Genomics and Proteomics Engineering in Medicine and Biology

by Akay, Metin

• ISBN13: 9780471631811
• ISBN10: 0471631817
• Edition: 1st
• Format: Hardcover
• Copyright: 2007-01-02
• Publisher: Wiley-IEEE Press

Summary

Genomics and Proteomics Engineering in Medicine and Biology highlights current applications of biomedical informatics, as well as advancements in genomics-proteomics areas. Structures and algorithms are used to analyze genomic data and develop computational solutions for pathological understanding.

Author Biography

METIN AKAY, PHD, is the Interim Chair and Professor of Bioengineering for the Harrington Department of Bioengineering at the Arizona State University. Dr. Akay is the founding Series Editor of the IEEE Press Series on Biomedical Engineering. In 1997, he received the prestigious Early Career Achievement Award from the IEEE Engineering in Medicine and Biology Society (EMBS). He was the program chair of both the annual IEEE EMBS Conference and Summer School for 2001. Dr. Akay has published several papers in the field and authored, coauthored, or edited fourteen books. He is also the editor in chief of the Wiley Encyclopedia of Biomedical Engineering.

Table of Contents

Preface	xi
Contributors	xiii
Qualitative Knowledge Models in Functional Genomics and Proteomics	1	(24)
Mor Peleg
Irene S. Gabashvili
Russ B. Altman
Introduction	1	(2)
Methods and Tools	3	(3)
Modeling Approach and Results	6	(13)
Discussion	19	(1)
Conclusion	20	(5)
References	21	(4)
Interpreting Microarray Data and Related Applications Using Nonlinear System Identification	25	(30)
Michael Korenberg
Introduction	25	(1)
Background	25	(5)
Parallel Cascade Identification	30	(4)
Constructing Class Predictors	34	(1)
Prediction Based on Gene Expression Profiling	35	(11)
Comparing Different Predictors Over the Same Data Set	46	(2)
Concluding Remarks	48	(7)
References	49	(6)
Gene Regulation Bioinformatics of Microarray Data	55	(44)
Gert Thijs
Frank De Smet
Yves Moreau
Kathleen Marchal
Bart De Moor
Introduction	55	(2)
Introduction to Transcriptional Regulation	57	(2)
Measuring Gene Expression Profiles	59	(2)
Preprocessing of Data	61	(2)
Clustering of Gene Expression Profiles	63	(7)
Cluster Validation	70	(6)
Searching for Common Binding Sites of Coregulated Genes	76	(11)
Inclusive: Online Integrated Analysis of Microarray Data	87	(2)
Further Integrative Steps	89	(1)
Conclusion	90	(9)
References	91	(8)
Robust Methods for Microarray Analysis	99	(32)
George S. Davidson
Shawn Martin
Kevin W. Boyack
Brian N. Wylie
Juanita Martinez
Anthony Aragon
Margaret Werner-Washburne
Monica Mosquera-Caro
Cheryl Willman
Introduction	99	(1)
Microarray Experiments and Analysis Methods	100	(3)
Unsupervised Methods	103	(14)
Supervised Methods	117	(10)
Conclusion	127	(4)
References	128	(3)
In Silico Radiation Oncology: A Platform for Understanding Cancer Behavior and Optimizing Radiation Therapy Treatment	131	(26)
G. Stamatakos
D. Dionysiou
N. Uzunoglu
Philosophiae Tumoralis Principia Algorithmica: Algorithmic Principles of Simulating Cancer on Computer	131	(2)
Brief Literature Review	133	(2)
Paradigm of Four-Dimensional Simulation of Tumor Growth and Response to Radiation Therapy In Vivo	135	(13)
Discussion	148	(2)
Future Trends	150	(7)
References	150	(7)
Genomewide Motif Identification Using a Dictionary Model	157	(16)
Chiara Sabatti
Kenneth Lange
Introduction	157	(3)
Unified Model	160	(4)
Algorithms for Likelihood Evaluation	164	(3)
Parameter Estimation via Minorization--Maximization Algorithm	167	(3)
Examples	170	(1)
Discussion and Conclusion	171	(2)
References	172	(1)
Error Control Codes and the Genome	173	(36)
Elebeoba E. May
Error Control and Communication: A Review	173	(7)
Central Dogma as Communication System	180	(4)
Reverse Engineering the Genetic Error Control System	184	(19)
Applications of Biological Coding Theory	203	(6)
References	205	(4)
Complex Life Science Multidatabase Queries	209	(18)
Zina Ben Miled
Nianhua Li
Yue He
Malika Mahoui
Omran Bukhres
Introduction	209	(3)
Architecture	212	(2)
Query Execution Plans	214	(5)
Related Work	219	(3)
Future Trends	222	(5)
References	223	(4)
Computational Analysis of Proteins	227	(30)
Dimitrios I. Fotiadis
Yorgos Goletsis
Christos Lampros
Costas Papaloukas
Introduction: Definitions	227	(2)
Databases	229	(3)
Sequence Motifs and Domains	232	(3)
Sequence Alignment	235	(6)
Modeling	241	(1)
Classification and Prediction	242	(6)
Natural Language Processing	248	(4)
Future Trends	252	(5)
References	252	(5)
Computational Analysis of Interactions Between Tumor and Tumor Suppressor Proteins	257	(32)
E. Pirogova
M. Akay
I. Cosic
Introduction	257	(4)
Methodology: Resonant Recognition Model	261	(4)
Results and Discussions	265	(19)
Conclusion	284	(5)
References	285	(4)
Index	289	(10)
About the Editor	299