks. PhD Thesis, Computer Science, Ludwig-Maximilians-Universität München, 2004.

Volker Hintermair. Characterisation and Visualisation of Protein Families based on Multicriterial Clustering. Bachelor's Thesis, November 2004.

Liebich, D. Packungsprobleme bei Proteinen. PhD Thesis, Computer Science, Friedrich-Wilhelms-Universität Bonn, 2004.

Thomas Obkircher. Eine erweiterte Bioinformatik Umgebung zur kriterienbasierten Protein Identifizierung Bachelor's Thesis, January 2004.

Andreas Spitzmüller. JRDP - Ein Java Framework fr Rekursive Dynamische Programmierung. Bachelor's Thesis, June 2004.


2003

Papers:

Aigner, T., A. Zien, D. Hanisch, R. Zimmer. Gene expression in chondrocytes assessed with use of microarrays. J Bone Joint Surg Am 85-A Suppl 2: 117-23, 2003.

Aigner, T., R. Zimmer. The promise and limitations of DNA microarray analysis: comment on the editorial by Firestein and Pisetsky. Arthritis Rheum 48(3): 860; author reply 862, 2003.

Hanisch, D., J. Fluck, H. T. Mevissen, R. Zimmer. Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput: 403-14, 2003.

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. Discrete Applied Mathematics, Vol. 127, No. 1, 163-177, 2003. [DOI 10.1016/S0166-218X(02)00382-7]

Volker Heun. Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices. In: Computational Molecular Biology, S. Istrail, P. Pevzner, R. Shamir (Eds.), Topics in Discrete Mathematics, Vol. 12, North-Holland, 2003.

Thomas Martinetz, Jan E. Gewehr, Jan T. Kim. Statistical Learning for Detecting Protein-DNA Binding Sites. In: D. C. Wunsch II, M. Hasselmo, and K. Venayagamoorthy (eds.): Proc. of the IEEE International Joint Conference on Neural Networks (IJCNN) 2003, IEEE Press, 2940-2945, 2003. (PDF)

Sohler, F., D. Hanisch, R. Zimmer. New methods for joint analysis of biological networks and expression data. Proceedings of the German Conference on Bioinformatics 2003 (GCB'03): 141-146, 2003.

von Oehsen, N., I. Sommer, R. Zimmer. Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput: 252-63, 2003.

Zien, A., J. Fluck, R. Zimmer, T. Lengauer. Microarrays: how many do you need? J Comput Biol 10(3-4): 653-67, 2003.


Books:

Volker Heun. Grundlegende Algorithmen - Einführung in den Entwurf und die Analyse effizienter Algorithmen. Zweite durchgesehene und überarbeitete Auflage, Vieweg Verlag, xiv+370, ISBN 3-528-11340-5, 2003.


Abstracts, Posters:

Jan E. Gewehr, Jan T. Kim, Thomas Martinetz. On the Correspondence between Scoring Matrices and Binding Site Sequence Distributions. Poster at Eleventh International Conference on Intelligent Systems for Molecular Biology (ISMB) 2003, Brisbane, Australia.

Jan T. Kim, Jan E. Gewehr, Thomas Martinetz. The Binding Matrix: A High Specificity Method for Finding Transcription Factor Binding Sites. Poster at Bioinformatics 2003, Helsinki, Finland.

Daniel Hanisch, Florian Sohler, Ralf Zimmer. ToPNet - an application for interactive analysis of expression data and biological networks. Poster at RECOMB 2003, Berlin, Germany.


Theses:

Cornelia Donner. Erkennung von Gennamen in wissenschaftlichen Texten - automatische Generierung von Synonymlisten und Prärozessierung der Texte. Bachelor's Thesis, June 2003.

Caroline C. Friedel. Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems. Bachelor's Thesis, June 2003.

William Travis Holton. Evaluation of mapping consistency between public gene and protein databases. Bachelor's Thesis, November 2003.

Zien, A. Computational Methods for Gene Expression Data Analysis. PhD Thesis, Computer Science, Friedrich-Wilhelms-Universität Bonn: 190, 2003.


2002

Papers:

Aigner, T., E. Bartnik, A. Zien, R. Zimmer. Functional genomics of osteoarthritis. Pharmacogenomics 3(5): 635-50, 2002.

Albrecht, M., D. Hanisch, R. Zimmer, T. Lengauer. Improving fold recognition of protein threading by experimental distance constraints. In Silico Biol 2(3): 325-37, 2002.

Freudenberg, J., R. Zimmer, D. Hanisch, T. Lengauer. A hypergraph-based method for unification of existing protein structure- and sequence-families. In Silico Biol 2(3): 339-49, 2002.

Hanisch, D., A. Zien, R. Zimmer, T. Lengauer. Co-clustering of biological networks and gene expression data. Bioinformatics 18 Suppl 1: S145-S154, 2002.

Hanisch, D., R. Zimmer, T. Lengauer. ProML - the protein markup language for specification of protein sequences, structures and families. In Silico Biol 2(3): 313-24, 2002.

Sommer, I., A. Zien, N. von Oehsen, R. Zimmer, T. Lengauer. Confidence measures for protein fold recognition. Bioinformatics 18(6): 802-12, 2002.

Zien, A., J. Fluck, T. Lengauer, R. Zimmer. Microarrays: How many do you need? RECOMB 2002, Washington, DC, ACM Press, New York, 2002.


Abstracts, Posters:

Thomas Martinetz, Jan E. Gewehr, Jan T. Kim. A Statistical Learning Approach to Predicting Protein-DNA-Binding Sites. Poster at European Conference on Computational Biology (ECCB) 2002, Saarbrücken, Germany.


2001

Papers:

Albrecht, M., D. Hanisch, R. Zimmer, T. Lengauer. Improving fold recognition of protein threading by experimental distance constraints. German Conference on Bioinformatics (GCB 2001), Braunschweig, 2001.

Freudenberg, J., R. Zimmer, D. Hanisch, T. Lengauer. A new method for unification of existing protein structure- and sequence-families. German Conference on Bioinformatics (GCB 2001), Braunschweig, 2001.

Hanisch, D., R. Zimmer, T. Lengauer. ProML - The protein markup language for specification of protein sequences, structures and families. German Conference on Bioinformatics (GCB 2001), Braunschweig, 2001.

Hoffmann, D., V. Schnaible, S. Wefing, M. Albrecht, D. Hanisch, R. Zimmer. Fast solution of Protein-3D-structures. Coupling of Biological and Electronic Systems, Proceedings of the 2nd caesarium, Bonn, Springer Verlag, 2001.

von Oehsen, N., R. Zimmer. Improving profile-profile alignments via log average scoring. Algorithms in Bioinformatics (WABI 2001), Aarhus, Springer, 2001.

Zien, A., T. Aigner, R. Zimmer, T. Lengauer. Centralization: a new method for the normalization of gene expression data. Bioinformatics 17 Suppl 1: S323-S331, 2001.

Zimmer, R., T. Lengauer. Protein Structure Prediction. Chapter in Bioinformatics - From Genomes to Drugs. T. Lengauer, Wiley-VCH: 237-313, 2001.


Patents:

Zimmer, R.. Frei programmierbares, universelles Parallel-Rechnersystem zur Durchfhrung von allgemeinen Berechnungen, 2001, Appl-No.: PCT Patent application, European patent office 15.04.1998, Patent-No.: EP 0 976 060 B1


Abstracts, Posters:

Albrecht, M., R. Zimmer. Protein structure prediction by threading with experimental constraints. Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001, Poster), 2001.

Hanisch, D., R. Zimmer, T. Lengauer. Evaluation of structure prediction models using the ProML specification language. Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001, Poster), 2001.