publications2

This folder holds the following references to publications, sorted by year and author.

There are 251 references in this bibliography folder.

Mazemondet, O, John, M, Leye, S, Rolfs, A, and Uhrmacher, A (accepted).
Elucidating the sources of β-catenin dynamics in human neural progenitor cells
PLOS-One.

Jaeger, A, Baake, J, Weiss, D, and Kriehuber, R (2013).
Glycogen synthase kinase-3beta regulates differentiation-induced apoptosis of human neural progenitor cells.
Int J Dev Neurosci, 31(1):61-68.

Holzhüter, C, Lex, A, Schmalstieg, D, Schulz, H, Schumann, H, and Streit, M (2012 (to appear)).
Visualizing Uncertainty in Biological Expression Data
In: Proceedings of the Visualization and Data Analysis VDA'12.

Luboschik, M, Tominski, C, Bittig, A, Uhrmacher, AM, and Schumann, H (2012 (accepted)).
Towards Interactive Visual Analysis of Microscopic-Level Simulation Data
In: Proceedings of SIGRAD 2012 – Interactive Visual Analysis of Data, citeulike-article-id = 11450119.

Bittig, AT, Haack, F, Maus, C, and Uhrmacher, AM (2011).
Adapting Rule-based Model Descriptions for Simulating in Continuous and Hybrid Space
In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, pp. 161-170, New York, NY, USA, ACM. CMSB '11.

Courtot, M, Juty, N, Knüpfer, C, Waltemath, D, Zhukova, A, and c (2011).
Controlled vocabularies and semantics in systems biology
Nature Molecular Systems Biology, 7(543).

Giese, A, Frahm, J, Hübner, R, Luo, J, Wree, A, Frech, MJ, Rolfs, A, and Ortinau, S (2011).
Erythropoietin and the effect of oxygen during proliferation and differentiation of human neural progenitor cells
BMC Cell Biology.

Hadlak, S, Schulz, H, and Schumann, H (2011).
In Situ Exploration of Large Dynamic Networks
IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2011), 17(12).

Jeschke, M, Ewald, R, and Uhrmacher, AM (2011).
Exploring the Performance of Spatial Stochastic Simulation Algorithms
Journal of Computational Physics, 230(7):2562-2574.

John, M, Schulz, H, Schumann, H, Uhrmacher, A, and Unger, A (2011).
Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models
Formal Aspects of Computing, Online First.

Lex, A, Schulz, H, Streit, M, Partl, C, and Schmalstieg, D (2011).
VisBricks: Multiform Visualization of Large, Inhomogeneous Data
IEEE Transactions on Visualization and Computer Graphics, 17(12).

Maciuszek, D and Martens, A (2011).
A reference architecture for game-based intelligent tutoring
In: Handbook of Research on Improving Learning and Motivation through Educational Games: Multidisciplinary Approaches, ed. by Patrick Felicia, IGI Global, Hershey, PA.

Maciuszek, D, Ladhoff, S, and Martens, A (2011).
Content design patterns for game-based learning
International Journal of Game-Based Learning.

Maus, C, Rybacki, S, and Uhrmacher, AM (2011).
Formal Rule-based Multi-Level Modeling
Poster, Heidelberg/Mannheim, Germany, 12th International Conference on Systems Biology (ICSB).

Maus, C, Rybacki, S, and Uhrmacher, AM (2011).
Rule-based multi-level modeling of cell biological systems
BMC Systems Biology, 5(166).

Mazemondet, O, Hybner, R, Frahm, J, Koszan, D, Bader, BM, Weiss, DG, Uhrmacher, AM, Frech, MJ, Rolfs, A, and Luo, J (2011).
Quantitative und kinetic profile of Wnt/ß-catenin signaling components during human neural progenitor cell differentiation
Cellular & Molecular Biology Letters, 16(4):515-538.

Schmitz, Y, Wolkenhauer, O, and Rateitschak, K (2011).
Nucleo-cytoplasmic shuttling of APC can maximize beta-catenin/TCF concentration
Journal of Theoretical Biology, 279:132-142.

Schulz, H (2011).
treevis.net - A Tree Visualization Reference
IEEE Computer Graphics and Applications, 31(6):6-10.

Schulz, H, Hadlak, S, and Schumann, H (2011).
The Design Space of Implicit Hierarchy Visualizations: A Survey
IEEE Transactions on Visualization and Computer Graphics, 17(4):393-411.

Schulz, H, Hadlak, S, and Schumann, H (2011).
Point-Based Visualization for Large Hierarchies
IEEE Transactions on Visualization and Computer Graphics, 17(5):598-611.

Schulz, H, Uhrmacher, A, and Schumann, H (2011).
Visual Analytics for Stochastic Simulation in Cell Biology
In: Proceedings of the Special Track on Theory and Applications of Visual Analytics (TAVA) of the i-Know'11 Conference, ACM.

Streit, M, Schulz, H, Lex, A, Schmalstieg, D, and Schumann, H (2011).
Model-Driven Design for the Visual Analysis of Heterogeneous Data
IEEE Transactions on Visualization and Computer Graphics.

Waltemath, D, Adams, R, Beard, DA, Bergmann, FT, Bhalla, US, Britten, R, Chelliah, V, Cooling, MT, Cooper, J, Crampin, E, Garny, A, Hoops, S, Hucka, M, Hunter, P, Klipp, E, Laibe, C, MIller, A, Moraru, I, Nickerson, D, Nielsen, P, Nikolski, M, Sahle, S, Sauro, H, Schmidt, H, Snoep, J, Tolle, D, Wolkenhauer, O, and Le Novère, N (2011).
Minimum Information About a Simulation Experiment (MIASE)
PLoS Computational Biology, 7(4).

Waltemath, D, Adams, R, Bergmann, F, Hucka, M, Kolpakov, F, Miller, A, Moraru, I, Nickerson, D, Sahle, S, Snoep, J, and Le Novere, N (2011).
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
BMC Systems Biology, 5(198).

Waltemath, D, Bergmann, FT, Adams, R, and Le Novère, N (2011).
Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
Webpublished, http://precedings.nature.com/documents/5846/version/1.