Contents
Preface. .................................................................... v
Contributors................................................................. ix
1 DNA Sequencing Data Analysis........................................... 1
Keyi Long, Lei Cai, and Lin He
2 Transcriptome Sequencing: RNA-Seq..................................... 15
Hong Zhang, Lin He, and Lei Cai
3 Capture Hybridization of Long-Range DNA Fragments
for High-Throughput Sequencing.. ...................................... 29
Xing Chen, Gang Ni, Kai He, Zhao-Li Ding, Gui-Mei Li,
Adeniyi C. Adeola, Robert W. Murphy, Wen-Zhi Wang, and Ya-Ping Zhang
4 The Introduction and Clinical Application of Cell-Free Tumor DNA. ......... 45
Jun Li, Renzhong Liu, Cuihong Huang, Shifu Chen, and Mingyan Xu
5 Bioinformatics Analysis for Cell-Free Tumor DNA Sequencing Data. ......... 67
Shifu Chen, Ming Liu, and Yanqing Zhou
6 An Overview of Genome-Wide Association Studies. ........................ 97
Michelle Chang, Lin He, and Lei Cai
7 Integrative Analysis of Omics Big Data.................................... 109
Xiang-Tian Yu and Tao Zeng
8 The Reconstruction and Analysis of Gene Regulatory Networks.............. 137
Guangyong Zheng and Tao Huang
9 Differential Coexpression Network Analysis for Gene Expression Data........ 155
Bao-Hong Liu10 iSeq: Web-Based RNA-seq Data Analysis and Visualization.. ................ 167
Chao Zhang, Caoqi Fan, Jingbo Gan, Ping Zhu, Lei Kong, and Cheng Li
11 Revisit of Machine Learning Supported Biological and Biomedical Studies..... 183
Xiang-tian Yu, Lu Wang, and Tao Zeng
12 Identifying Interactions Between Long Noncoding RNAs
and Diseases Based on Computational Methods............................ 205
Wei Lan, Liyu Huang, Dehuan Lai, and Qingfeng Chen
13 Survey of Computational Approaches for Prediction
of DNA-Binding Residues on Protein Surfaces............................. 223
Yi Xiong, Xiaolei Zhu, Hao Dai, and Dong-Qing Wei
14 Computational Prediction of Protein O-GlcNAc Modification............... 235
Cangzhi Jia and Yun Zuo
15 Machine Learning-Based Modeling of Drug Toxicity........................ 247
Jing Lu, Dong Lu, Zunyun Fu, Mingyue Zheng, and Xiaomin Luo
16 Metabolomics: A High-Throughput Platform for Metabolite
Profile Exploration. ..................................................... 265
Jing Cheng, Wenxian Lan, Guangyong Zheng, and Xianfu Gao
vii