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E-raamat: Statistical Analysis of Next Generation Sequencing Data

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Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized medicine.





About the editors:

Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics.

Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University.  He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology and bioinformatics.

Arvustused

From the book reviews:

This book is an excellent collection of 20 chapters presenting the state of art (as of 2014) of algorithms developed for the analysis of next generation sequencing (NGS) data. This book is a valuable and well-timed collection of articles on the statistical methods that can be applied on NGS data. Even if no prior NGS knowledge is required, the book is addressed mainly to researchers at postgraduate and post-doc levels. (Irina Ioana Mohorianu, zbMATH, Vol. 1297, 2014)

1 Statistical Analyses of Next Generation Sequencing Data: An Overview
1(24)
Riten Mitra
Ryan Gill
Susmita Datta
Somnath Datta
2 Using RNA-seq Data to Detect Differentially Expressed Genes
25(26)
Douglas J. Lorenz
Ryan S. Gill
Ritendranath Mitra
Susmita Datta
3 Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR
51(24)
Yunshun Chen
Aaron T.L. Lun
Gordon K. Smyth
4 Analysis of Next Generation Sequencing Data Using Integrated Nested Laplace Approximation (INLA)
75(18)
Andrea Riebler
Mark D. Robinson
Mark A. van de Wiel
5 Design of RNA Sequencing Experiments
93(22)
Dan Nettleton
6 Measurement, Summary, and Methodological Variation in RNA-sequencing
115(14)
Alyssa C. Frazee
Leonardo Collado Torres
Andrew E. Jaffe
Ben Langmead
Jeffrey T. Leek
7 DE-FPCA: Testing Gene Differential Expression and Exon Usage Through Functional Principal Component Analysis
129(16)
Hao Xiong
James Bentley Brown
Nathan Boley
Peter J. Bickel
Haiyan Huang
8 Mapping of Expression Quantitative Trait Loci Using RNA-seq Data
145(24)
Wei Sun
Yijuan Hu
9 The Role of Spike-In Standards in the Normalization of RNA-seq
169(22)
Davide Risso
John Ngai
Terence P. Speed
Sandrine Dudoit
10 Cluster Analysis of RNA-Sequencing Data
191(28)
Peng Liu
Yaqing Si
11 Classification of RNA-seq Data
219(28)
Kean Ming Tan
Ashley Petersen
Daniela Witten
12 Isoform Expression Analysis Based on RNA-seq Data
247(14)
Hongzhe Li
13 RNA Isoform Discovery Through Goodness of Fit Diagnostics
261(16)
Julia Salzman
14 MOSAiCS-HMM: A Model-Based Approach for Detecting Regions of Histone Modifications from ChIP-Seq Data
277(20)
Dongjun Chung
Qi Zhang
Sunduz Keles
15 Hierarchical Bayesian Models for ChIP-seq Data
297(18)
Riten Mitra
Peter Muller
16 Genotype Calling and Haplotype Phasing from Next Generation Sequencing Data
315(20)
Degui Zhi
Kui Zhang
17 Analysis of Metagenomic Data
335(20)
Ruofei Du
Zhide Fang
18 Detecting Copy Number Changes and Structural Rearrangements Using DNA Sequencing
355(24)
Venkatraman E. Seshan
19 Statistical Methods for the Analysis of Next Generation Sequencing Data from Paired Tumor-Normal Samples
379(26)
Mengjie Chen
Lin Hou
Hongyu Zhao
20 Statistical Considerations in the Analysis of Rare Variants
405(18)
Debashis Ghosh
Santhosh Girirajan
Index 423
About the editors:

Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics, and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics.

Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University.  He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology, and bioinformatics.