Dr.-Ing. Thomas Nocke


Associated Phd student

defended: Nov 30 2007


"Visual Data Mining and Visualization Design for Climate Research"

          Reviewers:   Heidrun Schumann (Universität Rostock, Germany)
                                Helwig Hauser (University of Bergen, Norway)
                                Holger Theisel (Otto-von-Guericke-Universität Magdeburg, Germany)

Dr.-Ing. Mathias Röhl


Associated Phd student

defended: May 20 2008


"Definition und Realisierung einer Plattform zur modellbasierten Komposition von Simulationsmodellen"

          Reviewers:   Adelinde Uhrmacher (Universität Rostock, Germany)
                                Axel Lehmann (Universität der Bundeswehr München, Germany)
                                Andreas Tolk (Old Dominion University, Norfolk, Virginia, USA)

Dr.-Ing. Andrea Unger


Phd student

defended: May 14 2010


"Visual Support for the Modeling and Simulation of Cell Biological Processes"

          Reviewers:   Heidrun Schumann (Universität Rostock, Germany)
                                Bernhard Preim (Otto-von-Guericke-Universität Magdeburg, Germany)
                                James J. Thomas (Pacific Northwest National Laboratory, Richland, Washington, USA)

Project S1: Visual Support for the Development of Methods and Models for Regenerative Systems

Dr. rer. nat. Alexandra Jaeger


Phd student

defended: May 31 2010


"Charakterisierung von Apoptoseprozessen während der Differenzierung von humanen neuralen VM197-Progenitorzellen in vitro"

          Reviewers:   Dieter G. Weiss (Universität Rostock, Germany)
                                Arndt Rolfs (Albrecht-Kossel-Institut für Neuroregeneration, Universität Rostock, Germany)
                                Jochen Prehn (Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Irland)

Project W2: Interference of the canonical Wnt pathway and apoptosis signaling pathways during proliferation and differentiation of neuronal progenitor cells

Dr. rer. nat. Rayk Hübner


Phd student

defended: May 31 2010


"Rolle of Wnt Signaling in Proliferation and Differentiation of ReNcell VM cells"

          Reviewers:   Arndt Rolfs (Albrecht-Kossel-Institut für Neuroregeneration, Universität Rostock, Germany)
                                Dieter G. Weiss (Universität Rostock, Germany)
                                Conny Noguchi (National Institute of Helth (NIH), Bethesda, USA)

Project R2: The Wnt dependent calcium signal path in the differentiation of human neural progenitor cells

Dr. rer. nat. Benjamin M. Bader


Phd student

defended: Jun 07 2010


"Spatio-temporal control of Wnt/beta-catenin signaling during fate commitment of human neural progenitor cells"

          Reviewers:   Dieter G. Weiss (Universität Rostock, Germany)
                                Ernest Arenas (Karolinska Institute, Stockholm, Schweden)

Project W1: Wnt Signaling mediated changes in the cytoskeleton motor enzyme system: Active and passive role in the differentiation of neural progenitor cells

Dr.-Ing. Hans-Jörg Schulz


Phd student

defended: Jun 09 2010


"Explorative Graph Visualization"

          Reviewers:   Heidrun Schumann (Universität Rostock, Germany)
                                Keith Andrews (Technical University Graz, Austria)
                                James Abello (DIMACS Institute, Rutgers University, USA)

Project S2: Visual Data Mining of Complex Structures

Dr.-Ing. Mathias John


Phd student

defended: Aug 26 2010


"Reaction Constraints for the π-Calculus: A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                Joachim Niehren (INRIA Lille Nord Europe, France)
                                Corrado Priami (Microsoft Research, University of Trento, Italy)

Project U1: Structure and space in modeling regenerative systems

Dr.-Ing. Roland Ewald


Associated Phd student

defended: Oct 15 2010


"Automatic Algorithm Selection for Complex Simulation Problems"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                David M. Nicol (University of Illinois at Urbana-Champaign, USA)
                                Georgios K. Theodoropoulos (University of Birmingham, UK)

Dr.-Ing. Matthias Jeschke


Phd student

defended: Oct 19 2010


"Efficient non-spatial and spatial simulation of biochemical reaction networks"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                Kevin Burrage (Oxford University, UK)
                                Koichi Takahashi (RIKIN Institute Yokohama, Japan)

Project U2: Efficient and flexible simulators for cell biological systems

Dr. rer. nat. Anne Schmöle


Associated Phd student

defended: Mar 21 2011


"Novel small molecules as GSK-3β inhibitors in human neural progenitor cells"

          Reviewers:   Arndt Rolfs (Albrecht-Kossel-Institut für Neuroregeneration, Universität Rostock, Germany)
                                Matthias Beller (Leibniz-Institut für Katalyse, Universität Rostock, Germany)
                                Sergei Kuznetsov (Institut für Biowissenschaften, Universität Rostock, Germany)
                                Johannes Schwarz (Klinik für Neurologie, Universität Leipzig, Germany)

Dr. techn. Marc Streit


Associated Phd student

defended: Apr 13 2011


"Guided Visual Analysis of Heterogeneous Data"

          Reviewers:   Dieter Schmalstieg (Graz University of Technology, Austria)
                                Heidrun Schumann (Universität Rostock, Germany)

Dr. -Ing. Orianne Mazemondet


Phd student

defended: Jul 01 2011


"Spatio-temporal Dynamics of the Wnt/beta-catenin Signaling Pathway: A Computational Systems Biology Approach"

          Reviewers:  Adelinde M. Uhrmacher (Universität Rostock, Germany)
                               Arndt Rolfs (Universität  Rostock, Germany)
                               James R. Faeder (University of Pittsburg, USA)

Project R1: Analysis of the functional impact of the canonical WNT/Fz/Dsh/GSK-3β/β-Catenin-signaling pathways for the differentiation of human neural progenitor cells.

Project Rolf_K1: in vitro and in silico exploration of the Wnt/β-catenin signaling pathway during differentiation oh human neural progenitor cells

Dr. -Ing. Simone Frey


Phd student

defended: Jul 12 2011


"A systems biology approach to dynamic modelling of the AMP-activated kinase pathway"

          Reviewers:  Olaf Wolkenhauer (Universität Rostock, Germany)
                               Ursula Kummer (Universität  Heidelberg, Germany)
                               Mattias Goksör (University of Gothenburg, Sweden)

Project Wolk_A1: A systems biology approach to dynamic modeling of signaling pathways and their characterization through quantitative measures.

Dr. -Ing. Dagmar Waltemath


Phd student

defended: Jul 27 2011


"Annotation-based storage and retrieval of models and simulation descriptions in computational biology"

          Reviewers:  Andreas Heuer (Universität Rostock, Germany)
                               Nicolas Le Novère (European Bioinformatics Institute, Cambridge, UK)
                               Ulf Leser (Humboldt-Universität zu Berlin, Germany)

Project H1: Defining and storing model components.

Dr. -Ing. Carsten Maus


Phd student

defended: Mar 25 2013


"Toward Accessible Multilevel Modeling in Systems Biology. A Rule-based Language Concept"

          Reviewers:  Adelinde M. Uhrmacher (Universität Rostock, Germany)
                               James R. Faeder (University of Pittsburgh, USA)
                               Ursula Kummer (Universität Heidelberg, Germany)

Project Uhrm_A1: Multi-level modeling of cell-biological systems.

Dr. rer. nat. Heiko Lemcke


Phd student

defended: Oct 28 2013


"The role of gap junctional intercellular communication and connexin s in the differentiation of human neural progenitor cells"

          Reviewers:  Sergei Kuznetsov (Institut für Biowissenschaften, Universität Rostock, Germany)
                               Arndt Rolfs (Albrecht Kossel Institut für Neuroregeneration, Universität Rostock, Germany)

Project Weis_A1: The reorganization of the cytoskeleton during Wnt-mediated neuronal differentiation

Dr. -Ing. Yvonne Schmitz


Phd student

defended: Dec 19 2013


"Compartmental Modelling of the Wnt Pathway: Elucidating the role of nucleo-cytoplasmic shuttling of β -catenin and its antagonists"

          Reviewers:  Olaf Wolkenhauer (Universität Rostock, Germany)
                               Adelinde M. Uhrmacher (Universität Rostock, Germany)
                               Helen M. Byrne (University of Oxford, UK)

Project Wo1: The influence of spatial aspects and feedbacks on the dynamics of intercellular signal transmission.

Project Wolk_K1: Mathematical modelling of cellular signal transduction: kinetic properties of the Wnt-signalling pathway.

Dr.-Ing. Stefan Leye


Associated Phd student

defended: Jan 07 2014


"Toward Guiding Simulation Experiments"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                Luiz Felipe Perrone (Bucknell University, USA)
                                Corrado Priami (Centre for Computational and Systems Biology, University of Trento, Italy)

Dr.-Ing. Steffen Hadlak


Phd student

defended: Nov 27 2014


"Graph visualization in space and time"

          Reviewers:   Heidrun Schumann (Universität Rostock, Germany)
                                Bodo Urban (Fraunhofer-IGD, Universität Rostock, Germany)
                                Andreas Kerren (Linnaeus University, Sweden)

Project Schu_A2: Multi-Level Visualization of Dynamic Complex Graphs.

Dr. rer. nat. Carolin Mußmann (geb. Mahler)


Phd student

defended: Dec 05 2014


"The network of signaling pathways: Analys is of the Notch and Wnt signaling pathway in the differentiation of human neural progenitor cells "

          Reviewers:  Reinhard Schröder (Universität Rostock, Germany)
                               Arndt Rolfs (Albrecht Kossel Institut für Neuroregeneration, Universität Rostock, Germany)

Project Rolf_A2: Effects of Wnt5a and Wnt7a on the differentiation of human neural progenitor cells

Dr.-Ing. Youwei Zheng


Phd student

defended: Nov 13 2015


"Contributions to Models of Single Neuron Computation in Striatum and Cortex "

          Reviewers:  Adelinde Uhrmacher (Universität Rostock, Germany)
                               Lars Schwabe (Xplosion Interactive GmbH)
                               D. James Surmeier (Northwestern University, USA)

Project Schw_A1: Multi-scale modeling and simulation of neural systems.

Dr.-Ing. Fiete Haack


Associated Phd student

defended: Apr 29 2016


"Exploring the spatio-temporal dynamics of lipid rafts and their role in signal transduction. A Modeling and Simulation approach"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                Kevin Burrage (University of Oxford, UK)
                                Edda Klipp (Humboldt-Universität zu Berlin, Germany)

Dr.-Ing. Stefan Rybacki


Associated Phd student

defended: Jul 21 2016


"Towards reproducible simulation studies with JAMES II"

          Reviewers:   Adelinde M. Uhrmacher (Universität Rostock, Germany)
                                Oliver Rose (University of the Federal Armed Forces Munich, Germany)
                                uiz Felipe Perrone (Bucknell University, USA)

Dr. -Ing. Arne Bittig


Phd student

defended: Jan 31 2017


"ML-Space: Hybrid Spatial Gillespie and Brownian Motion Simulation at Multiple Levels, and a Rule-based Description Language"

          Reviewers:  Adelinde M. Uhrmacher (Universität Rostock, Germany)
                               James R. Faeder (University of Pittsburgh, USA)
                               Heinz Koeppl (Technische Univerität Darmstadt, Germany)

Project Uhrm_A2: Stochastic, Discrete Modelling of Cell Biological Processes in Continuous Space.