List of Contributors .......................................... vii
Preface ........................................................ xi
1 An Introduction to Next-Generation Biological Platforms
Virginia Mohlere, Wenting Wang, and Ganiraju Manyam .......... 1
2 An Introduction to The Cancer Genome Atlas
Bradley M. Broom and Rehan Akbani ........................... 31
3 DNA Variant Calling in Targeted Sequencing Data
Wenyi Wang, Yu Fan, and Terence P. Speed .................... 54
4 Statistical Analysis of Mapped Reads from mRNA-Seq Data
Ernest Turro and Alex Lewin ................................. 11
5 Model-Based Methods for Transcript Expression-Level
Quantification in RNA-Seq
Zhaonan Sun, Han Wu, Zhaohui Qin, and Yu Zhu ............... 105
6 Bayesian Model-Based Approaches for Solexa Sequencing
Data
Riten Mitra, Peter Mueller, and Yuan Ji .................... 126
7 Statistical Aspects of ChlP-Seq Analysis
Jonathan Cairns, Andy G. Lynch, and Simon Tavaré ........... 138
8 Bayesian Modeling of ChlP-Seq Data from Transcription
Factor to Nucleosome Positioning
Raphael Gottardo and Sangsoon Woo .......................... 170
9 Multivariate Linear Models for GWAS
Chiara Sabatti ............................................. 188
10 Bayesian Model Averaging for Genetic Association Studies
Christine Peterson, Michael Swartz, Sanjay Shete, and
Marina Vannucci ............................................ 208
11 Whole-Genome Multi-SNP-Phenotype Association Analysis
Yongtao Guan and Kai Wang .................................. 224
12 Methods for the Analysis of Copy Number Data in Cancer
Research
Bradley M. Broom, Kim-Anh Do, Melissa Bondy, Patricia
Thompson, and Kevin Coombes ................................ 244
13 Bayesian Models for Integrative Genomics
Francesco C. Stingo and Marina Vannucci .................... 272
14 Bayesian Graphical Models for Integrating Multiplatform
Genomics Data
Wenting Wang, Veerabhadran Baladandayuthapani, Chris
С. Holmes, and Kim-Anh Do .................................. 292
15 Genetical Genomics Data: Some Statistical Problems and
Solutions
Hongzhe Li ................................................. 312
16 A Bayesian Framework for Integrating Copy Number and
Gene Expression Data
Yuan Ji, Filippo Trentini, and Peter Mueller ............... 331
17 Application of Bayesian Sparse Factor Analysis Models in
Bioinformatics
Haisu Ma and Hongyu Zhao ................................... 350
18 Predicting Cancer Subtypes Using Survival-Supervised
Latent Dirichlet Allocation Models
Keegan Korthauer, John Dawson, and Christina Kendziorski ... 366
19 Regularization Techniques for Highly Correlated Gene
Expression Data with Unknown Group Structure
Brent A. Johnson ........................................... 382
20 Optimized Cross-Study Analysis of Microarray-Based
Predictors
Xiaogang Zhong, Luigi Marchionni, Leslie Cope, Edwin
S. Iversen, Elizabeth S. Garrett-Mayer, Edward
Gabrielson, and Giovanni Parmigiani ........................ 398
21 Functional Enrichment Testing: A Survey of
Statistical Method
Laila M. Poisson and Debashis Ghosh ........................ 423
22 Discover Trend and Progression Underlying High-
Dimensional Data
Peng Qiu ................................................... 445
23 Bayesian Phylogenetics Adapts to Comprehensive Infectious
Disease Sequence Data
Jennifer A. Tom, Janet S. Sinsheimer, and Marc A. Suchard .. 460
Index ......................................................... 10l
Color plates follow ........................................... 104
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