Data Management of Protein Interaction Networks (PDF)

LIST OF FIGURES xiii LIST OF TABLES xix FOREWORD xxi PREFACE xxiii ACKNOWLEDGMENTS xxix INTRODUCTION xxxi ACRONYMS xxxiii 1 INTERACTOMICS 1 1.1 Interactomics and Omics Sciences / 1 1.2 Genomics and Proteomics / 4 1.3 Representation and Management of Protein Interaction Data / 5 1.4 Analysis of Protein Interaction Networks / 5 1.5 Visualization of Protein Interaction Networks / 6 1.6 Models for Biological Networks / 7 1.7 Flow of Information in Interactomics / 8 1.8 Applications of Interactomics in Biology and Medicine / 10 1.9 Summary / 11 2 TECHNOLOGIES FOR DISCOVERING PROTEIN INTERACTIONS 13 2.1 Introduction / 13 2.2 Techniques Investigating Physical Interactions / 14 2.3 Technologies Investigating Kinetic Dynamics / 17 2.4 Summary / 18 3 GRAPH THEORY AND APPLICATIONS 21 3.1 Introduction / 21 3.2 Graph Data Structures / 22 3.3 Graph-Based Problems and Algorithms / 28 3.4 Summary / 31 4 PROTEIN-TO-PROTEIN INTERACTION DATA 33 4.1 Introduction / 33 4.2 HUPO PSI-MI / 34 4.3 Summary / 41 5 PROTEIN-TO-PROTEIN INTERACTION DATABASES 43 5.1 Introduction / 43 5.2 Databases of Experimentally Determined Interactions / 45 5.3 Databases of Predicted Interactions / 55 5.4 Metadatabases: Integration of PPI Databases / 62 5.5 Summary / 70 6 MODELS FOR PROTEIN INTERACTION NETWORKS 71 6.1 Introduction / 71 6.2 Random Graph Model / 72 6.3 Scale-Free Model / 73 6.4 Geometric Random Graph Model / 73 6.5 Stickiness Index (STICKY) Model / 74 6.6 Degree-Weighted Model / 74 6.7 Network Scoring Models / 75 6.8 Summary / 76 7 ALGORITHMS ANALYZING FEATURES OF PROTEIN INTERACTION NETWORKS 79 7.1 Introduction / 79 7.2 Analysis of Protein Interaction Networks through Centrality Measures / 80 7.3 Extraction of Network Motifs / 81 7.4 Individuation of Protein Complexes / 88 7.5 Summary / 99 8 ALGORITHMS COMPARING PROTEIN INTERACTION NETWORKS 101 8.1 Introduction / 101 8.2 Local Alignment Algorithms / 104 8.3 Global Alignment Algorithms / 109 8.4 Summary / 111 9 ONTOLOGY-BASED ANALYSIS OF PROTEIN

MARIO CANNATARO, PhD, is Associate Professor of ComputerEngineering at the Magna Græcia University of Catanzaro. Hisresearch explores bioinformatics, computational proteomics andgenomics, medical informatics, grid and parallel computing, andadaptive web systems. Dr. Cannataro has published three books andmore than 150 papers in international journals and conferenceproceedings.

PIETRO HIRAM GUZZI, PhD, is Assistant Professor ofComputer Engineering at the Magna Græcia University ofCatanzaro. His research focuses on the analysis of proteininteraction networks and the use of biological knowledge encoded inontologies for modeling, querying, and analyzing proteininteraction networks.

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