Methods for detecting protein-protein interactions (PPIs) have given researchers a global picture of protein interactions on a genomic scale.
Biological Data Mining in Protein Interaction Networks explains bioinformatic methods for predicting PPIs, as well as data mining methods to mine or analyze various protein interaction networks. A defining body of research within the field, this book discovers underlying interaction mechanisms by studying intra-molecular features that form the common denominator of various PPIs.
Reviewer: Omer Iqbal, MD, FACC, FESC (Loyola University Medical Center) Description: This well-illustrated book explains bioinformatic methods for predicting protein-protein interactions and provides the inner working mechanisms of cells leading to the understanding of underlying disease pathways and discovery of new drugs to benefit mankind. Purpose: The purpose is to disseminate research results and best practice from cross-disciplinary researchers and practitioners interested in and working on bioinformatics, data mining, and proteomics. Audience: The book targets researchers in the areas of bioinformatics, data mining, machine learning, and data structure. It also is intended for practitioners in the industry in these areas and for instructors and postgraduate students in colleges and universities. The authors are recognized authorities in this field. Features: The first of the book's five sections is constituted of an introduction and two chapters on the molecular biology of protein-protein interactions for computer scientists and data mining for biologists. The second section details the protein-protein interaction network connection and cleaning as well as various aspects of protein-protein interactions. The third section explores knowledge discovery from protein-protein interaction networks and the fourth section explains biological applications using protein-protein interaction analysis. The last section on tools for analysis of protein-protein interaction networks covers graphical analysis and visualization and module finding for protein-protein interactions as well as network querying techniques for protein-protein interaction network comparison. The detailed table of contents is helpful. The use of color in different illustrations may have enhanced clarity and helped comprehension. Assessment: This is a valuable resource for researchers, biologists, computer scientists, postgraduate students, and others interested in the field of biological data mining in protein-protein interaction networks that will help illuminate the inner working mechanisms of cells, thereby enabling understanding of underlying disease pathways and discovery of new drugs.
Product dimensions: 8.70 (w) x 11.30 (h) x 1.30 (d)
Table of Contents
Ch. I Molecular Biology of Protein-Protein Interactions for Computer Scientists Christian Schonbach Schonbach, Christian 1
Ch. II Data Mining for Biologists Koji Tsuda Tsuda, Koji 14
Ch. III Domain-Based Prediction and Analysis of Protein-Protein Interactions Tatsuya Akutsu Morihiro Hayashida Hayashida, Tatsuya Akutsu Morihiro 29
Ch. IV Incorporating Graph Features for Predicting Protein-Protein Interactions Martin S. R. Paradesi Doina Caragea Caragea, Martin S. R. Paradesi Doina William H. Hsu Hsu, William H. 45
Ch. V Discovering Protein-Protein Interaction Sites from Sequence and Structure David La La, David Daisuke Kihara Kihara, Daisuke 64
Ch. VI Network Cleansing: Reliable Interaction Networks Paolo Marcatili Marcatili, Paolo Anna Tramontano Tramontano, Anna 80
Ch. VII Discovering Interaction Motifs from Protein Interaction Networks Hugo Willy Willy, Hugo 99
Ch. VIII Discovering Network Motifs in Protein Interaction Networks Raymond Wan Wan, Raymond Hiroshi Mamitsuka Mamitsuka, Hiroshi 117
Ch. IX Discovering Protein Complexes in Protein Interaction Networks Clara Pizzuti Pizzuti, Clara Simona Ester Rombo Rombo, Simona Ester 144
Ch. X Evolutionary Analyses of Protein Interaction Networks Takashi Makino Makino, Takashi Aoife McLysaght McLysaght, Aoife 169
Ch. XI Discovering Lethal Proteins in Protein Interaction Networks Kar Leong Tew Tew, Kar Leong Xiao-Li Li Li, Xiao-Li 183
Ch. XII Predicting Protein Functions from Protein Interaction Networks Hon Nian Chua Chua, Hon Nian Limsoon Wong Wong, Limsoon 203
Ch. XIII Protein Interactions for Functional Genomics Pablo Minguez Minguez, Pablo Joaquin Dopazo Dopazo, Joaquin 223
Ch. XIV Prioritizing Disease Genesand Understanding Disease Pathways Xiaoyue Zhao Zhao, Xiaoyue Lilia M. Iakoucheva Iakoucheva, Lilia M. Michael Q. Zhang Zhang, Michael Q. 239
Ch. XV Dynamics of Protein-Protein Interaction Network in Plasmodium Falciparum Smita Mohanty Mohanty, Smita Shashi Bhushan Pandit Pandit, Shashi Bhushan Narayanaswamy Srinivasan Srinivasan, Narayanaswamy 257
Ch. XVI Graphical Analysis and Visualization Tools for Protein Interaction Networks Sirisha Gollapudi Gollapudi, Sirisha Alex Marshall Marshall, Alex Daniel Zadik Zadik, Daniel Charlie Hodgman Hodgman, Charlie 286
Ch. XVII Network Querying Techniques for PPI Network Comparison Valeria Fionda Fionda, Valeria Luigi Palopoli Palopoli, Luigi 312
Ch. XVIII Module Finding Approaches for Protein Interaction Networks Tero Aittokallio Aittokallio, Tero 335
More About This Textbook
Overview
Methods for detecting protein-protein interactions (PPIs) have given researchers a global picture of protein interactions on a genomic scale.
Biological Data Mining in Protein Interaction Networks explains bioinformatic methods for predicting PPIs, as well as data mining methods to mine or analyze various protein interaction networks. A defining body of research within the field, this book discovers underlying interaction mechanisms by studying intra-molecular features that form the common denominator of various PPIs.
Editorial Reviews
Doody's Review Service
Reviewer: Omer Iqbal, MD, FACC, FESC (Loyola University Medical Center)Description: This well-illustrated book explains bioinformatic methods for predicting protein-protein interactions and provides the inner working mechanisms of cells leading to the understanding of underlying disease pathways and discovery of new drugs to benefit mankind.
Purpose: The purpose is to disseminate research results and best practice from cross-disciplinary researchers and practitioners interested in and working on bioinformatics, data mining, and proteomics.
Audience: The book targets researchers in the areas of bioinformatics, data mining, machine learning, and data structure. It also is intended for practitioners in the industry in these areas and for instructors and postgraduate students in colleges and universities. The authors are recognized authorities in this field.
Features: The first of the book's five sections is constituted of an introduction and two chapters on the molecular biology of protein-protein interactions for computer scientists and data mining for biologists. The second section details the protein-protein interaction network connection and cleaning as well as various aspects of protein-protein interactions. The third section explores knowledge discovery from protein-protein interaction networks and the fourth section explains biological applications using protein-protein interaction analysis. The last section on tools for analysis of protein-protein interaction networks covers graphical analysis and visualization and module finding for protein-protein interactions as well as network querying techniques for protein-protein interaction network comparison. The detailed table of contents is helpful. The use of color in different illustrations may have enhanced clarity and helped comprehension.
Assessment: This is a valuable resource for researchers, biologists, computer scientists, postgraduate students, and others interested in the field of biological data mining in protein-protein interaction networks that will help illuminate the inner working mechanisms of cells, thereby enabling understanding of underlying disease pathways and discovery of new drugs.
Product Details
Table of Contents
Ch. I Molecular Biology of Protein-Protein Interactions for Computer Scientists Christian Schonbach Schonbach, Christian 1
Ch. II Data Mining for Biologists Koji Tsuda Tsuda, Koji 14
Ch. III Domain-Based Prediction and Analysis of Protein-Protein Interactions Tatsuya Akutsu Morihiro Hayashida Hayashida, Tatsuya Akutsu Morihiro 29
Ch. IV Incorporating Graph Features for Predicting Protein-Protein Interactions Martin S. R. Paradesi Doina Caragea Caragea, Martin S. R. Paradesi Doina William H. Hsu Hsu, William H. 45
Ch. V Discovering Protein-Protein Interaction Sites from Sequence and Structure David La La, David Daisuke Kihara Kihara, Daisuke 64
Ch. VI Network Cleansing: Reliable Interaction Networks Paolo Marcatili Marcatili, Paolo Anna Tramontano Tramontano, Anna 80
Ch. VII Discovering Interaction Motifs from Protein Interaction Networks Hugo Willy Willy, Hugo 99
Ch. VIII Discovering Network Motifs in Protein Interaction Networks Raymond Wan Wan, Raymond Hiroshi Mamitsuka Mamitsuka, Hiroshi 117
Ch. IX Discovering Protein Complexes in Protein Interaction Networks Clara Pizzuti Pizzuti, Clara Simona Ester Rombo Rombo, Simona Ester 144
Ch. X Evolutionary Analyses of Protein Interaction Networks Takashi Makino Makino, Takashi Aoife McLysaght McLysaght, Aoife 169
Ch. XI Discovering Lethal Proteins in Protein Interaction Networks Kar Leong Tew Tew, Kar Leong Xiao-Li Li Li, Xiao-Li 183
Ch. XII Predicting Protein Functions from Protein Interaction Networks Hon Nian Chua Chua, Hon Nian Limsoon Wong Wong, Limsoon 203
Ch. XIII Protein Interactions for Functional Genomics Pablo Minguez Minguez, Pablo Joaquin Dopazo Dopazo, Joaquin 223
Ch. XIV Prioritizing Disease Genesand Understanding Disease Pathways Xiaoyue Zhao Zhao, Xiaoyue Lilia M. Iakoucheva Iakoucheva, Lilia M. Michael Q. Zhang Zhang, Michael Q. 239
Ch. XV Dynamics of Protein-Protein Interaction Network in Plasmodium Falciparum Smita Mohanty Mohanty, Smita Shashi Bhushan Pandit Pandit, Shashi Bhushan Narayanaswamy Srinivasan Srinivasan, Narayanaswamy 257
Ch. XVI Graphical Analysis and Visualization Tools for Protein Interaction Networks Sirisha Gollapudi Gollapudi, Sirisha Alex Marshall Marshall, Alex Daniel Zadik Zadik, Daniel Charlie Hodgman Hodgman, Charlie 286
Ch. XVII Network Querying Techniques for PPI Network Comparison Valeria Fionda Fionda, Valeria Luigi Palopoli Palopoli, Luigi 312
Ch. XVIII Module Finding Approaches for Protein Interaction Networks Tero Aittokallio Aittokallio, Tero 335
Compilation of References 354
Index 408