Computational Methods in Cell Biology

Computational methods are playing an ever increasing role in cell biology.  The Volume focuses on computational methods, emphasizing their intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment. Table of Contents: Principles of model building: an experimentation-aided approach to development of models for signaling networks Ambhighainath Ganesan and Andre Levchenko Integrated Inference and Analysis of Regulatory Networks From Multi-Level Measurements Christopher S. Poultney, Alex Greenfield, and Richard Bonneau Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets Shao-shan Carol Huang and Ernest Fraenkel A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness Paul Loriaux and Alexander Hoffmann Stochastic Modeling of Cellular Networks Jacob Stewart-Ornstein and Hana El-Samad Quantifying Traction Stresses in Adherent Cells Casey M. Kraning-Rush, Shawn P. Carey, Joseph P. Califano, and Cynthia A. Reinhart-King CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution Robert F. Murphy Spatial Modeling of Cell Signaling Networks Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, and Leslie M. Loew Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics Erik S. Welf and Jason M. Haugh Nonparametric Variable Selection and Modeling for Spatial and Temporal Regulatory Networks Anil Aswani, Mark D. Biggin, Peter Bickel and Claire Tomlin Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding Tommy Kaplan and Mark D. Biggin 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 Multi-scale modeling of tissues using CompuCell3D Maciej H. Swat, Gilberto L. Thomas, Julio M. Belmonte, Abbas Shirinifard, Mitja Hmeljak, and James A. Glazier 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