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


"<link annotation-based storage and retrieval of models simulation descriptions in computational external-link internen>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. med. Venkata Ajay Narendra Talabattula


Phd student

defended: Jan 18 2017
 


"Wnt3a induces neuronal differentiation and crosstalk between Wnt/Ca2+-pathway and Wnt/β-catenin pathway"

          Reviewers:  Arndt Rolfs  (Universitätsmedizin Rostock, Germany)
                               Hugo Murua Escobar (Universitätsmedizin Rostock, Germany)
                               Gabriele M. Rune (Universitätsklinikum Hamburg-Eppendorft, Germany)

Project Rolf_A1 - Effects of Wnt/calcium-pathway on the differentiation of ReNcell VM cells.

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.

Dr. -Ing. Ron Henkel


Phd student

defended: Jun 14 2023
 


"Contributions to the reuse and reproducibility of computational biology models"

          Reviewers:  Dagmar Walthemath   (Universität Greifswald, Germany)
                               Jacky Snoep (Stellenbosch University, South Africa)
                               Kurt Sandkuhl (Univerität Rostock, Germany)

Project H3_1 - Distributed information retrieval using web based nets