GoFORSYS Partner Project: Modelling the Circadian Clock of Chlamydomonas reinhardtii and Its Influences on Nitrogen Use and Photosynthetic Capacity

Edited Books

M. Gheorghe, T. Hinze, G. Paun, G. Rozenberg, A. Salomaa (Editors). Membrane Computing. Eleventh International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers. Series Lecture Notes in Computer Science, Vol. 6501, ISBN 978-3-642-18122-1, Springer-Verlag Berlin, Heidelberg, 393 p., 2010
M. Gheorghe, T. Hinze, G. Paun (Editors). Proceedings of the Eleventh International Conference on Membrane Computing (CMC11). ISBN 978-3-86805-721-8, Verlag ProBusiness Berlin, 482 p., 2010
H. Bordihn, R. Freund, T. Hinze, M. Holzer, M. Kutrib, F. Otto (Editors). Proceedings of the Second Workshop on Non-Classical Models for Automata and Applications (NCMA2010). ISBN 978-3-85403-263-2, Volume 263, Österreichische Computer Gesellschaft, 196 p., 2010
J. Behre, G. Escuela, T. Hinze (Editors). Proceedings Compendium of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC2010) and of the First Workshop on Applications of Membrane Computing, Concurrency, and Agent-based Modelling in Population Biology (AMCA-POP2010). ISBN 978-3-86805-767-6, Verlag ProBusiness Berlin, 238 p., 2010

Journal Articles, Book Chapters, and Conference Papers (peer review)

T. Hinze, C. Bodenstein, B. Schau, I. Heiland, S. Schuster. Chemical Analog Computers for Clock Frequency Control Based on P Modules. Proceedings of the Twelfth International Conference on Membrane Computing, to appear within series Lecture Notes in Computer Science, Springer Verlag, 2011, accepted
G. Gruenert, G. Escuela, P. Dittrich, T. Hinze. Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problems. Proceedings of the Twelfth International Conference on Membrane Computing, to appear within series Lecture Notes in Computer Science, Springer Verlag, 2011, accepted
T. Hinze, C. Bodenstein, I. Heiland, S. Schuster. Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization. ISSN 0926-4981, ERCIM News 85:27-29, 2011
T. Hinze, M. Schumann, S. Schuster. Synchronisation of Biological Clock Signals: Capturing Coupled Repressilators from a Control Systems Perspective. In F. Babiloni, A. Fred, J. Filipe, H. Gamboa (Eds.), Proceedings of the Fourth International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS2011), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, ISBN 978-989-8425-35-5, pp. 101-106, SciTePress, 2011
T. Hinze, J. Decraene, G.G. Mitchell, J. Behre, S. Schuster. Towards a Unified Approach for the Modelling, Analysis, and Simulation of Cell Signalling Networks. In Z. Zhao (Ed.), Sequence and Genome Analysis: Methods and Applications. ISBN 978-0-9807330-4-4, iConcept Press, 2010
J. Decraene, T. Hinze. A Multidisciplinary Survey of Computational Techniques for the Modelling, Simulation and Analysis of Biochemical Networks. ISSN 0948-695x, Journal of Universal Computer Science 16(9):1152-1175, 2010
G. Gruenert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich. Rule-based spatial modeling with diffusing, geometrically constrained molecules. ISSN 1471-2105, BMC Bioinformatics 11:307, 2010
T. Schulze, K. Prager, H. Dathe, J. Kelm, P. Kießling, M. Mittag. How the green algae Chlamydomonas reinhardtii keeps time. Protoplasma, 2010, in press
T. Hinze, T. Lenser, G. Escuela, I. Heiland, S. Schuster. Modelling Signalling Networks with Incomplete Information about Protein Activation States: A P System Framework of the KaiABC Oscillator. In G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, G. Rozenberg, A. Salomaa (Eds.), Membrane Computing. Proceedings Tenth International Workshop on Membrane Computing (WMC10). Revised, Selected and Invited Papers, Series Lecture Notes in Computer Science, ISBN 978-3-642-11466-3, Vol. 5957, pp. 316-334, © Springer Verlag, 2010
S.B. Seitz, W. Weisheit, M. Mittag. Multiple roles and interaction factors of an E-box element in Chlamydomonas reinhardtii. Plant Physiol. 152:2243-2257, 2010
N. Matsumaru, T. Hinze, P. Dittrich. Organization-Oriented Chemical Programming of Distributed Artifacts. ISSN 1941-6318, International Journal of Nanotechnology and Molecular Computation 1(4):54-70, 2009
T. Hinze, R. Fassler, G. Escuela, B. Ibrahim, S. Schuster. Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics. In K. Ambos-Spies, B. Löwe, W. Merkle (Eds.), Proceedings Booklet Fifth Conference on Computability in Europe (CiE2009), pp. 186-195, University of Heidelberg, 2009
T. Hinze, R. Fassler, T. Lenser, P. Dittrich. Register Machine Computations on Binary Numbers by Oscillating and Catalytic Chemical Reactions Modelled using Mass-Action Kinetics. ISSN 0129-0541, International Journal of Foundations of Computer Science 20(3):411-426, 2009
T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich. Event-Driven Metamorphoses of P Systems. In D. Corne, P. Frisco, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Membrane Computing. Proceedings Ninth International Workshop on Membrane Computing (WMC9), Series Lecture Notes in Computer Science, ISBN 978-3-540-95884-0, Vol. 5391, pp. 231-245, © Springer Verlag, 2009

Abstracts

M. Schumann, T. Hinze, S. Schuster. Synchronisation of Clocks: Comparing Mechanisms in Biological and Technical Distributed Systems. In D. Schomburg, A. Grote (Eds.), Abstract Booklet, German Conference on Bioinformatics (GCB2010), p. 67, Carolo-Wilhelmina University of Technology Braunschweig, 2010
P. Kießling, J. Kelm, O. Voytsekh, S. Schäuble, I. Heiland, S. Schuster, M. Mittag. A systems biology approach to improve nitrate-uptake in Chlamydomonas reinhardtii during day-phase. 14th International Conference on the Cell and Molecular Biology of Chlamydomonas, Norton, MA, USA, 2010
M. Mittag, S. Seitz, O. Voytsekh. Multiple roles of an E-box element within the circadian controlled promoter of the c3 gene. 14th International Conference on the Cell and Molecular Biology of Chlamydomonas, Norton, MA, USA, 2010
M. Mittag, O. Voytsekh, S. Seitz. Molecular components of the circadian system of Chlamydomonas reinhardtii and their role in temperature entrainment. Dreizehnte Wissenschaftliche Tagung der Sektion Phykologie, Insel Reichenau, 2010
R. Haberland, T. Hinze. Prolog-based XML processing for compact representation and deductive evaluation of biological reaction networks. In G. Antranikian, D. Chiu, F. Keil, A. Liese, T. Scheper, A.-P. Zeng (Eds.), Abstract Booklet, International Conference Biosystems Analysis and Engineering (BioSys2009), p. 27, Hamburg University of Technology, 2009
T. Hinze, I. Heiland, B. Schau, T. Lenser, S. Schuster. Reverse Engineering by Artificial Network Evolution. In R. Guthke, M. Pfaff (Eds.), Abstract Booklet, International Workshop Integrative Network Inference in Systems Biology (IWINISB2009), pp. 32-33, Leibniz Institute for Natural Product Research and Infection Biology Jena - Hans Knöll Institute, 2009
B. Schau, T. Hinze, T. Lenser, I. Heiland, S. Schuster. Control System-Based Reverse Engineering of Circadian Oscillators. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (Eds.), Abstract Booklet, German Conference on Bioinformatics (GCB2009), p. 126-127, Martin-Luther University Halle-Wittenberg, 2009
I. Heiland, T. Hinze, O. Voytsekh, M. Mittag, S. Schuster. Temperature Regulation of Circadian Rhythms. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (Eds.), Abstract Booklet, German Conference on Bioinformatics (GCB2009), p. 40, Martin-Luther University Halle-Wittenberg, 2009
S. Schäuble, I. Heiland, O. Voytsekh, M. Mittag, S. Schuster. Modelling Changes in Amino Acid Metabolism during Day-Night Cycles. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (Eds.), Abstract Booklet, German Conference on Bioinformatics (GCB2009), p. 39, Martin-Luther University Halle-Wittenberg, 2009
P. Kießling, J. Kelm, O. Voytsekh, M. Mittag. Improvement of nitrogen-uptake in Chlamydomonas reinhardtii during day-phase by genetic manipulation of relevant genes. Zweites Interdisziplinäres Doktorandensymposium, Potsdam Graduate School, 2009
I. Heiland, T. Hinze, O. Voytsekh, O. Ebenhöh, M. Mittag, S. Schuster. The Role of Phosphorylation in Circadian Rhythms. German Symposium on Systems Biology, Heidelberg, 2009
O. Voytsekh, S. Schäuble, P. Kießling, J. Kelm, I. Heiland, S. Schuster, M. Mittag. A Systems Biology Approach to Improve Nitrogen-Uptake in Chlamydomonas reinhardtii during Day-Phase. Abstract Booklet, Gordon Conference Chronobiology, Newport, USA, 2009
T. Hinze, T. Lenser, S. Schuster. Backtracking Membrane Systems Unravel Stable Oscillatory Behaviour in Space and Topology of Distributed Reaction Networks. In J. Brown (Ed.), Proceedings The IET Conference on Synthetic Biology, Systems Biology and Bioinformatics (BioSysBio2009), pp. 194-195, IET Press, 2009
O. Voytsekh, S. Seitz, D. Iliev, M. Mittag. The circadian RNA-binding protein CHLAMY1 can integrate temperature information. Annual Conference of the Association for General and Applied Microbiology, Ruhr-Universität Bochum, 2009
I. Heiland, T. Hinze, O. Voytsekh, O. Ebenhöh, M. Mittag, S. Schuster. The Role of Phosphorylation in Circadian Rhythms. FEBS-SysBio2009: The Third FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function, Alpbach, Austria, p. 86, Federation of European Biochemical Societies, 2009