Computational systems biology / edited by Jason McDermott [and others].

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Bibliographic Details
Uniform Title:Methods in molecular biology (Clifton, N.J.) ; v. 541.
Springer protocols (Series)
Other Authors: McDermott, Jason
Language:English
Published: Totowa, N.J. : Humana, [2009], ©2009.
Series:Methods in molecular biology (Clifton, N.J.) ; v. 541.
Springer protocols (Series)
Subjects:
Computational biology.
Systems biology.
Bioinformatics.
Computational Biology.
Systems Biology.
Physical Description:xviii, 587 pages, 5 unnumbered pages of plates : illustrations (some color) ; 27 cm.
Format: Book
Contents:
  • Part 1. Network components
  • 1. Identification of cis-regulatory elements in gene co-expression networks using A-GLAM / Leonardo Mariño-Ramírez ... [et al.]
  • 2. Structure-based Ab initio prediction of transcription factor-binding sites / L. Angela Liu and Joel S. Bader
  • 3. Inferring protein-protein interactions from multiple protein domain combinations / Simon P. Kanaan ... [et al.]
  • 4. Prediction of protein-protein interactions: a study of the co-evolution model / Itai Sharon, Jason V. Davis, and Golan Yona
  • 5. Computational reconstruction of protein-protein interaction networks: algorithms and issues / Eric Franzosa, Bolan Linghu, and Yu Xia
  • 6. Prediction and integration of regulatory and protein-protein interactions / Duangdao Wichadakul, Jason McDermott, and Ram Samudrala
  • 7. Detecting hierarchical modularity in biological networks / Erzsebet Ravasz
  • Part 2. Network inference
  • 8. Methods to reconstruct and compare transcriptional regulatory networks / M. Madan Babu, Benjamin Lang, and L. Aravind
  • 9. Learning global models of transcriptional regulatory networks from data / Aviv Madar and Richard Bonneau
  • 10. Inferring molecular interactions pathways from eQTL data / Imran Rashid, Jason McDermott, and Ram Samudrala
  • 11. Methods for the inference of biological pathways and networks / Roger E. Bumgarner and Ka Yee Yeung
  • Part 3. Network dynamics
  • 12. Exploring pathways from gene co-expression to network dynamics / Huai Li, Yu Sun, and Ming Zhan
  • 13. Network dynamics / Herbert M. Sauro
  • 14. Kinetic modeling of biological systems / Haluk Resat, Linda Petzold, and Michel F. Pettigrew
  • 15. Guidance for data collection and computational modelling of regulatory networks / Adam Christopher Palmer, and Keith Edward Shearwin
  • Part 4. Function and evolutionary systems biology
  • 16. Maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure / Liran Carmel, ... [et al.]
  • 17. Enzyme function prediction with interpretable models / Umar Syed and Golan Yona
  • 18. Using evolutionary information to find specificity-determining and co-evolving residues / Grigory Kolesov and Leonid A. Mirny
  • 19. Connecting protein interaction data, mutations, and disease using bioinformatics / Jake Y. Chen, Eunseog Youn, and Sean D. Mooney
  • 20. Effects of functional bias on supervised learning of a gene network model / Insuk Lee and Edward M. Marcotte
  • Part 5. Computational infrastructure for systems biology
  • 21. Comparing algorithms for clustering of expression data: how to assess gene clusters / Golan Yona, William Dirks, and Shafquat Rahman
  • 22. Bioverse API and web application / Michal Guerquin ... [et al.]
  • 23. Computational representation of biological systems / Zach Frazier ... [et al.]
  • 24. Biological network inference and analysis using SEBINI and CABIN / Ronald Taylor and Mudita Singhal.