Dr. Thomas Hinze

Postanschrift     Friedrich-Schiller-Universität Jena     Biologisch-Pharmazeutische Fakultät     Fachbereich Bioinformatik     Ernst-Abbe-Platz 1-4     07743 Jena

Telefon, Fax, E-Mail     Telefon: (03641) 9 46463     Fax: (03641) 9 46452     E-Mail:

Besucheradresse     Ernst-Abbe-Platz 2     Raum 3407     Jena

Veröffentlichungen

Bücher

T. Hinze, M. Sturm. Rechnen mit DNA - Eine Einführung in Theorie und Praxis. ISBN 3-486-27530-5, Oldenbourg Wissenschaftsverlag München, 316 S., 2004

Bücher als Herausgeber

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 S., 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 S., 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, Band 263 der Österreichischen Computer Gesellschaft, 196 S., 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 S., 2010

Patente

• M. Sturm, T. Hinze. Verfahren zur Ausführung von mathematischen Operationen mittels eines DNA-Computers und DNA-Computer hierzu. Deutsches Patent DE 101 59 886 B4, IPC G06N 3/00, Deutsches Patentamt München, erteilt 2010
• E.P. Stoschek, M. Sturm, T. Hinze, et al. Molekularbiologisches Verfahren zur Lösung von NP-Problemen. Deutsches Patent DE 198 53 726 C2, IPC C12N 15/10, Deutsches Patentamt München, erteilt 2003

Dissertation

• T. Hinze. Universelle Modelle und ausgewählte Algorithmen des DNA-Computing. Dissertation (summa cum laude), TU Dresden, 2002

Buchkapitel

• 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, Chapter 13, pp. 227-257, iConcept Press, 2010
• N. Matsumaru, T. Lenser, T. Hinze, P. Dittrich. Toward Organization-Oriented Chemical Programming: A Case Study with the Maximal Independent Set Problem. In F. Dressler, I. Carreras (Eds.), Advances in Biologically Inspired Information Systems: Models, Methods, and Tools. Series Studies in Computational Intelligence, ISBN 978-3-540-72692-0, Vol. 69, pp. 147-163, © Springer Verlag, 2007

Journal- und Konferenzbeiträge (peer review)

• I. Heiland, C. Bodenstein, T. Hinze, O. Weisheit, O. Ebenhöh, M. Mittag, S. Schuster. Modelling Temperature Entrainment of Circadian Clocks using the Arrhenius Equation and a Reconstructed Model from Chlamydomonas reinhardtii. ISSN 0092-0606, Journal of Biological Physics, 2012
• T. Hinze, C. Bodenstein, B. Schau, I. Heiland, S. Schuster. Chemical Analog Computers for Clock Frequency Control Based on P Modules. In M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, S. Verlan (Eds.), Membrane Computing. 12th International Conference. Revised Selected Papers. Series Lecture Notes in Computer Science, ISBN 978-3-642-28023-8, Vol. 7184, pp. 182-202, © Springer Verlag, 2012
• T. Hinze, M. Schumann, C. Bodenstein, I. Heiland, S. Schuster. Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In-silico Study of Modules for Circadian Clock Systems. ISSN 1687-5265, Computational Intelligence and Neuroscience, vol. 2011, article ID 262189, 9 pp., 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
• 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. In M. Gheorghe, G. Paun, S. Verlan (Eds.), Proceedings of the Twelfth International Conference on Membrane Computing (CMC12), pp. 169-190, Laboratoire d'Algorithmique Complexite et Logique, University of Paris Est, 2011
• 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
• 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
• G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno-Alvarez. Applying Membrane Systems in Food Engineering. In M.A. Martinez-del-Amor, G. Paun, I. Perez-Hurtado, A. Riscos-Nunez (Eds.), Proceedings of the Eight Brainstorming Week on Membrane Computing (8BWMC). ISBN 978-84-614-2357-6, pp. 109-121, Fenix Editora, 2010
• 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
• G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno-Alvarez. Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. In A. Fred, J. Filipe, H. Gamboa (Eds.), Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS2010), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, ISBN 978-989-674-018-4, pp. 306-311, INSTICC press, 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, 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, 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, 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
• N. Matsumaru, T. Lenser, F. Centler, P. Speroni di Fenizio, T. Hinze, P. Dittrich. Common Organizational Structures within Two Chemical Flip-Flops. In Y. Suzuki, A. Adamatzky, M. Hagiya, H. Umeo (Eds.), Natural Computing. Proceedings Third International Workshop on Natural Computing (IWNC2008), ISBN 4-915905-35-7, pp. 50-59, Japan Society for Artificial Intelligence, 2008
• S. Hayat, T. Hinze. Toward integration of in vivo molecular computing devices: successes and challenges. ISSN 1955-2068, HFSP Journal 2(5):239-243, 2008
• T. Lenser, N. Matsumaru, T. Hinze, P. Dittrich. Tracking the Evolution of Chemical Computing Networks. In S. Bullock, J. Noble, R. Watson, M.A. Bedau (Eds.), Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems (Artificial Life XI), ISBN 978-0-262-75017-2, pp. 343-350, MIT Press, 2008
• R. Fassler, T. Hinze, T. Lenser, P. Dittrich. Construction of Oscillating Chemical Register Machines on Binary Numbers using Mass-Action Kinetics. In O.H. Ibarra, P. Sosik (Eds.), Proceedings Prague International Workshop on Membrane Computing in conjunction with DNA14 (PIWMC2008), ISBN 978-80-7248-468-3, pp. 11-22, Silesian University Press, 2008
• H. Rohn, B. Ibrahim, T. Lenser, T. Hinze, P. Dittrich. Enhancing Parameter Estimation of Biochemical Networks by Exponentially Scaled Search Steps. In E. Marchiori, J.H. Moore (Eds.), Proceedings Sixth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO2008), Series Lecture Notes in Computer Science, ISBN 978-3-540-78756-3, Vol. 4973, pp. 177-187, © Springer Verlag, 2008
• T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich. Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks. In P. Encarnacao, A. Veloso (Eds.), Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS2008), ISBN 978-989-8111-18-0, Vol. 1, pp. 162-169, IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2008
• T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich. Hill Kinetics Meets P Systems. In G. Eleftherakis, P. Kefalas, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Membrane Computing, Series Lecture Notes in Computer Science, ISBN 978-3-540-77311-5, Vol. 4860, pp. 320-335, © Springer Verlag, 2007
• N. Matsumaru, T. Lenser, T. Hinze, P. Dittrich. Designing a chemical program using chemical organization theory. BMC Systems Biology, ISSN 1752-0509, Special Issue BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology 1(1):P26, 2007
• T. Lenser, T. Hinze, B. Ibrahim, P. Dittrich. Towards Evolutionary Network Reconstruction Tools for Systems Biology. In E. Marchiori, J.H. Moore, J.C. Rajapakse (Eds.), Proceedings Fifth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO2007), Series Lecture Notes in Computer Science, ISBN 3-540-71782-9, Vol. 4447, pp. 132-142, © Springer Verlag, 2007
• T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich. Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo. In G. Eleftherakis, P. Kefalas, G. Paun (Eds.), Proceedings of the Eight Workshop on Membrane Computing (WMC8), ISBN 978-960-89629-2-7, pp. 363-381, SEERC Publishers, 2007
• T. Hinze, T. Lenser, P. Dittrich. A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks. In H.J. Hoogeboom, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Proceedings Seventh Workshop on Membrane Computing (WMC7), Series Lecture Notes in Computer Science, ISBN 3-540-69088-7, Vol. 4361, pp. 409-423, © Springer Verlag, 2006
• T. Hinze, U. Hatnik, M. Sturm. An Object Oriented Simulation of Real Occurring Molecular Biological Processes for DNA Computing and Its Experimental Verification. In N. Jonoska, N.C. Seeman (Eds.), DNA Computing. Proceedings Seventh International Meeting on DNA-Based Computers (DNA7), Tampa, FL, USA, 2001, Revised Papers. Series Lecture Notes in Computer Science, ISBN 3-540-43775-4, Vol. 2340, pp. 1-13, © Springer Verlag, 2002
• M. Sturm, T. Hinze. Distributed Splicing of RE with 6 Test Tubes. Romanian Journal of Information Science and Technology, ISSN 1453-8245, Editura Academiei Romane 4(1-2):211-234, 2001
• U. Hatnik, T. Hinze, M. Sturm. A Probabilistic Approach to Description of Molecular Biological Processes on DNA and Their Object Oriented Simulation. In V.V. Kluev, N.E. Mastorakis (Eds.), Proceedings WSES International Conference on Simulation (SIM2001), ISBN 960-8052-40-8, Malta, 01-06 September, 2001
• E.P. Stoschek, M. Sturm, T. Hinze. DNA-Computing - ein funktionales Modell im laborpraktischen Experiment. Informatik Forschung und Entwicklung, ISSN 0178-3564, © Springer Verlag 16(1):35-52, 2001
• O.N. Koufaki, T. Hinze. Mutation Database of Three Genes Located on Chromosome 10q(23-24). Third Human Chromosome 10 Workshop (3CHR10), The Sanger Centre, Wellcome Trust Genome Campus Hinxton, Cambridge, UK, 30 September-02 October, 1999, The Genome Database (GDB) ID: CIT:777941 and in P. Deloukas, L. French, T. Meitinger, N.K. Moschonas. Report of the third international workshop on human chromosome 10 mapping and sequencing 1999, Cytogenetics and Cell Genetics, ISSN 0301-0171, Verlag S. Karger, Basel 90(1-2):1-12, 2000

Tagungsbeiträge und Kurzfassungen

• C. Bodenstein, B. Schau, I. Heiland, S. Schuster, T. Hinze. Modelling Biological Frequency Control of Circadian Rhythms using a Phase-locked Loop. In R. Eils, P. Bork, U. Klingmüller, T. Höfer, U. Kummer, P. Sorger (Eds.), Abstract Booklet, Twelfth International Conference on Systems Biology (ICSB2011), p. 148, University of Heidelberg, 2011
• 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
• 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
• 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
• I. Heiland, T. Hinze, O. Voytsekh, O. Ebenhöh, M. Mittag, S. Schuster. The Role of Phosphorylation in Circadian Rhythms. Third FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function (FEBS-SysBio2009), Alpbach, Austria, p. 86, Federation of European Biochemical Societies, 2009
• P. Dittrich, T. Hinze, B. Ibrahim, T. Lenser, N. Matsumaru. Hierarchically Evolvable Components for Complex Systems: Biologically Inspired Algorithmic Design. In J. Jost, D. Helbing, H. Kantz, A. Deutsch (Eds.), Proceedings of the European Conference on Complex Systems (ECCS2007), p. 85, TU Dresden, 2007
• T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich. Effizient chemisch rechnen durch deterministische Reaktionssysteme mit Regelpriorisierung. In M. Droste, M. Lohrey (Hrsg.), Proceedings 17. Theorietag Automaten und Formale Sprachen, pp. 68-73, Universität Leipzig, 2007
• J. Decraene, P. Dittrich, T. Hinze, T. Lenser, B. McMullin, G. Mitchell. A Multidisciplinary Survey of Modeling Techniques for Biochemical Networks. Proceedings Integrative Post-Genomics (IPG'06), p. 19, INSA Lyon, 2006
• T. Hinze, T. Lenser, P. Dittrich. Zellsignalnetzwerke - Biologische Computer mit universeller Berechnungsstärke. In R. Freund, M. Oswald (Hrsg.), Proceedings 16. Theorietag Automaten und Formale Sprachen, pp. 73-77, TU Wien, 2006
• T. Hinze, M. Sturm. Eine DNA-Arithmetik auf der Basis von Chomsky-Grammatiken. In S. Bensch, O. Boldt, H. Bordihn, H. Jürgensen (Hrsg.), Tagungsband 14. Theorietag "Automaten und Formale Sprachen", Caputh, ISSN 0946-7580, Universität Potsdam, 2004
• T. Hinze, M. Sturm. Towards an in-vitro Implementation of a Universal Distributed Splicing Model for DNA Computation. In R. Freund (Hrsg.), Proceedings Theorietag 2000 (TT2000), ISBN 3-85028-325-9, TU Wien, Austria, pp. 185-189, 25-27 September, 2000

Berichte

• E. Hellwig, T. Hinze, T. Lenser, P. Dittrich. Beispiele und künstliche Evolution oszillierender biochemischer Netzwerke: eine experimentelle Studie. Technical Report on Computer Science 08-05, FSU Jena, 2008
• C. Schmidt, T. Hinze, T. Lenser, P. Dittrich. Selected Public Databases and Software Tools with Relevance to the ESIGNET Project. Technical Report on Computer Science 06-24, FSU Jena, 2006
• T. Hinze, M. Sturm. A universal functional approach to DNA computing and its experimental practicability. In A. Condon, G. Rozenberg (Eds.), Preliminary Proceedings Sixth International Meeting on DNA Based Computers (DNA6), University of Leiden, Leiden, The Netherlands, p. 257, 13-17 June, 2000 and Technical Report TUD-FI00-05, ISSN 1430-211X, TU Dresden, 2000
• M. Sturm, T. Hinze. Distributed Splicing of RE with 6 Test Tubes. In C.S. Calude, M.J. Dinnen, G. Paun (Eds.), Preliminary Proceedings Workshop on Multiset Processing (WMP2000), Curtea de Arges, Romania, CDMTCS Research Report No. 140, pp. 236-248, 21-25 August, 2000
• E.P. Stoschek, M. Sturm, T. Hinze. On a DNA experiment for solving a certain NP-complete problem. Technical Report TUD-FI99-02, ISSN 1430-211X, TU Dresden, 1999