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Jena Centre for Bioinformatics

Jena Centre for Bioinformatics. Spokesman: Stefan Schuster Deputy Spokesman: Sebastian Böcker. History of JCB. Founded in 2001 Funded by German Ministry of Education and Research (BMBF) 2001-2008 Since 2008, „low-budget“ network with funding from various sources

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Jena Centre for Bioinformatics

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  1. Jena Centre for Bioinformatics Spokesman: Stefan Schuster Deputy Spokesman: Sebastian Böcker

  2. History of JCB • Founded in 2001 • Funded by German Ministry of Education and Research (BMBF) 2001-2008 • Since 2008, „low-budget“ network withfunding from various sources • Coordinator/Spokesman2001-2007: Jürgen Sühnel, since January 2008: Sebastian Böcker and Stefan Schuster in rotary annual change • Manager:Margit Leitner

  3. Beutenberg Campus Technology and Innovation Park BioCentiv GmbH – Centreof Competence for Bioinstruments Max Planck Institute forBiogeochemistry Max Planck Institute for Chemical Ecology Abbe Centre FSU - CentreforMolecularBiomedicine Hans Knöll Institute Institute ofPhotonic Technology Wacker Biotech GmbH FSU - Institute forVirologyand Antiviral Therapy FSU - Institute for Applied Physics Fraunhofer Institute for Applied Opticsand Precision Engineering Fritz Lipmann Institute

  4. Interaction with other research networks in Jena • Jena School of Microbial Communication • International Max Planck Research School on Ecological Interactions • Jena Centre for Systems Biology of Ageing • Jena Life Science Forum • and others

  5. BMBF Call: Systems Biology for Health in Old Age – GerontoSys • Since 2009: JenAge (GerontoSys program funded by BMBF) • 4 Million Euro for 3 years, 5 groups out of 10 are from JCB

  6. JCB membersin JenAge Udo Hahn: Department of German Linguistics, Jena University Language & Information Engineering Lab - JULIE Stefan Schuster: Department of Bioinformatics Reinhard Guthke: Systems Biology/ Bioinformatics Group Matthias Platzer: Genome Analysis Group (sequenced several bacteria and part of human genome)Jürgen Sühnel: Biocomputing Group

  7. Strong interest in theoretical questions • For example, in FSU Jena, School of Mathematics and Computer Science: • Sebastian Böcker: Bioinformatics (phylogenetic trees, algorithms for mass spectrometry) • Rolf Niedermeier: Theoretical Computer Science, e.g. fixed-parameter tractability problems • Clemens Beckstein: Artificial Intelligence • E.G. Schukat-Talamazzini: Pattern Recognition • Peter Dittrich: Biosystems Analysis • FSU Jena, School of Biology and Pharmaceutics: • Thomas Hinze (in Schuster lab): DNA and membrane computing, biological oscillations

  8. Conferences/Meetings in which JCB was/is involved (e.g. by sponsoring) • Jena Life Science Forum, 18-20 June 2009 and 23-27 August 2010, Organizers: B.O. Küppers, S. Artmann, S. Schuster, (assisted by T. Hinze), S. Heinemann • Annual International Workshops "Integrative Network Inference in Systems Biology", Jena, Organizers: R. Guthke ans M. Pfaff • 11th International Conference on Membrane Computing - CMC11, 24-27 August 2010, Jena, Main organizer: T. Hinze assisted by Dittrich and Schuster labs • International Workshop “Metabolic Pathway Analysis 2005” (Schuster) in Jena, sequels: “Metabolic Pathways Analysis 2009” in Leiden (NL) and 2011 in Chester (UK) • and others

  9. JCB Seminars/Lectures, Workshops • 20-30 Seminars/Lectures per year: Speakers from all over Germany, and from France, Spain, England, U.S., Israel, New Zealand, Uruguay, Montenegro and others • 21 so far in 2010 • Annual or biannual workshops, last workshop in February 2010 together with JSMC

  10. Selected joint publications of JCB groups in 2009/10 S. Schuster, J.U. Kreft, N. Brenner, F. Wessely, G. Theißen, E. Ruppin, A. Schroeter: Cooperation and cheating in microbial exoenzyme production - Theoretical analysis for biotechnological applications. Biotechnol. J. 5 (2010) 751-758. (Schuster, Theißen) G. Grünert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich: Rule-based spatial modeling with diffusing, geometrically constrained molecules. BMC Bioinformatics, 11 (2010) 307 (Dittrich, Schuster/Hinze) Dom M, Jiong Guo J, Hüffner F, Niedermeier R, Truss A (2009) Fixed-parameter tractability results for feedback set problems in tournaments. J. Discrete Alg. 8 (2010) 76–86 (Böcker, Niedermeier) Lenser T, Theissen G, Dittrich P (2009) Developmental robustness by obligate interaction of Class B Floral Homeotic Genes and Proteins PLoS Comput. Biol. 5: e1000264. (Dittrich, Theissen) Wollbold J, Huber R, Pohlers D, Koczan D, Guthke R, Kinne RW, Gausmann U (2009) Adapted Boolean network models for extracellular matrix formation. BMC Syst. Biol. 3: 77. (Guthke, Kinne, Platzer)

  11. Joint publications of JCB groups 2009 (cont.) Sinha R, Nikolajewa S, Szafranski K, Hiller M, Jahn N, Huse K, Platzer M, Backofen R (2009) Accurate prediction of NAGNAG alternative splicing. Nucl. Acids Res. 37, 3569- 3579. (Backofen, Guthke, Platzer) Lehmann K, Müller JP, Schlott B, Skroblin P, Barz D, Norgauer J, Wetzker R (2009) PI3Kgamma controls oxidative burst in neutrophils via interaction with PKCalpha and p47phox. Biochem. J. 419, 603-610 (Müller, Wetzker) Pudimat R, Backofen R, Schukat-Talamazzini EG (2009). Fast feature subset selection in biological sequence analysis. Intern. J. PatternRecogn. Artific. Intell., 23, 191-207. (Backofen, Schukat-Talamazzini) Hinze T, Fassler R, Lenser T, Dittrich P (2009) Register machine computations on binary numbers by oscillating and catalytic chemical reactions modelled using mass-action kinetics. Intern. J. Found. Comput. Sci., 20, 411-426. (Dittrich, Schuster) Kaleta C, Richter S, Dittrich P (2009) Using chemical organization theory for model- checking. Bioinformatics 25, 1915-1922 (Dittrich, Schuster)

  12. Much interest in innovative approaches • Such as membrane computing • Example: Dittrich lab involved in DFG-funded research network „Organic computing“, EU-funded programme on in-vivo chemical computing etc. • The JCB wishes all participants of CMC11 a most interesting and enjoyable conference!!

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