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• Coordinator/Spokesman 2001-2007: Jürgen

Sühnel, since January 2008: Sebastian Böcker and Stefan Schuster in rotary annual change

• Manager: Margit Leitner

Beutenberg CampusBeutenberg Campus

Hans Knöll InstituteHans Knöll InstituteMax Planck Institute for Chemical EcologyMax Planck Institute for Chemical Ecology FSU - Centre for Molecular BiomedicineFSU - Centre for Molecular Biomedicine

Institute of Photonic TechnologyInstitute of Photonic Technology FSU - Institute for Virology and Antiviral TherapyFSU - Institute for Virology and Antiviral Therapy

Abbe CentreAbbe Centre

Wacker Biotech GmbHWacker Biotech GmbH

Max Planck Institute for BiogeochemistryMax Planck Institute for Biogeochemistry

BioCentiv GmbH – Centre of Competence for BioinstrumentsBioCentiv GmbH – Centre of Competence for BioinstrumentsTechnology and Innovation Park Technology and Innovation Park

Fritz Lipmann InstituteFritz Lipmann InstituteFraunhofer Institute for Applied Optics and Precision EngineeringFraunhofer Institute for Applied Optics and Precision EngineeringFSU - Institute for Applied PhysicsFSU - Institute for Applied Physics

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

BMBF Call: BMBF Call: Systems Biology for Health in Old Age – GerontoSysSystems 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

JCB membersJCB members in JenAgeJenAge

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

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

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

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

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)

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. Pattern Recogn. 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)

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!!