MolBI

Previous Years

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

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

  3. Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I (2008) 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. Grunwald S, Speer A, Ackermann J, Koch I (2008) Petri net modelling of gene regulation of the Duchenne muscular dystrophy BioSystems 92:189-205, doi:10.1016/j.biosystems.2008.02.005.  PubMed

  5. Koch I, Heiner M (2008) 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

  6. Sackmann A, Formanowicz D, Formanowicz P, Koch I, Blazewicz J (2007) An analysis of the Petri net based model of the human body iron homeostasis process Computational Biology and Chemistry 31:1-10, doi: 10.1016/j.ejro.2022.100459.  PubMed

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

  8. Scheer M, Klawonn F, Münch R, Grote A, Hiller K, Choi C, Koch I, Schobert M, Härtig E, Klages U, Jahn D (2006) JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Nucleic Acids Research 34:W510-W515, doi: 10.1093/nar/gkl329  PubMed

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

  10. Koch I, Björn H. Junker, Heiner M (2005) Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics 21:1219-1226, doi: 10.1093/bioinformatics/bti145  PubMed, 

  11. Trißl S, Rother K, Müller H, Steinke T, Koch I, Preissner R, Frömmel C, Leser U (2005) Columba: an integrated database of proteins, structures, and annotations BMC Bioinformatics 6:81, doi: 10.1186/1471-2105-6-81  PubMed

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

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

  14. Popova-Zeugmann L, Heiner M, Koch I (2004) 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

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

  16. Heiner M, Koch I (2004) 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

  17. May P, Barthel S, Koch I (2004) PTGL - Protein Topology Graph Library. Bioinformatics 20(17):3277-3279  PubMed

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

  19. Rother K, Müller H, Trissl S, Koch I, Steinke T, Preissner R, Frömmel C, Leser U (2004) 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

  20. Sifringer M, Uhlenberg B, Lammel S, Hanke R, Neumann B, von Moers A, Koch I, Speer A (2003) 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 PubMed

  21. Heiner M, Koch I, Will J (2003) 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, LNCS 2602:173 

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

  23. Patrick May, Koch I (2003) 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 

  24. Rother K, Trissl S, Müller H, May P, Heek R, Preissner R, Steinke T, Koch I, Leser U, Frömmel C (2003) 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: pp.109-110

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

  26. Kriventseva EV, Koch I, Appweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S (2003) Increase of functional diversity by alternative splicing. Trends in Genetics 19:124-128  PubMed

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

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

  29. Heiner M, Koch I, Voss K (2001) 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

  30. Sunyaev S, Ramensky V, Koch I, Lathe III W, Kondrashov AS, Bork P (2001)  Prediction of Deleterious Human Alleles Human Molecular Genetics 10(6):591-597

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

  32. Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T (2000) 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

  33. Koch I, Schuster S, Heiner M (2000) 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

  34. Koch I, Schuster S, Heiner M (1999) 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

  35. O'Connel JR, Margetic N, Farrall M, Lathrop GM, Weeks DE, Demenais F, Martinez M, Durrieu G, Koch I, Rohde K Dissecting complex diseases with FINESSE. Genetic Epidemiology 15:521-522

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

  37. Koch I, Lengauer T (1997) 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

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

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

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

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

  42. Selbig J, Koch I, Kaden F (1991) 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

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

  44. Kaden F, Koch I, Selbig J (1989) Knowledge-based prediction of protein structures. Report DAI-PEE-1, ZKI - Central Institute for Cybernetics and Information Processes of the Academy of Sciences, Berlin, Germany 

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