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Homepage of Gerd Grünert @ Bio Systems Analysis

Gerd Gruenert

Contact

Gerd Grünert
Biosystem Analysis Research Group
Department of Mathematics and Computer Science
Friedrich Schiller University Jena

Ernst-Abbe-Platz 1-3
Room 3430
07743 Jena
Germany

Phone: +49 (3641) 9 46461
Email: gerd.gruenert [at] uni-jena.de
Web: you already found this page ;-)


Software

biosys  SRSim: rule-based simulation of reaction networks in 3d space (based on the LAMMPS molecular dynamics simulator), doi:10.1186/1471-2105-11-307
 DropsimScreenshot  DropSim: event-based simulation of self-exciting droplet computers, using for example the from Belousov-Zhabotinsky reaction (see paper)



Research Interests

artificial life: evolutionary algorithms, genetic programming, self-assembly & self-organization, molecular machines, self-modifying programs

machine learning: data mining, autonomous experimentation, information theory, artificial neural networks, brain-machine interfaces, network plasticity, artificial intelligence

evolution: evo-devo, origins of life, generation of novelties, multicellularity, pattern formation

systems biology: neuro biology, spatial simulation & modeling, genomics, cell biology, cellular transport processes

computer science: parallel computing, efficient algorithms, big data, high-performance computing, cryptography, 3D visualization, unconventional programming & computing


short CV

2002 - 2008 Diplom BioInformatics (Computational Biology) at the Friedrich Schiller University of Jena Germany (Including one semster at the Universidad de Navarra in Pamplona, Spain)
- Thesis Title: "Spatial Rule-Based Simulation of Reaction Networks"
 Aug 2008 - Sept 2008 Research assistant at the Bio Systems Analysis Group, FSU Jena, head: Prof. Dr. Peter Dittrich
- Publishing my diploma thesis' results: 'spatial, rule-based modeling of reaction systems'
 Mar 2009 - Jun 2009 Research assistant at Justin O'Sullivan's Research Group, Massey University, Auckland, New Zealand
- RNA-Seq data analysis and 3D chromatin modeling
 Aug 2009 - Oct 2009 Research assistant at the Biophysics of Macromolecules Group at the German Cancer Research Center (DKFZ) Heidelberg, head: Prof. Dr. Jörg Langowski
- 3D structure reconstruction of the yeast nucleus
 Nov 2009 - now
PhD Thesis,  Bio Systems Analysis Group, FSU Jena, head: Prof. Dr. Peter Dittrich
- Thesis Title: "Unconventional Programming: Programming Non-programmable Systems"



Publications


Gerd Grünert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, Peter Dittrich (2010)
Rule-based spatial modeling with diffusing, geometrically constrained molecules
BMC Bioinformatics, 11:307


Gerd Grünert, Gabi Escuela, Peter Dittrich, Thomas Hinze (2011)
Morphological Algorithms: Membrane Receptor-ligand Interactions and Rule-based Molecule Graph Evolution for Exact Set Cover Problem
Proceedings of CMC12, France, 2011


Gerd Grünert, Peter Dittrich (2011)
Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems
Membrane Computing, LNCS, Springer Berlin, 2011


Gerd Grünert, Peter Dittrich, Klaus-Peter Zauner (2011)
Artificial wet neuronal networks from compartmentalised excitable chemical media
ERCIM News, 85(85):30-32, 2011


Lutz R. Gehlen, Gerd Grünert, M. Beatrix Jones, Chris D. Rodley, Jörg Langowski, J.M .O'Sullivan (2012)
Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
Nucleus (Austin, Tex.), 3(4):370


Gerd Grünert, Gabi Escuela, Peter Dittrich (2012)
Symbol representations in Evolving Droplet Computers
J. Durand-Lose, N. Jonoska (Eds.): Unconventional Computation and Natural Computation - 11th International Conference, UCNC 2012, Orlean, France, Sept. 3-7, 2012. Proceedings. LNCS 7445, Springer, 2012


Alexandra Diem, Gerd Grünert, Peter Dittrich (2012)
Evolution and growth of molecular networks for disease classification
In Book of Abstracts, European Conference on Complex Systems, page 44, Brussels, September 2012


Ayse Koca Caydasi, Maiko Lohel, Gerd Grünert, Peter Dittrich, Gislene Pereira, Bashar Ibrahim (2012)
A Dynamical Model of the Spindle Position Checkpoint
Molecular Systems Biology, 8(582)


Bashar Ibrahim, Richard Henze, Gerd Grünert, Matthew Egbert, Jan Huwald, Peter Dittrich (2013)
Spatial Rule-Based Modeling: A method and its application to the human mitotic kinetochore
Cells, 2:506-544


Dennis Görlich, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2013)
Molecular Codes Through Complex Formation in a Model of the Human Inner Kinetochore.
Biosemiotics, pages 223-247, 2013


Sergej Tschernyschkow, Sabine Herda, Gerd Grünert, Volker Döring, Dennis Görlich, Antje Hofmeister, Christian Hoischen, Stephan Diekmann, Peter Dittrich, Bashar Ibrahim (2013)
Rule-based Modeling and Simulations of the Inner Kinetochore Structure
Progress in Biophysics and Molecular Biology, 113(1):33 - 45, 2013


Gerd Grünert, Jan Szymanski, Julian Holley, Gabi Escuela, Alexandra Diem, Bashar Ibrahim, Andrew Adamatzky, Jerzy Gorecki, Peter Dittrich (2013)
Multi-scale Modelling of Computers made from Excitable Chemical Droplets
International Journal of Unconventional Computing, 9(3-4)


Gabi Escuela, Gerd Grünert, Peter Dittrich (2014)
Symbol representations and signal dynamics in evolving droplet computers
Natural Computing, 13(2): 247-256


Matthew Egbert, Gerd Grünert, Gabi Escuela, Peter Dittrich (2013)
Synthetic signalling protocell networks as models of neural computation
Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems


Konrad Gizynski, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2014)
Strategy of teaching for a chemical classifier constructed with photosensitive droplets
IEEE Transactions on Evolutionary Computation, in review, 2014


Gerd Grünert, Konrad Gizynski, Gabi Escuela, Bashar Ibrahim, Peter Dittrich (2014)
Understanding networks of computing chemical droplet neurons based on information flow
Int. J. Neur. Syst. DOI: 10.1142/S0129065714500324
other links:

Thomas Hinze, Jörn Behre, Christian Bodenstein, Gabi Escuela, Gerd Grünert, Petra Hofstedt, Peter Sauer, Sikander Hayat, Peter Dittrich (2014)
Membrane systems and tools combining dynamical structures with reaction kinetics for applications in chronobiology
In Applications of Membrane Computing in Systems and Synthetic Biology, pages 133-173. Springer International Publishing, 2014