PD Dr.-Ing. habil. Thomas Hinze Senior University Lecturer and Independent Research Fellow

Postal Address     Friedrich Schiller University Jena     Faculty of Biological Sciences     Dpt. of Bioinformatics at Matthias-Schleiden Institute     Ernst-Abbe-Platz 2     D-07743 Jena     Germany

Phone, fax, e-mail     mobile: +49 172 79 79 603     phone/fax: +49 3641 9 46452     e-mail:

Address for Visitors     Ernst-Abbe-Platz 2     Room 3407 (fourth floor)     Jena

Publications

Books

G. Zhang, M.J. Perez-Jimenez, A. Riscos-Nunez, S. Verlan, S. Konur, T. Hinze, M. Gheorghe. Membrane Computing Models: Implementations. ISBN 978-981-16-1565-8, Springer-Verlag, 301 p., 2021

T. Hinze. Computer der Natur. Ausgewählte molekulare Prinzipien der biologisch inspirierten Informationsverarbeitung. ISBN 978-87-403-0378-0, Verlag bookboon.com, London, 118 p., 2013 (in German)

T. Hinze, M. Sturm. Rechnen mit DNA - Eine Einführung in Theorie und Praxis. (Computing with DNA: An Introduction into Theory and Practice.) ISBN 3-486-27530-5, Oldenbourg Wissenschaftsverlag München, 316 p., 2004 (in German)

Edited Books

T. Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Editors). Membrane Computing. 19th International Conference, CMC 2018, Dresden, Germany, September 4-7, 2018, Revised Selected Papers. Series Lecture Notes in Computer Science, Vol. 11399 ISBN 978-3-030-12797-8, Springer-Verlag Berlin, Heidelberg, 288 p., 2019

T. Hinze, J. Behre (Editors). Preliminary Proceedings of the Nineteenth International Conference on Membrane Computing (CMC19). ISBN 978-3-96409-030-0, Verlag ProBusiness Berlin, 276 p., 2018

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

Patents

• M. Sturm, T. Hinze. Verfahren zur Ausführung von mathematischen Operationen mittels eines DNA-Computers und DNA-Computer hierzu. German Patent DE 101 59 886 B4, IPC G06N 3/00, Deutsches Patentamt München, granted 2010 (in German)
• E.P. Stoschek, M. Sturm, T. Hinze, et al. Molecular Biological Method for Solving NP Problems. German Patent DE 198 53 726 C2, IPC C12N 15/10, Deutsches Patentamt München, granted 2003

Professorial Dissertation and PhD Thesis

• T. Hinze. Molecular Computing. Professorial Dissertation, FSU Jena, 2012
• T. Hinze. Universal Models and Selected Algorithms for DNA Computing. PhD Thesis (summa cum laude), TU Dresden, 2002 (in German)

Book Chapters

• T. Hinze. The Java Environment for Nature-inspired Approaches (JENA): A Workbench for BioComputing and BioModelling Enthusiasts. In C. Graciani, A. Riscos-Nunez, Gh. Paun, G. Rozenberg, A. Salomaa (Eds.), Enjoying Natural Computing, Series Lecture Notes in Computer Science, Vol. 11270, pp. 155-169, ISBN 978-3-030-00264-0, Springer Verlag, 2018, invited paper
• T. Hinze, J. Behre, K. Kirkici, Pa. Sauer, Pe. Sauer, S. Hayat. Passion to P for Polymorphic Processes in Practice. In M. Gheorghe, I. Petre, M.J. Perez-Jimenez, G. Rozenberg, A. Salomaa (Eds.), Multidisciplinary Creativity. Homage to Gheorghe Paun on His 65th Birthday. ISBN 978-606-8401-63-8, Spandugino, 2016
• T. Hinze, J. Behre, C. Bodenstein, G. Escuela, G. Grünert, P. Hofstedt, P. Sauer, S. Hayat, P. Dittrich. Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology. In P. Frisco, M. Gheorghe, M.J. Perez-Jimenez (Eds.), Applications of Membrane Computing in Systems and Synthetic Biology., Series Emergence, Complexity, and Computation, Vol. 7, pp. 133-173, ISBN 978-3-319-03190-3, © Springer Verlag, 2014, supplementary material
• 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 Articles and Conference Papers (peer review)

• B. Förster, T. Hinze, P. Langendörfer. Topology- and Resource-based Distribution Scheme for Collaborative Security-focused Design Space Exploration in Large-scale Static WSNs. IEEE International Telecommunication Networks and Applications Conference (ITNAC2024), 2024, submitted
• H. Rehr, F. Kretschmer, C. Höner zu Siederdissen, C. Grelck, E. Barth, M. Mundhenk, T. Hinze. A Chomsky Grammar Simulator Written in the J Language. In T. Koß, F. Manea, S. Siemer (Eds.), Theorietag 2024, Technical Report, pp. 27-30, Georg-August Universität Göttingen, 2024
• B. Förster, P. Langendörfer, T. Hinze. Determining Distributions of Security Means for WSNs based on the Model of a Neighbourhood Watch. IEEE Access 12:74343-74366, 2024
• B. Förster, T. Hinze, P. Langendörfer. Security Mean Distribution in WSNs for Cooperative Schemes. Tagungsband iCampus Cottbus Conference 2024, ISBN 978-3-910600-00-3, pp. 38-41, AMA Service GmbH, 2024
• N. Civiero, A. Henderson, T. Hinze, R. Nicolescu, C. Zandron. Implementing Perceptrons by Means of Water Based Computing. Journal of Membrane Computing 6(1):29-41, Springer Verlag, 2024
• B. Förster, P. Langendörfer, T. Hinze. Novel Approach to a Plant Inspired Distributed Security Scheme for Wireless Sensor Networks. In R. Stojanovic, L. Jozwiak, B. Lutovac, D. Jurisic (Eds.), Proceedings of the 12th Mediterranean Conference on Embedded Computing (MECO), ISBN 979-8-3503-2291-0, pp. 353-358, IEEE (Catalog Number CFP2339T-ART), 2023
• A. Henderson, R. Nicolescu, M.J. Dinneen, T. Chan, H. Happe, T. Hinze. Programmable and Parallel Water Computing. Journal of Membrane Computing 5(1):25-54, Springer Verlag, 2023
• R. Starke, I. Vukorep, K. Frommelt, A. Melcher, T. Hinze. Towards Artificial Ossification for Bone-inspired Technical Structures. In M.F. Hvejsel and P.J.S. Cruz (Eds.), Structures and Architecture, Vol. 2, ISBN 978-0-367-90281-0, pp. 1211-1218, CRC Press (Taylor and Francis Group), 2022
• A. Henderson, R. Nicolescu, M.J. Dinneen, T. Chan, H. Happe, T. Hinze. Turing Completeness of Water Computing. Journal of Membrane Computing 3(3):182-193, Springer Verlag, 2021
• T. Hinze. Coping with Dynamical Reaction System Topologies using Deterministic P Modules: A Case Study of Photosynthesis. Journal of Membrane Computing 2(4):281-289, Springer Verlag, 2020
• T. Hinze, H. Happe, A. Henderson, R. Nicolescu. Membrane Computing with Water. Journal of Membrane Computing 2(2):121-136, Springer Verlag, 2020
• A. Melcher, I. Vukorep, T. Hinze. Construction of Stable and Lightweight Technical Structures Inspired by Ossification of Bones using Osteogenetic P Systems. In T. Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 19th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-030-12797-8, Vol. 11399, pp. 208-228, © Springer Verlag, 2019, Best Paper Award
• B. Förster, T. Hinze. Towards Automated Analysis of Belousov-Zhabotinsky Reactions in a Petri Dish by Membrane Computing using Optic Flow. In T. Hinze, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 19th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-030-12797-8, Vol. 11399, pp. 131-141, © Springer Verlag, 2019
• T. Hinze, B. Förster. Event-based Life in a Nutshell: How Evaluation of Individual Life Cycles Can Reveal Statistical Inferences using Action-accumulating P Systems. In M. Gheorghe, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 18th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-319-73358-6, Vol. 10725, pp. 129-150, © Springer Verlag, 2018
• T. Hinze. Coping with Dynamical Structures for Interdisciplinary Applications of Membrane Computing. In A. Leporati, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 17th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-319-54071-9, Vol. 10105, pp. 16-27, © Springer Verlag, 2017, invited paper
• T. Hinze, L. Weber, U. Hatnik. Walking Membranes: Grid-exploring P Systems with Artificial Evolution for Multi-purpose Topological Optimisation of Cascaded Processes. In A. Leporati, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 17th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-319-54071-9, Vol. 10105, pp. 251-271, © Springer Verlag, 2017, Springer Award
• T. Hinze, K. Kirkici, Pa. Sauer, Pe. Sauer, J. Behre. Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. In G. Rozenberg, A. Salomaa, J.M. Sempere, C. Zandron (Eds.), Membrane Computing. 16th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-319-28474-3, Vol. 9504, pp. 215-235, © Springer Verlag, 2016
• T. Hinze, K. Grützmann, B. Höckner, P. Sauer, S. Hayat. Categorised Counting Mediated by Blotting Membrane Systems for Particle-based Data Mining and Numerical Algorithms. In M.Gheorghe, G. Rozenberg, A. Salomaa, P. Sosik, C. Zandron (Eds.), Membrane Computing. 15th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-319-14370-5, Vol. 8961, pp. 241-257, © Springer Verlag, 2014
• T. Hinze. Unraveling Oscillating Structures by Means of P Systems. In M. Gheorghe, G. Paun, M.J. Perez-Jimenez, G. Rozenberg (Eds.), Research Frontiers of Membrane Computing: Open Problems and Research Topics. International Journal of Foundations of Computer Science 24(5):547-623, 2013
• B. Höckner, P. Hofstedt, T. Vörtler, P. Sauer, T. Hinze. Constraint-based Approach for an Early Inspection of the Feasibility of Cyber Physical Systems. In M. Hanus, R. Rocha (Eds.), 20th International Conference on Applications of Declarative Programming and Knowledge Management, Technical Report 1306, ISSN 2192-6247, pp. 183-197, Christian-Albrechts-Universität zu Kiel, Institut für Informatik, 2013
• T. Hinze, B. Schell, M. Schumann, C. Bodenstein. Maintenance of Chronobiological Information by P System Mediated Assembly of Control Units for Oscillatory Waveforms and Frequency. In E. Csuhaj-Varju, M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, G. Vaszil (Eds.), Membrane Computing. 13th International Conference. Series Lecture Notes in Computer Science, ISBN 978-3-642-36750-2, Vol. 7762, pp. 208-227, © Springer Verlag, 2013
• 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 38:449-464, 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 (in German)
• 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

Extended Abstracts and Abstracts

• T. Hinze. Unraveling Oscillating Structures by Means of P Systems. In M. Gheorghe, G. Paun, M.J. Perez-Jimenez (Eds.), Research Topics in Membrane Computing, pp. 39-42, University of Sevilla, 2012
• 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, Dresden University of Technology, 2007
• T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich. Efficient Chemical Computing using Deterministic Reaction Systems with Prioritisation of Rules. In M. Droste, M. Lohrey (Eds.), Proceedings 17. Theorietag Automaten und Formale Sprachen, pp. 68-73, University of Leipzig, 2007 (in German)
• 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. Cell Signalling Networks: Biological Computers with Universal Computational Capacity. In R. Freund, M. Oswald (Eds.), Proceedings 16. Theorietag Automaten und Formale Sprachen, pp. 73-77, Technische Universität Wien, 2006 (in German)
• T. Hinze, M. Sturm. DNA Arithmetics Based on Chomsky Grammars. In S. Bensch, O. Boldt, H. Bordihn, H. Jürgensen (Eds.), Proceedings 14. Theorietag "Automaten und Formale Sprachen", Caputh, ISSN 0946-7580, Universität Potsdam, 2004 (in German)
• T. Hinze, M. Sturm. Towards an in-vitro Implementation of a Universal Distributed Splicing Model for DNA Computation. In R. Freund (Ed.), Proceedings Theorietag 2000 (TT2000), ISBN 3-85028-325-9, TU Wien, Austria, pp. 185-189, 25-27 September, 2000

Reports

• T. Hinze. Interview with Gheorghe Paun. Bulletin of the International Membrane Computing Society, issue December 2017
• H. Lieske, D. Noack, C. Schwalbe, E. Vogel, T. Hinze. Fascination of Molecular Computing: Student's Contributions Convey Findings of Interdisciplinary Research. Computer Science Report 01/2016, ISSN 1437-7969, Brandenburg University of Technology Cottbus-Senftenberg, 2016
• 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 (in German)
• 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