Computer Methods, Part C

The combination of faster, more advanced computers and more quantitatively oriented biomedical researchers has recently yielded new and more precise methods for the analysis of biomedical data. These better analyses have enhanced the conclusions that can be drawn from biomedical data, and they have changed the way that experiments are designed and performed. This volume, along with the 2 previous Computer Methods volumes for the Methods in Enzymology serial, aims to inform biomedical researchers about recent applications of modern data analysis and simulation methods as applied to biomedical research.

Presents step-by-step computer methods and discusses the techniques in detail to enable their implementation in solving a wide range of problemsInforms biomedical researchers of the modern data analysis methods that have developed alongside computer hardwarePresents methods at the "nuts and bolts" level to identify and resolve a problem and analyze what the results mean

1. Predicting Fluorescence Lifetimes and Spectra of Biopolymers

Patrik R. Callis

2. Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock

Elizabeth Y. Scribner, Hassan M. Fathallah-Shaykh

3. Strategies for articulated multibody-based adaptive coarse grain simulation of RNA

Mohammad Poursina, Kishor D. Bhalerao, Samuel C. Flores , Kurt S. Anderson, Alain Laederach

4. Modeling Loop Entropy

Gregory S. Chirikjian

5. Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles

Radhakrishnan Nagarajan

6. Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation

E. S. Zeron, M. Santill_an

7. How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology

Didier Gonze, Wassim Abou-Jaoud´e, Adama Ouattara, and Jos´e Halloy

8. Computational modelling of biological pathways by executable biology

Maria Luisa Guerriero John K. Heath

9. Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes

Don Kulasiri

10. Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory

David McMillen, Brian Ingalls, Jordan Ang

11. Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases

Alberto Marin-Sanguino, Shailendra K. Gupta, Eberhard O. Voit and Julio Vera

12. Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example

Necmettin Yildirim, Caner Kazanci F

13. Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data.

Joshua S. Richman MD, PhD

14. Scaling differences of heartbeat excursions between wake and sleep periods

L. Guzm´an-Vargas, I. Reyes-Ram´ırez, R. Hern´andez-P´erez, F. Angulo-Brown

15. Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments

John F. Beausang, Yale E. Goldman, and Philip C. Nelson

16. Inferring mechanisms from dose-response curves

Carson C. Chow, Karen M. Ong, Edward J. Dougherty, and S. Stoney Simons, Jr.

17. Spatial Aspects in Biological System Simulations

Haluk Resat, Michelle N. Costa, and Harish Shankaran

18. Computational Approaches to Modeling Viral Structure and Assembly

Stephen C. Harvey, Anton S. Petrov, Batsal Devkota and Mustafa Burak Boz

19. An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

Andrew Leaver-Fay, Michael Tyka, Steven M. Lewis, Oliver F. Lange, James Thompson, Ron Jacak, Kristian Kaufman, P. Douglas Renfrew, Colin A. Smith, Will Sheffler, Ian W. Davis, Seth Cooper, Adrien Treuille, Daniel J. Mandell, Florian Richter, Yih-En Andrew Ban, Sarel J. Fleishman, Jacob E. Corn, David E. Kim, Sergey Lyskov, Monica Berrondo, Stuart Mentzer, Zoran Popović, James J. Havranek, John Karanicolas, Rhiju Das, Jens Meiler, Tanja Kortemme, Jeffrey J. Gray, Brian Kuhlman¹, David Baker, and Philip Bradley

20. Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly

Vikas Nanda, Sohail Zahid, Fei Xu, Daniel Levine