Computational Methods in Cell Biology

Content: 
Front Matter
Pages i-iii

Copyright
Page iv

Contributors
Pages xi-xiii

Preface
Pages xv-xvi
Anand R. Asthagiri, Adam P. Arkin

Chapter 1 - Principles of Model Building: An Experimentation-Aided Approach to Development of Models for Signaling Networks
Pages 1-17
Ambhighainath Ganesan, Andre Levchenko

Chapter 2 - Integrated Inference and Analysis of Regulatory Networks from Multi-Level Measurements
Pages 19-56
Christopher S. Poultney, Alex Greenfield, Richard Bonneau

Chapter 3 - Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple “-Omics” Datasets
Pages 57-80
Shao-shan Carol Huang, Ernest Fraenkel

Chapter 4 - A Framework for Modeling the Relationship Between Cellular Steady-state and Stimulus-responsiveness
Pages 81-109
Paul M. Loriaux, Alexander Hoffmann

Chapter 5 - Stochastic Modeling of Cellular Networks
Pages 111-137
Jacob Stewart-Ornstein, Hana El-Samad

Chapter 6 - Quantifying Traction Stresses in Adherent Cells
Pages 139-178
Casey M. Kraning-Rush, Shawn P. Carey, Joseph P. Califano, Cynthia A. Reinhart-King

Chapter 7 - CellOrganizer: Image-Derived Models of Subcellular Organization and Protein Distribution
Pages 179-193
Robert F. Murphy

Chapter 8 - Spatial Modeling of Cell Signaling Networks
Pages 195-221
Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, Leslie M. Loew

Chapter 9 - Stochastic Models of Cell Protrusion Arising From Spatiotemporal Signaling and Adhesion Dynamics
Pages 223-241
Erik S. Welf, Jason M. Haugh

Chapter 10 - Nonparametric Variable Selection and Modeling for Spatial and Temporal Regulatory Networks
Pages 243-261
Anil Aswani, Mark D. Biggin, Peter Bickel, Claire Tomlin

Chapter 11 - Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding
Pages 263-283
Tommy Kaplan, Mark D. Biggin

Chapter 12 - Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant
Pages 285-323
Alexandre Cunha, Paul T. Tarr, Adrienne H.K. Roeder, Alphan Altinok, Eric Mjolsness, Elliot M. Meyerowitz

Chapter 13 - Multi-Scale Modeling of Tissues Using CompuCell3D
Pages 325-366
Maciej H. Swat, Gilberto L. Thomas, Julio M. Belmonte, Abbas Shirinifard, Dimitrij Hmeljak, James A. Glazier

Chapter 14 - Multiscale Model of Fibrin Accumulation on the Blood Clot Surface and Platelet Dynamics
Pages 367-388
Zhiliang Xu, Scott Christley, Joshua Lioi, Oleg Kim, Cameron Harvey, Wenzhao Sun, Elliot D. Rosen, Mark Alber

Index
Pages 389-400

Volumes in series
Pages 401-410