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E-raamat: Network Biology: Methods and Applications

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While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting parts lists that are usually insufficient to unlock mechanistic insights on their own right.  Fortunately, as Network Biology: Methods and Applications examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way.  This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field.  Written in the highly successful Methods in Molecular Biology series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Comprehensive and accessible, Network Biology: Methods and Applications provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets.
Preface v
Contributors xi
1 Analysis of Protein--Protein Interactions Using High-Throughput Yeast Two-Hybrid Screens
1(30)
Seesandra V. Rajagopala
Peter Uetz
2 Identification of Mammalian Protein Complexes by Lentiviral-Based Affinity Purification and Mass Spectrometry
31(16)
Zuyao Ni
Jonathan B. Olsen
Andrew Emili
Jack F. Greenblatt
3 Protein Networks Involved in Vesicle Fusion, Transport, and Storage Revealed by Array-Based Proteomics
47(12)
Mikael Bauer
Magdalena Maj
Ludwig Wagner
Dolores J. Cahill
Sara Linse
David J. O'Connell
4 Identification and Relative Quantification of Native and Proteolytically Generated Protein C-Termini from Complex Proteomes: C-Terminome Analysis
59(12)
Oliver Schilling
Pitter F. Huesgen
Olivier Barre
Christopher M. Overall
5 Construction of Protein Interaction Networks Based on the Label-Free Quantitative Proteomics
71(16)
Mihaela E. Sardiu
Michael P. Washburn
6 Studying Binding Specificities of Peptide Recognition Modules by High-Throughput Phage Display Selections
87(12)
Haiming Huang
Sachdev S. Sidhu
7 Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli
99(28)
Mohan Babu
Alla Gagarinova
Andrew Emili
8 Advanced Methods for High-Throughput Microscopy Screening of Genetically Modified Yeast Libraries
127(34)
Yifat Cohen
Maya Schuldiner
9 Pooled Lentiviral shRNA Screening for Functional Genomics in Mammalian Cells
161(22)
Kim Blakely
Troy Ketela
Jason Moffat
10 Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences
183(54)
Susana S. Neves
Laura L. Forrest
11 Using Coevolution to Predict Protein--Protein Interactions
237(20)
Gregory W. Clark
Vaqaar-un-Nisa Dar
Alexandr Bezginov
Jinghao M. Yang
Robert L. Charlebois
Elisabeth R.M. Tillier
12 Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
257(22)
Daniele Merico
Ruth Isserlin
Gary D. Bader
13 Quality Control Methodology for High-Throughput Protein Protein Interaction Screening
279(16)
Alexei Vazquez
Jean-Francois Rual
Kavitha Venkatesan
14 Filtering and Interpreting Large-Scale Experimental Protein--Protein Interaction Data
295(16)
Gabriel Musso
Andrew Emili
Zhaolei Zhang
15 Classification of Cancer Patients Using Pathway Analysis and Network Clustering
311(26)
David C.Y. Fung
Amy Lo
Lucy Jankova
Stephan J. Clarke
Mark Molloy
Graham R. Robertson
Marc R. Wilkins
16 Statistical Analysis of Dynamic Transcriptional Regulatory Network Structure
337(16)
Jennifer J. Smith
Ramsey A. Saleem
John D. Aitchison
17 Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs
353(10)
Colm Ryan
Gerard Cagney
Nevan Krogan
Padraig Cunningham
Derek Greene
18 Displaying Chemical Information on a Biological Network Using Cytoscape
363(14)
Iain M. Wallace
Gary D. Bader
Guri Giaever
Corey Nislow
19 Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform
377(22)
Benjamin Webb
Keren Lasker
Dina Schneidman-Duhovny
Elina Tjioe
Jeremy Phillips
Seung Joong Kim
Javier Velazquez-Muriel
Daniel Russel
Andrej Sali
20 Predicting Node Characteristics from Molecular Networks
399(16)
Sara Mostafavi
Anna Goldenberg
Quaid Morris
21 Mathematical Modeling of Biomolecular Network Dynamics
415(20)
Alexander V. Ratushny
Stephen A. Ramsey
John D. Aitchison
Index 435