NDLI: Computational Modeling of Cellular Signaling Processes Embedded into Dynamic Spatial Contexts

Content Provider	PubMed Central
Author	Angermann, Bastian R. Frederick, Klauschen Garcia, Alex D. Thorsten, Prustel Zhang, Fengkai Germain, Ronald N. Martin, Meier-schellersheim
Abstract	Cellular signaling processes depend on specific spatiotemporal distributions of their molecular components. Multi-color high-resolution microscopy now permits detailed assessment of such distributions, providing the input for fine-grained computational models that explore the mechanisms governing dynamic assembly of multi-molecular complexes and their role in shaping cellular behavior. However, incorporating into such models both complex molecular reaction cascades and the spatial localization of signaling components within dynamic cellular morphologies presents substantial challenges. Here we introduce an approach that addresses these challenges by automatically generating computational representations of complex reaction networks based on simple bi-molecular interaction rules embedded into detailed, adaptive models of cellular morphology. Using examples of receptor-mediated cellular adhesion and signal-induced localized MAPK activation in yeast, we illustrate the capacity of this simulation technique to provide insights into cell biological processes. The modeling algorithms, implemented in a version of the Simmune tool set, are accessible through intuitive graphical interfaces as well as programming libraries.
Related Links	http://dx.doi.org/10.1038/nmeth.1861
Ending Page	289
Page Count	7
Starting Page	283
File Format	PDF
ISSN	15487091
e-ISSN	15487105
Journal	Nature methods
Issue Number	3
Volume Number	9
Language	English
Publisher Date	2012-01-01
Access Restriction	Open
Subject Keyword	Biotechnology Cell Biology Biochemistry Molecular Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology Biotechnology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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