New Developments in Biostatistics and Bioinformatics

by Fan, Jianqing; Lin, Xihong; Liu, Jun S.

• ISBN13: 9789812837431
• ISBN10: 9812837434
• Format: Hardcover
• Copyright: 2009-05-31
• Publisher: World Scientific Pub Co Inc

Summary

This book presents an overview of recent developments in biostatistics and bioinformatics. Written by active researchers in these emerging areas, it is intended to give graduate students and new researchers an idea of where the frontiers of biostatistics and bioinformatics are as well as a forum to learn common techniques in use, so that they can advance the fields via developing new techniques and new results. Extensive references are provided so that researchers can follow the threads to learn more comprehensively what the literature is and to conduct their own research. In particulars, the book covers three important and rapidly advancing topics in biostatistics: analysis of survival and longitudinal data, statistical methods for epidemiology, and bioinformatics.

Table of Contents

Preface
Analysis of Survival and Longitudinal Data
Non- and Semi- Parametric Modeling in Survival Analysis	p. 3
Introduction	p. 3
Cox's type of models	p. 4
Multivariate Cox's type of models	p. 14
Model selection on Cox's models	p. 24
Validating Cox's type of models	p. 27
Transformation models	p. 28
Concluding remarks	p. 30
References	p. 30
Additive-Accelerated Rate Model for Recurrent Event	p. 35
Introduction	p. 35
Inference procedure and asymptotic properties	p. 37
Assessing additive and accelerated covariates	p. 40
Simulation studies	p. 41
Application	p. 42
Remarks	p. 43
Acknowledgements	p. 44
Appendix	p. 44
References	p. 48
An Overview on Quadratic Inference Function Approaches for Longitudinal Data	p. 49
Introduction	p. 49
The quadratic inference function approach	p. 51
Penalized quadratic inference function	p. 56
Some applications of QIF	p. 60
Further research and concluding remarks	p. 65
Acknowledgements	p. 68
References	p. 68
Modeling and Analysis of Spatially Correlated Data	p. 73
Introduction	p. 73
Basic concepts of spatial process	p. 76
Spatial models for non-normal/discrete data	p. 82
Spatial models for censored outcome data	p. 88
Concluding remarks	p. 96
References	p. 96
Statistical Methods for Epidemiology
Study Designs for Biomarker-Based Treatment Selection	p. 103
Introduction	p. 103
Definition of study designs	p. 104
Test of hypotheses and sample size calculation	p. 108
Sample size calculation	p. 111
Numerical comparisons of efficiency	p. 116
Conclusions	p. 118
Acknowledgements	p. 121
Appendix	p. 122
References	p. 126
Statistical Methods for Analyzing Two-Phase Studies	p. 127
Introduction	p. 127
Two-phase case-control or cross-sectional studies	p. 130
Two-phase designs in cohort studies	p. 136
Conclusions	p. 149
References	p. 151
Bioinformatics
Protein Interaction Predictions from Diverse Sources	p. 159
Introduction	p. 159
Data sources useful for protein interaction predictions	p. 161
Domain-based methods	p. 163
Classification methods	p. 169
Complex detection methods	p. 172
Conclusions	p. 175
Acknowledgements	p. 175
References	p. 175
Regulatory Motif Discovery: From Decoding to Meta-Analysis	p. 179
Introduction	p. 179
A Bayesian approach to motif discovery	p. 181
Discovery of regulatory modules	p. 184
Motif discovery in multiple species	p. 189
Motif learning on ChIP-chip data	p. 195
Using nucleosome positioning information in motif discovery	p. 201
Conclusion	p. 204
References	p. 205
Analysis of Cancer Genome Alterations Using Single Nucleotide Polymorphism (SNP) Microarrays	p. 209
Background	p. 209
Loss of heterozygosity analysis using SNP arrays	p. 212
Copy number analysis using SNP arrays	p. 216
High-level analysis using LOH and copy number data	p. 224
Software for cancer alteration analysis using SNP arrays	p. 229
Prospects	p. 231
Acknowledgements	p. 231
References	p. 231
Analysis of ChIP-chip Data on Genome Tiling Microarrays	p. 239
Background molecular biology	p. 239
A ChIP-chip experiment	p. 241
Data description and analysis	p. 244
Follow-up analysis	p. 249
Conclusion	p. 254
References	p. 254
Subject Index	p. 259
Author Index	p. 261
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