Thorsten Lenser

Bio Systems Analysis Group
Institute of Computer Science
Friedrich-Schiller-University Jena
07743 Jena, Germany

Office: Ernst-Abbe-Platz 2, Room 3431
Phone: +49 (0)3641-9-46463
Fax:     +49 (0)3641-9-46302
Email:

Please note: As of May 2010, I have moved to Carl Zeiss MicroImaging, Jena.
You can still reach me at the email address given above.

Research interests

• Modelling and evolving signalling and regulatory networks (EU-project ESIGNET)
  This is also the project I am working on for my PhD thesis

• Stochastic aspects of gene regulation

• Self-organisation in biological systems (from cells to swarms)

• Evolutionary design and robust control of nonlinear systems in nature

• Mathematical and computational modelling of biological phenomena

Education

• 2004/05: MRes in Mathematics in the Living Environment at the University of York, UK
  Masters thesis at the Australian Antarctic Division in Hobart, Tasmania

• 2001-04: Study of Mathematics and Computer Science at FSU Jena

Publications

Journal Papers and Book Chapters

• Peter Brand, Thorsten Lenser, Peter Hemmerich (2010)
  Assembly Dynamics of PML Nuclear Bodies in Living Cells
  PMC Biophysics 3:3, 2010

• Thorsten Lenser, Günter Theißen, Peter Dittrich (2009)
  Developmental robustness by obligate interaction of class B floral homeotic genes and proteins
  PLoS Computational Biology, 5(1):e1000264, 2009

• Stefanie Weidtkamp-Peters, Thorsten Lenser (shared first authorship), Dmitri Negorev, Norman Gerstner, Thomas G. Hofmann, Georg Schwanitz, Christian Hoischen, Gerd Maul, Peter Dittrich, Peter Hemmerich (2008)
  Dynamics of Component Exchange at PML nuclear bodies
  Journal of Cell Science 121:2731-2743, 2008

• Naoki Matsumaru, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2007)
  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, (Series: Studies in Computational Intelligence, Vol. 69), p. 147-163, Springer, Berlin

• Thorsten Lenser, Andrew Constable (2007)
  A nonparametric algorithm to model movement between polygon subdomains in a spatially explicit ecosystem model
  Ecological Modelling 206(1-2), pp 79-92, 2007

Conference Proceedings

• Thomas Hinze, Thorsten Lenser, Gabi Escuela, Ines Heiland, Stefan Schuster (2010)
  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, A. Salomaa (Eds.), Membrane Computing. Proceedings Tenth International Workshop on Membrane Computing (WMC10). Revised, Selected and Invited Papers, Series Lecture Notes in Computer Science, ISSN 0302-9743, Vol. 5957, pp. 316-334, © Springer Verlag, 2010 (in press)

• Thomas Hinze, Raffael Fassler, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2009)
  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

• Thorsten Lenser, Naoki Matsumaru, Thomas Hinze, Peter Dittrich (2008)
  Tracking the Evolution of Chemical Computing Networks
  In S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.) Proceedings of the Eleventh International Conference on Artificial Life, pp.343-350, MIT Press, Cambridge, MA, 2008

• Naoki Matsumaru, Thorsten Lenser, Florian Centler, Pietro Speroni di Fenizio, Thomas Hinze, Peter Dittrich (2008)
  Common Organizational Structures within Two Chemical Flip-Flops
  In Y. Suzuki, A. Adamatzky, M. Hagiya, H. Umeo (Eds.) Proceedings Third International Workshop on Natural Computing (IWNC2008), ISBN 4-915905-35-7, pp. 50-59, Japan Society for Artificial Intelligence, 2008

• Hendrik Rohn, Bashar Ibrahim, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2008)
  Enhancing Parameter Estimation of Biochemical Networks by Exponentially Scaled Search Steps
  In: E. Marchiori, J.H. Moore (Eds.), Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings EvoBio 2008, Naples, Series Lecture Notes in Computer Science, Vol. 4973, pp. 177-187, Springer Verlag, 2008

• Raffael Fassler, Thomas Hinze, Thorsten Lenser, Peter Dittrich (2008)
  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), pp. 11-22, Silesian University Press, 2008

• Thomas Hinze, Sikander Hayat, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2008)
  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, 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

• Thomas Hinze, Sikander Hayat, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2007)
  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, Vol. 4860, pp. 320-335, Springer Verlag, 2007

• Thomas Hinze, Raffael Fassler, Thorsten Lenser, Naoki Matsumaru, Peter Dittrich (2007)
  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 (partially in German)

• Thorsten Lenser, Thomas Hinze, Bashar Ibrahim, Peter Dittrich (2007)
  Towards Evolutionary Network Reconstruction Tools for Systems Biology
  In: E. Marchiori, J.H. Moore, J.C. Rajapakse (Eds.), Proceedings of the Fifth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO), Valencia, LNCS 4447, pp 132-142, Springer Verlag, 2007

• Thomas Hinze, Thorsten Lenser, Peter Dittrich (2006)
  A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks
  In: H.J. Hoogeboom, G. Paun, G. Rozenberg (Eds.), Proceedings Seventh Workshop on Membrane Computing (WMC7), Leiden, LNCS 4361, pp. 409-423, Springer Verlag, 2006

• Thomas Hinze, Thorsten Lenser, Peter Dittrich (2006)
  Zellsignalnetzwerke - Biologische Computer mit universeller Berechnungsstärke
  In: R. Freund, M. Oswald (Eds.), Proc. 16. Theorietag Automaten und Formale Sprachen, p. 73--77, TU Wien, 2006

Posters

• Benedikt Schau, Thomas Hinze, Thorsten Lenser, Ines Heiland, Stefan Schuster (2009)
  Control System-Based Reverse Engineering of Circadian Oscillators.
  German Conference on Bioinformatics (GCB2009), Martin-Luther University Halle-Wittenberg, 2009

• Thomas Hinze, Thorsten Lenser, Ines Heiland, Stefan Schuster (2009)
  Backtracking Membrane Systems Unravel Stable Oscillations in Distributed Reaction Networks.
  The IET Conference on Synthetic Biology, Systems Biology and Bioinformatics (BioSysBio2009), University of Cambridge, UK, 2009

• Peter Dittrich, Bashar Ibrahim, Thomas Hinze, Thorsten Lenser, Naoki Matsumaru (2007)
  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

• Naoki Matsumaru, Thorsten Lenser, Thomas Hinze, Peter Dittrich (2007)
  Designing a Chemical Program Using Chemical Organization Theory
  BioSysBio 2007, Manchester, UK (Runner-up for best poster award), BMC Systems Biology, 1(Suppl 1):P26, 2007

• Thorsten Lenser, Thomas Hinze, Peter Dittrich (2006)
  Evolving Biological Networks
  UC '06 - 5th International Conference on Unconventional Computation, York, UK

• James Decraene, Peter Dittrich, Thomas Hinze, Thorsten Lenser, Barry McMullin, George Mitchell (2006)
  A Multidisciplinary Survey of Modeling Techniques for Biochemical Networks
  Proceedings Integrative Post-Genomics (IPG'06), p. 19, INSA Lyon-France, 2006

Teaching

• WS 2006/7:
  Exercises for lecture "Angewandte Biosystemanalyse" (in german)

• SS 2006:
  Exercises for lecture "Evolutionäre Algorithmen" (in german)