Informatics in proteomics / edited by Sudhir Srivastava.

Format:

Book

Contributor:

Srivastava, Sudhir, 1954-

Language:

English

Subjects (All):

Proteomics--Data processing.

Proteomics.

Bioinformatics.

Computational Biology.

Medical Subjects:

Proteomics.

Computational Biology.

Physical Description:

436 pages, 16 unnumbered pages of plates : illustrations (some color) ; 25 cm

Place of Publication:

Boca Raton, FL : Taylor & Francis/CRC Press, 2005.

Summary:

The handling and analysis of data generated by proteomics investigations represent a challenge for computer scientists, biostaticians, and biologists to develop tools for storing, retrieving, visualizing, and analyzing genomic data. Informatics in Proteomics examines the ongoing advances in the application of bioinformatics to proteomics research and analysis.

Through computer simulations, scientists can determine more about how diseases affect cells, predict how various drug interventions would work, and ultimately use proteins as therapeutic targets. This book first addresses the infrastructure needed for public protein databases. It discusses information management systems and user interfaces for storage, retrieval, and visualization of the data as well as issues surrounding data standardization and integration of protein sequences recorded in the last two decades. The authors subsequently examine the application of statistical and bioinformatic tools to data analysis, data presentation, and data mining. They discuss the implementation of algorithms, statistical methods, and computer applications that facilitate pattern recognition and biomarker discovery by integrating data from multiple sources.

This book offers a well-rounded resource of informatic approaches to data storage, retrieval, and protein analysis as well as application-specific bioinformatic tools that can be used in disease detection, diagnosis, and treatment. Informatics in Proteomics captures the current state-of-the-art and provides a valuable foundation for future directions.

Contents:

Chapter 1 The Promise of Proteomics: Biology, Applications, and Challenges / Paul D. Wagner, Sudhir Srivastava 1

Chapter 2 Proteomics Technologies and Bioinformatics / Sudhir Srivastava, Mukesh Verma 17

Chapter 3 Creating a National Virtual Knowledge Environment for Proteomics and Information Management / Daniel Crichton, Heather Kincaid, Sean Kelly, Sudhir Srivastava, J. Steven Hughes, Donald Johnsey 31

Chapter 4 Public Protein Databases and Interfaces / Jane Meejung Chang Oh 53

Chapter 5 Proteomics Knowledge Databases: Facilitating Collaboration and Interaction between Academia, Industry, and Federal Agencies / Denise B. Warzel, Marcy Winget, Cim Edelstein, Chenwei Lin, Mark Thornquist 79

Chapter 6 Proteome Knowledge Bases in the Context of Cancer / Djamel Medjahed, Peter A. Lemkin 109

Chapter 7 Data Standards in Proteomics: Promises and Challenges / Veerasamy Ravichandran, Ram D. Sriram, Gary L. Gilliland, Sudhir Srivastava 141

Chapter 8 Data Standardization and Integration in Collaborative Proteomics Studies / Marcin Adamski, David J. States, Gilbert S. Omenn 163

Chapter 9 Informatics Tools for Functional Pathway Analysis Using Genomics and Proteomics / Chad Creighton, Samir M. Hanash 193

Chapter 10 Data Mining in Proteomics / R. Gangal 205

Chapter 11 Protein Expression Analysis / Guoan Chen, David G. Beer 227

Chapter 12 Nonparametric, Distance-Based, Supervised Protein Array Analysis / Mei-Fen Yeh, Jeanne Kowalski, Nicole White, Zhen Zhang 255

Chapter 13 Protein Identification by Searching Collections of Sequences with Mass Spectrometric Data / D. Fenyo, J. Eriksson, R.C. Beavis 267

Chapter 14 Bioinformatics Tools for Differential Analysis of Proteomic Expression Profiling Data from Clinical Samples / Zhen Zhang 277

Chapter 15 Sample Characterization Using Large Data Sets / Brian T. Luke 293

Chapter 16 Computational Tools for Tandem Mass Spectrometry-Based High-Throughput Quantitative Proteomics / Jimmy K. Eng, Andrew Keller, Xiao-jun Li, Alexey I. Nesvizhskii, Ruedi Aebersold 335

Chapter 17 Pattern Recognition Algorithms and Disease Biomarkers / Ben A. Hitt, Emanuel Petricoin, Lance Liotta 353

Chapter 18 Statistical Design and Analytical Strategies for Discovery of Disease-Specific Protein Patterns / Ziding Feng, Yutaka Yasui, Dale McLerran, Bao-Ling Adam, John Semmes 367

Chapter 19 Image Analysis in Proteomics / Stephen Lockett 391.

Notes:

Includes bibliographical references and index.

ISBN:

1574444808

OCLC:

56955960