Computational Methods in Cell Biology

Computational Methods in Cell Biology

1st Edition - April 13, 2012

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  • Editors: Anand R. Asthagiri, Adam Arkin
  • eBook ISBN: 9780123884213
  • Hardcover ISBN: 9780123884039

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Description

Computational methods are playing an ever increasing role in cell biology.  This volume of Methods in Cell Biology focuses on Computational Methods in Cell Biology and consists of two parts: (1) data extraction and analysis to distill models and mechanisms, and (2) developing and simulating models to make predictions and testable hypotheses. 

Key Features

  • Focuses on computational methods in cell biology
  • Split into 2 parts--data extraction and analysis to distill models and mechanisms, and developing and simulating models to make predictions and testable hypotheses
  • Emphasizes the intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment

Readership

Researchers and students in cell, molecular and developmental biology

Table of Contents

    1. Principles of model building: an experimentation-aided approach to development of models for signaling networks
    2. Ambhighainath Ganesan and Andre Levchenko

    3. Integrated Inference and Analysis of Regulatory Networks From Multi-Level Measurements
    4. Christopher S. Poultney, Alex Greenfield, and Richard Bonneau

    5. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets
    6. Shao-shan Carol Huang and Ernest Fraenkel

    7. A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness
    8. Paul Loriaux and Alexander Hoffmann

    9. Stochastic Modeling of Cellular Networks
    10. Jacob Stewart-Ornstein and Hana El-Samad

    11. Quantifying Traction Stresses in Adherent Cells
    12. Casey M. Kraning-Rush, Shawn P. Carey, Joseph P. Califano, and Cynthia A. Reinhart-King

    13. CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution
    14. Robert F. Murphy

    15. Spatial Modeling of Cell Signaling Networks
    16. Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, and Leslie M. Loew

    17. Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics
    18. Erik S. Welf and Jason M. Haugh

    19. Nonparametric Variable Selection and Modeling for Spatial and Temporal Regulatory Networks
    20. Anil Aswani, Mark D. Biggin, Peter Bickel and Claire Tomlin

    21. Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding
    22. Tommy Kaplan and Mark D. Biggin

    23. Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant
    24. Alexandre Cunha, Paul T. Tarr, Adrienne H. K. Roeder, Alphan Altinok, Eric Mjolsness, and Elliot M. Meyerowitz

    25. Multi-scale modeling of tissues using CompuCell3D
    26. Maciej H. Swat, Gilberto L. Thomas, Julio M. Belmonte, Abbas Shirinifard, Mitja Hmeljak, and James A. Glazier

    27. 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

Product details

  • No. of pages: 370
  • Language: English
  • Copyright: © Academic Press 2012
  • Published: April 13, 2012
  • Imprint: Academic Press
  • eBook ISBN: 9780123884213
  • Hardcover ISBN: 9780123884039

About the Serial Volume Editors

Anand R. Asthagiri

Adam Arkin

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