Computational Methods in Cell Biology (Methods in Cell Biology, Vol. 110)

Table of contents

1. Principles of model building: an experimentation-aided approach to development of models for signaling networks
   Ambhighainath Ganesan and Andre Levchenko
2. Integrated Inference and Analysis of Regulatory Networks From Multi-Level Measurements
   Christopher S. Poultney, Alex Greenfield, and Richard Bonneau
3. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets
   Shao-shan Carol Huang and Ernest Fraenkel
4. A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness
   Paul Loriaux and Alexander Hoffmann
5. Stochastic Modeling of Cellular Networks
   Jacob Stewart-Ornstein and Hana El-Samad
6. Quantifying Traction Stresses in Adherent Cells
   Casey M. Kraning-Rush, Shawn P. Carey, Joseph P. Califano, and Cynthia A. Reinhart-King
7. CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution
   Robert F. Murphy
8. Spatial Modeling of Cell Signaling Networks
   Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, and Leslie M. Loew
9. Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics
   Erik S. Welf and Jason M. Haugh
10. Nonparametric Variable Selection and Modeling for Spatial and Temporal Regulatory Networks
    Anil Aswani, Mark D. Biggin, Peter Bickel and Claire Tomlin
11. Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding
    Tommy Kaplan and Mark D. Biggin
12. Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant
    Alexandre Cunha, Paul T. Tarr, Adrienne H. K. Roeder, Alphan Altinok, Eric Mjolsness, and Elliot M. Meyerowitz
13. Multi-scale modeling of tissues using CompuCell3D
    Maciej H. Swat, Gilberto L. Thomas, Julio M. Belmonte, Abbas Shirinifard, Mitja Hmeljak, and James A. Glazier
14. Multiscale Model of Fibrin Accumulation on the Blood Clot Surface and Platelet Dynamics
    Zhiliang Xu, Scott Christley, Joshua Lioi, Cameron Harvey, Wenzhao Sun, Elliot D. Rosen, and Mark Alber