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PD Dr. Thomas Hinze

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Visiting researcher
About him Show content
PD Dr. Thomas Hinze Image: Dr. Thomas Hinze

PD Dr.-Ing. habil. Thomas Hinze

was born in Halle/Saale in 1971. He graduated from the Dresden University of Technology with Diploma degree in computer science in 1997. Afterwards, he was employed as a software developer within the field of SAP-based applications. Later, he returned to academic research equipped with a PhD scholarship by the Studienstiftung des Deutschen Volkes (German Academic Scholarship Foundation). He received the PhD at Dresden University of Technology with the level summa cum laude for his thesis entitled "Universal Models and Selected Algorithms of DNA Computing" in 2002. Subsequently, he moved to the Friedrich Schiller University Jena in 2006. Starting as a postdoctoral researcher in the BioSystems Analysis Group headed by apl. Prof. Peter Dittrich, he continued his stay as project leader at the Department of Bioinformatics headed by Prof. Stefan Schuster explorating principles of biological information processing from 2009. In 2012, he became a senior university lecturer at the Friedrich Schiller University Jena along with his professorial dissertation entitled "Molecular Computing". In the same year, he filled the position of a university lecturer at the Brandenburg University of Technology Cottbus and succeeded in self-dependent teaching and enhancing the research area of Membrane Computing. Since 2017, he acts as senior university lecturer and independent guest research fellow at Friedrich Schiller University Jena again. His list of publications comprises 78 records in total including two patents and two German-speaking textbooks ("Computing with DNA" and "Computers Found in Nature"). He is a steering committee member of the International Membrane Computing Society and editorial board member of the Springer Journal of Membrane Computing.

Link: personal web page http://users.minet.uni-jena.de/~hinze/index-en.html

Research interests Show content
  • Biologically Inspired Computing (in vitro, in vivo, in silico)
  • Molecular Computing (DNA-, RNA-, Protein-Computing, Chemical Computing, Dynamical Structures)
  • Membrane-, Cell-Based, Neural, Amorphous, Evolutionary Computing, Artificial Life,       Organic Computing
  • Systems, Synthetic, and Algebraic Biology for Exploration of Biological Information Processing
Publications Show content

http://users.minet.uni-jena.de/~hinze/publications.html

2019

T. Hinze, H. Happe, R. Nicolescu.
Membrane Computing with Water.
Accepted for 20th International Conference on Membrane Computing (CMC20), 2019

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

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

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

 

2018

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 S., 2018

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

Thomas Hinze, Benjamin Förster
Event-based Life in a Nutshell: How Evaluation of Individual Life Cycles Can Reveal Statistical Inferences using Action-accumulating P Systems
Lecture Notes in Computer Science 10725, 2018, 129-150, In: M. Gheorghe, G. Rozenberg, A. Salomaa, C. Zandron (Eds.), Membrane Computing. 18th International Conference. ISBN 978-3-319-73358-6, Springer Verlag
bibtex | abstract ]

2017

T. Hinze
Interview with Gheorghe Paun
Bulletin of the International Membrane Computing Society, 2017, to appear in issue December 2017
bibtex ]

T. Hinze
Coping with Dynamical Structures for Interdisciplinary Applications of Membrane Computing
Springer Series Lecture Notes in Computer Science 10105, 2017, 16-27
bibtex | abstract |  doi  ]

T. Hinze, L. Weber, U. Hatnik
Walking Membranes: Grid-exploring P Systems with Artificial Evolution for Multi-purpose Topological Optimisation of Cascaded Processes
Lecture Notes in Computer Science 10105 , 2017, 251-271
bibtex | abstract |  doi  ]

2016

T. Hinze, J. Behre, K. Kirkici, Pa. Sauer, Pe. Sauer, S. Hayat
Passion to P for Polymorphic Processes in Practice
In: Multidisciplinary Creativity. Homage to Gheorghe Paun on His 65th Birthday (eds. M. Gheorghe, I. Petre, M.J. Perez-Jimenez, G. Rozenberg, A. Salomaa), ISBN 978-606-8401-63-8, Spandugino, 2016, ch. 7, 77-88
bibtex | abstract ]

T. Hinze, K. Kirkici, Pa. Sauer, Pe. Sauer, J. Behre
Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential
Springer Lecture Notes in Computer Science 9504, 2016, 215-235
bibtex | abstract |  doi  |  url  ]

2015

P. Sauer, T. Hinze, P. Hofstedt
Dynamic Ad-hoc Topologies for Mobile Robot Navigation Based on Non-Uniform Grid Maps
International Journal of Mechanical and Mechatronics Engineering 2(6), 2015, 92-101
bibtex | abstract ]

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
Lecture Notes in Computer Science 8961, 2015, 241-257
bibtex | abstract |  doi  |  url  ]

2014

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: Applications of Membrane Computing in Systems and Synthetic Biology (eds. P. Frisco, M. Gheorghe, M.J. Perez-Jimenez), Springer Series Emergence, Complexity, and Computation, 2014, ch. 5, 133-173
bibtex |  doi  |  url  ]

2013

T. Hinze
Unraveling Oscillating Structures by Means of P Systems
International Journal of Foundations of Computer Science 24(5), 2013, 605-607
bibtex |  doi  ]

T. Hinze
Computer der Natur
T. Hinze, Verlag bookboon.com, ISBN 978-87-403-0378-0, 2013, eBook
bibtex |  url  ]

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: Membrane Computing. 13th International Conference (eds. E. Csuhaj-Varju, M. Gheorghe, G. Paun, G. Rozenberg, A. Salomaa, G. Vaszil), Vol. 7762, Springer Verlag, 2013, 208-227
bibtex |  doi  ]

2012

T. Hinze
Unraveling Oscillating Structures by Means of P Systems
In: Research Topics in Membrane Computing (eds. M. Gheorghe, G. Paun, M.J. Perez-Jimenez), University of Sevilla, 2012, 39-42
bibtex |  pdf  |  url  ]

I. Heiland, C. Bodenstein, T. Hinze, O. Weisheit, O. Ebenhoeh, M. Mittag and S. Schuster
Modelling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii
Journal of Biological Physics 38 (3), 2012, 449-464
bibtex | abstract |  doi  ]

T. Hinze, C. Bodenstein, B. Schau, I. Heiland, S. Schuster
Chemical Analog Computers for Clock Frequency Control Based on P Modules
In: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 182-202
bibtex | abstract |  doi  ]

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: Membrane Computing. Proceedings of the 12th International Conference (CMC12) (eds. M. Gheorghe, G. Paun, R. Rozenberg, A. Salomaa, S. Verlan), Springer Verlag, Vol. 7184, 2012, 160-181
bibtex | abstract |  doi  ]

2011

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.
Computational Intelligence and Neuroscience, vol. 2011, 2011, ID 262189
bibtex | abstract |  doi  |  url  |  PudMed-ID: 22046179 ]

T. Hinze, C. Bodenstein, I. Heiland, S. Schuster
Capturing Biological Frequency Control of Circadian Clocks by Reaction System Modularization
ERCIM News 85, 2011, 27-29
bibtex | abstract ]

T. Hinze, M. Schumann, S. Schuster
Synchronisation of Biological Clock Signals: Capturing Coupled Repressilators from a Control Systems Perspective
In: Proceedings of the Fourth International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS2011) (eds. F. Babiloni, A. Fred, J. Filipe, H. Gamboa), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, SciTePress, ISBN 978-989-8425-35-5, 2011, 101-106
bibtex | abstract ]

2010

Membrane Computing. Eleventh International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers.
M. Gheorghe, T. Hinze, G. Paun, G. Rozenberg, A. Salomaa (Eds.), Series: Lecture Notes in Computer Science (Vol. 6501), Subseries: Theoretical Computer Science and General Issues , Springer Verlag, Heidelberg 2010, 393, ISBN: 978-3642181221
bibtex | abstract ]

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)
J. Behre, G. Escuela, T. Hinze (Eds.), ProBusiness Verlag, Berlin 2010, 238, ISBN: 978-3-86805-767-6
bibtex ]

G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno
Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems
In: Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS2010) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, INSTICC press, 2010, 306-311, ISBN: 978-989-674-018-4
bibtex ]

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
bibtex | abstract |  doi  |  PudMed-ID: 20529264 ]

J. Decraene, T. Hinze
A Multidisciplinary Survey of Computational Techniques for the Modelling, Simulation and Analysis of Biochemical Networks
Journal of Universal Computer Science 16 (9), 2010, 1152-1175
bibtex | abstract |  url  ]

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 patent, Deutsches Patentamt München, 2010, granted 2010
bibtex ]

G. Escuela, T. Hinze, P. Dittrich, S. Schuster, M. Moreno-Alvarez
Applying Membrane Systems in Food Engineering
In: Eight Brainstorming Week on Membrane Computing (eds. M.A. Martinez-del-Amor, G. Paun, I. Perez-Hurtado, A. Riscos-Nunez), Fenix Editora, Sevilla 2010, 109-121, ISBN: 978-84-614-2357-6
bibtex ]

H. Bordihn, R. Freund, T. Hinze, M. Holzer, M. Kutrib, F. Otto
Proceedings of the Second Workshop on Non-Classical Models for Automata and Applications - Vol. 263 (NCMA2)
Austrian Computer Society 2010, ISBN: 978-3-85403-263-2
bibtex ]

M. Gheorghe T. Hinze, G. Paun
Proceedings of the Eleventh International Conference on Membrane Computing (CMC11)
ProBusiness Verlag, Berlin 2010, ISBN: 978-3-86805-721-8
bibtex ]

G. Gruenert, B. Ibrahim, T. Lenser, M. Lohel, T. Hinze, P. Dittrich
Rule-based spatial modeling with diffusing, geometrically constrained molecules.
BMC Bioinformatics 11, 2010, 307
bibtex |  PudMed-ID: 20529264 ]

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: Sequence and Genome Analysis: Methods and Applications (eds. Z. Zhao), iConcept Press, 2010, ch. 13, 227-257
bibtex |  pdf  ]

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: Proceedings of the 10th International Workshop on Membrane Computing (WMC) (eds. G. Paun, M.J. Perez-Jimenez, A. Riscos-Nunez, A. Salomaa), Springer Verlag, 2010, 316-334
bibtex ]

2009

R. Haberland, T. Hinze
Prolog-based XML processing for compact representation and deductive evaluation of biological reaction networks
In: Abstract Booklet, International Conference Biosystems Analysis and Engineering (BioSys) (eds. G. Antranikian, D. Chiu, F. Keil, A. Liese, T.Scheper, A.-P. Zeng), University of Technology Hamburg, 2009, 27
bibtex ]

T. Hinze, R. Faßler, G. Escuela, B. Ibrahim, S. Schuster
Computation by Synthetic Cell Signaling and Oscillating Processes Modelled using Mass-Action Kinetics
In: Proceedings Booklet Fifth Conference on Computability in Europe (CiE) (eds. K. Ambos-Spies, B. Löwe, W. Merkle), University of Heidelberg 2009, 186-195
bibtex ]

N. Matsumaru, T. Hinze, P. Dittrich
Organization-Oriented Chemical Programming of Distributed Artifacts
International Journal of Nanotechnology and Molecular Computation 1 (4), 2009, 54-70
bibtex ]

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
International Journal of Foundations of Computer Science 20, 2009, 411-426
bibtex ]

T. Hinze, R. Fassler, T. Lenser, N. Matsumaru, P. Dittrich
Event-Driven Metamorphoses of P Systems
Lecture Notes in Computer Science 5391, 2009, 231-245
bibtex ]

2008

T. Hinze, S. Hayat, T. Lenser, N. Matsumaru, P. Dittrich
Biosignal-Based Computing by AHL Induced Synthetic Gene Regulatory Networks
In: Proceedings of the First International Conference on Bio-Inspired Systems and Signal Processing (BIOSIGNALS) (eds. ), IEEE Engineering in Medicine and Biology Society, Institute for Systems and Technologies of Information Control and Communication, 2008, 162-169
bibtex ]

T. Lenser, N. Matsumaru, T. Hinze, P. Dittrich
Tracking the Evolution of Chemical Computing Networks
In: Proceedings of Artificial Life XI (eds. ), 2008, 343-350
bibtex ]

S. Hayat, T. Hinze
Toward integration of in vivo molecular computing devices: successes and challenges
HFSP Journal 2, 2008, 239-243
bibtex ]

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
Series Lecture Notes in Computer Science 4860, 2007, 320-335
bibtex ]

Teaching at the university Jena Show content

Informations about " Vorlesung und Projektübung Molekulare Algorithmen" in the summer term:

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