Computational and Statistical Approaches to Genomics

by Zhang, Wei; Shmulevich, Ilya

• ISBN13: 9780387262871
• ISBN10: 0387262873
• Edition: 2nd
• Format: Hardcover
• Copyright: 2006-06-30
• Publisher: Springer Verlag

Summary

The 2nd edition of this book adds 8 new contributors to reflect a modern cutting edge approach to genomics. The expanded scope includes coverage of statistical issues on single nucleotide polymorphism analysis array, CGH analysis, SAGE analysis, gene shaving and related methods for microarray data analysis, and cross-hybridization issues on oligo arrays. The authors of the 17 original chapters have updated the contents of their chapters, including references, on such topics as the development of novel engineering, statistical and computational principles, as well as methods, models, and tools from these disciplines applied to genomics.

Table of Contents

Preface	ix
1 Microarray Image Analysis and Gene Expression Ratio Statistics	1	(20)
Yidong Chen, Edward R. Dougherty, Michael L. Bittner, Paul Meltzer, and Jeffery Trent
2 Statistical Considerations in the Assessment of cDNA Microarray Data Obtained Using Amplification	21	(16)
Jing Wang, Kevin R. Coombes, Keith Baggerly, Limei Hu, Stanley R. Hamilton, and Wei Zhang
3 Sources of Variation in Microarray Experiments	37	(12)
Kathleen F. Kerr, Edward H. Leiter, Laurent Picard, and Gary A. Churchill
4 Studentizing Microarray Data	49	(12)
Keith A. Baggerly, Kevin R. Coombes, Kenneth R. Hess, David N. Stivers, Lynne V. Abruzzo, and Wei Zhang
5 Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains	61	(14)
Vella Oja, Janne Nikkilä, Petri Törönen, Garry Wong, Eero Castrén, and Samuel Kaski
6 Selecting Informative Genes for Cancer Classification Using Gene Expression Data	75	(14)
Tatsuya Akutsu and Satoru Miyano
7 Finding Functional Structures in Glioma Gene-Expressions Using Gene Shaving Clustering and MDL Principle	89	(30)
Ciprian D. Giurcaneanu, Cristian Mircean, Gregory N. Fuller, and Ioan Tabus
8 Design Issues and Comparison of Methods for Microarray-Based Classification	119	(18)
Edward R. Dougherty and Sanju N. Attoor
9 Analyzing Protein Sequences Using Signal Analysis Techniques	137	(26)
Karen M. Bloch and Gonzalo R. Arce
10 Scale-Dependent Statistics of the Numbers of Transcripts and Protein Sequences Encoded in the Genome	163	(46)
Vladimir A. Kuznetsov
11 Statistical Methods in Serial Analysis of Gene Expression (SAGE)	209	(26)
Ricardo Z.N. Vêncio and Helena Brentani
12 Normalized Maximum Likelihood Models for Boolean Regression with Application to Prediction and Classification in Genomics	235	(24)
Ioan Tabus, Jorma Rissanen, and Jaakko Astola
13 Inference of Genetic Regulatory Networks via Best-Fit Extensions	259	(20)
Harri Ländesmäki, Ilya Shmulevich, Olli Yli-Harja, and Jaakko Astola
14 Regularization and Noise Injection for Improving Genetic Network Models	279	(18)
Eugene van Someren, Lodewyk Wessels, Marcel Reinders, and Eric Backer
15 Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene Expression Relations	297	(14)
Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Michael L. Bittner, Yidong Chen, Daniel E. Russ, and Robert L. Martino
16 Single Nucleotide Polymorphisms and Their Applications	311	(40)
Rudy Guerra and Zhaoxia Yu
17 The Contribution of Alternative Transcription and Alternative Splicing to the Complexity of Mammalian Transcriptomes	351	(30)
Mihaela Zavolan and Christian Schönbach
18 Computational Imaging, and Statistical Analysis of Tissue Microarrays: Quantitative Automated Analysis of Tissue Microarrays	381	(24)
Aaron J. Berger Robert L. Camp, and David L. Rimm
Index	405