Previous Years


  1. Janice Kielbassa, Ralf Bortfeldt, Stefan Schuster, Ina Koch. Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets Computational Biology and Chemistry (2009) 33: 46-61, doi:10.1016/j.compbiolchem.2008.07.022.  PubMed

  2. Ina Koch, Georg Fuellen. A review of bioinformatics education in Germany Briefings in Bioinformatics 9(3):232-242 (2008) doi:10.1093/bib/bbn006.  PubMed

  3. Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Bjorn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch. Modularization of biochemical networks based on classification of Petri net t-invariants BMC Bioinformatics 9:90 (2008), doi:10.1186/1471-2105-9-90.  PubMed

  4. Stefanie Grunwald, Astrid Speer, Jörg Ackermann, Ina Koch. Petri net modelling of gene regulation of the Duchenne muscular dystrophy BioSystems 92: 189-205 (2008), doi:10.1016/j.biosystems.2008.02.005.  PubMed

  5. Ina Koch, Monika Heiner. Petri nets In: Analysis of Biological Networks Eds. Björn H. Junker, Falk Schreiber, Wiley Book Series in Bioinformatics (Series Eds. Yi Pan, Albert Y. Zomaya) chapter 7:139-180 (2008).

  6. Andrea Sackmann, Dorota Formanowicz, Pjotr Formanowicz, Ina Koch, Jacek Blazewicz. An analysis of the Petri net based model of the human body iron homeostasis process Computational Biology and Chemistry 31:1-10 (2007).  PubMed

  7. Andrea Sackmann, Monika Heiner, Ina Koch. Application of Petri net based analysis techniques to signal transduction pathways BMC Bioinformatics 7:482 (2006), doi:10.1186/1471-2105-7-482.  PubMed

  8. Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, Dieter Jahn. JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Nucleic Acids Research 34:W510-W515 (2006).  PubMed

  9. Louchka Popova-Zeugmann, Monika Heiner, Ina Koch. Time Petri Nets for Modelling and Analysis of Biochemical Networks Fundamenta Informaticae 67:149-162 (2005).

  10. Ina Koch, Björn H. Junker, Monika Heiner. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics 21:1219-1226 (2005).  PubMed

  11. Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser. Columba: an integrated database of proteins, structures, and annotations BMC Bioinformatics 6:81 (2005).  PubMed

  12. Ina Koch, Markus Schüler, Monika Heiner. STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks. In Silico Biol. 5(2):129-37 (2005)  PubMed

  13. Ina Koch, Markus Schüler, Monika Heiner. A Software Tool for Petri Net based based Analysis in Biochemical Networks. In Silico Biology 5, 0014 (2004).

  14. Louchka Popova-Zeugmann, Monika Heiner, Ina Koch. Modelling and Analysis of Biochemical Networks with Time Petri Nets. Proc. Workshop Concurrency, Specification & Programming 2004, Caputh, Sept. 24 - 26, Informatik-Berichte der HUB Nr. 170, 1:136-143 (2004).

  15. Ina Koch, Monika Heiner. Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets. Tutorial Notes, 5th Int. Conference on Systems Biology - ICSB 2004, Heidelberg/Germany, October (2004).

  16. Monika Heiner, Ina Koch. Petri Net Based Model Validation in Systems Biology. Proceedings 25th International Conference on Application and Theory of Petri Nets, ICATPN 2004. July, 21-25, Bologna, Italy, Springer Verlag Berlin LNCS 3099:216-237 (2004).

  17. Patrick May, Stefan Barthel, Ina Koch. PTGL - Protein Topology Graph Library. Bioinformatics 20(17):3277-3279 (2004).  PubMed

  18. Monika Heiner, Ina Koch, Jürgen Will. Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. Journal BioSystems, 75(1-3):15-28 (2004).  PubMed

  19. Kristian Rother, Heiko Müller, Silke Trissl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser. COLUMBA: Multidimensional Data Integration of Protein Annotations. Proceedings International Workshop of Data Integration in Life Sciences, DILS 2004. March, 25-26, Leipzig, Germany, Springer Verlag Berlin LCBI 2994:156-171 (2004).

  20. Marco Sifringer, Birgit Uhlenberg, Stefanie Lammel, Rita Hanke, Benjamin Neumann, Arpad von Moers, Ina Koch, Astrid Speer. Identification of transcripts from a subtraction library which might be responsible for the mild phenotype in an intrafamilially variable course of Duchenne muscular dystrophy. Human Molecular Genetics 114:149-156 (2003). PubMed

  21. Monika Heiner, Ina Koch, Jürgen Will. Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB Proc. - First International Workshop on Computational Methods in Systems Biology, Rovereto, Italy, ed. C. Priami, February 24-26, LNCS2602:173 (2003).

  22. Christian Köberle, Volker Patzel, Ina Koch. RNA Analysis and Antisense Oligodeoxyribonucleotide Prediction Tool - RAOPT. Currents in Computational Molecular Biology, eds. R. Spang, P. Beziat, M. Vingron. pp. 195-196 (2003).

  23. Patrick May, Ina Koch. PTGL - Protein Topology Graph Library. ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics; eds. C. Christophe, H.-P- Lenhof, M.-F. Sagot:193-194 (2003).

  24. Kristian Rother, Silke Trissl, H. Müller, Patrick May, R. Heek, Robert Preissner, Thomas Steinke, Ina Koch, Ulf Leser, Cornelius Frömmel. Columba - A Database of Annotations of Protein Structure. ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics; eds. C. Christophe, H.-P- Lenhof, M.-F. Sagot:109-110 (2003).

  25. Klaus Voss, Monika Heiner, Ina Koch. Steady State Analysis of Metabolic Pathways using Petri Nets. In Silico Biology 3(3):367-387 (2003).  PubMed

  26. Evgenia V. Kriventseva, Ina Koch, Rolf Appweiler, Martin Vingron, Peer Bork, Mikhail S. Gelfand, Shamil Sunyaev. Increase of functional diversity by alternative splicing. Trends in Genetics 19:124-128 (2003).  PubMed

  27. Stéphanie Boué, Martin Vingron, Evgenia V. Kriventseva, Ina Koch. Theoretical analysis of alternative splice forms using computational methods. ECCB-European Conference on Computational Biology, Oxford Press, Bioinformatics 18(suppl. 2): S65-S73 (2002).  PubMed

  28. Stefan Schuster, Thomas Pfeiffer, Ina Koch, Ferdinand Moldenhauer, Thomas Dandekar. Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae. Bioinformatics 18(2):351-361 (2002).

  29. Monika Heiner, Ina Koch, Klaus Voss. Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets. CPN'01-Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, University of Aarhus, Denmark, ed.K. Jensen,ISSN 0105-8517, pp.15-34 (2001).

  30. Shamil Sunyaev, Vasily Ramensky, Ina Koch, Warren Lathe III, Alexey S. Kondrashov, Peer Bork. Prediction of Deleterious Human Alleles. Human Molecular Genetics 10(6): 591-597 (2001).

  31. Ina Koch. Fundamental Study: Enumerating all connected maximal common subgraphs in two graphs. Theoretical Computer Science 250:1-30 (2001).

  32. Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar. Structural Analysis of metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma pneumoniae. Proc.Germ.Conf.Bioinf., eds. E.-B. Bauer, U.Rost, J. Stoye, M. Vingron, October, 5-7 Heidelberg, Germany, (2000), Logos Verlag Berlin, ISBN 3-89722-498-4, pp.115-120 (2000).

  33. Ina Koch, Stefan Schuster, Monika Heiner. Using time-dependent Petri nets for the analysis of metabolic networks. Workshop Modellierung und Simulation Metabolischer Netzwerke, eds. R. Hofestädt, K. Lautenbach, M. Lange, Preprint No.10, Faculty of Computer Science, Otto-von-Guericke University of Magdeburg, pp.15-21 (2000).

  34. Ina Koch, Stefan Schuster, Monika Heiner. Simulation and analysis of metabolic networks by time-dependent Petri nets. Computer Science and Biology - Proceedings of the German Conference on Bioinformatics 1999, pp.208-210 (1999).

  35. Jeff R. O'Connel, Nino Margetic, Martin Farrall, G.M. Lathrop, Daniel E. Weeks, Florence Demenais, Maria Martinez, Gilles Durrieu, Ina Koch, Klaus Rohde. Dissecting complex diseases with FINESSE. Genetic Epidemiology 15:521-522 (1998).

  36. Ina Koch. Ein graphentheoretischer Ansatz zum paarweisen und multiplen Vergleich von Proteinstrukturen. Wissenschaft und Technik Verlag, Berlin, ISBN 3-89685-446-1, (1998).

  37. Ina Koch, Thomas Lengauer. Detection of distant structural similarities in a set of proteins using a fast graph-based method. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, June, 21-26 (1997) in Halkidiki, Greece. AAAI Press, California. eds. T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, A. Valencia, pp.167-187 (1997).

  38. Ina Koch, Thomas Lengauer, Egon Wanke. An algorithm for finding maximal common subtopologies in a set of proteins. Journal of Computational Biology 3(2):289-306 (1996).

  39. Frieder Kaden, Ina Koch, Joachim Selbig. Heuristische Analyse und Vorhersage von Proteinstrukturen. Arbeitspapiere der GMD - Gesellschaft für Mathematik und Datenverarbeitung GmbH, 656 (1992).

  40. Ina Koch, Frieder Kaden, Joachim Selbig. Analysis of protein sheet topologies by graph-theoretical methods. Proteins: Structure, Function, and Genetics 12:314-324 (1992).

  41. Joachim Selbig, Frieder Kaden, Ina Koch. Applying machine learning methods for finding significant amino acid properties in proteins. FEBS Letters 297:1-6 (1992).

  42. Joachim Selbig, Ina Koch, Frieder Kaden. Automatic knowledge acquisition for the prediction of protein structures. Contributions to Artificial Intelligence; eds. U. Geske, D. Koch Akademie-Verlag Berlin, Germany, pp. 109-120 (1991).

  43. Frieder Kaden, Ina Koch, Joachim Selbig. Knowledge-based prediction of protein structures. Journal of Theoretical Biology 147(1):85-100 (1990).

  44. Frieder Kaden, Ina Koch, Joachim Selbig. Knowledge-based prediction of protein structures. Report DAI-PEE-1, ZKI - Central Institut for Cybernetics and Information Processes of Academy of Sciences, Berlin, Germany (1989).

  45. Ina Koch, Ada Markwald. Membranen mit trägergebundenem Transport (Carriermembranen) III. Polymermembranen mit fixierten funktionellen Gruppen. Literaturberichte, Academy of Sciences Berlin, Germany (1986).