This volume introduces the reader to the latest experimental and bioinformatics methods for DNA sequencing, RNA sequencing, cell-free tumour DNA sequencing, single cell sequencing, single-cell proteomics and metabolomics. Chapters detail advanced analysis methods, such as Genome-Wide Association Studies (GWAS), machine learning, reconstruction and analysis of gene regulatory networks and differential coexpression network analysis, and gave a practical guide for how to choose and use the right algorithm or software to handle specific high throughput data or multi-omics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Computational Systems Biology: Methods and Protocols aims to ensure successful results in the further study of this vital field.
1. DNA Sequencing Data Analysis
Keyi Long, Lei Cai, and Lin He
2. Transcriptome Sequencing: RNA-seq
Hong Zhang, Lin He, and Lei Cai
3. Capture Hybridization of Long-range DNA Fragments for High-throughput Sequencing
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
Jun Li, Renzhong Liu, Cuihong Huang, and Mingyan Xu
Shifu Chen, Ming Liu, and Yanqing Zhou
6. An Overview of Genome-Wide Association Studies
7. Integrative Analysis of Omics Big Data
Xiang-tian Yu, Tao Zeng
8. The Reconstruction and Analysis of Gene Regulatory Networks
Guangyong Zheng and Tao Huang
10. iSeq: Web-based RNA-seq Data Analysis and Visualization
Xiang-tian Yu, Lu Wang, and Tao Zeng
12. Identifying Interactions Between Long Non-coding RNAs and Diseases Based on Computational Methods
Wei Lan , Liyu Huang, Dehuan Lai, and Qingfeng Chen
13. Survey Of Computational Approaches For Prediction of DNA-binding Residues on Protein Surfaces
Yi Xiong, Xiaolei Zhu, Hao Dai, and Dong-Qing Wei
14. Computational Prediction of Protein O-GlcNAc Modification
Cangzhi Jia and Yun Zuo
15. Machine Learning Based Modeling of Drug Toxicity
Jing Lu, Dong Lu, Zunyun Fu, Mingyue Zheng, and Xiaomin Luo
16. Metabolomics: A High-throughput Platform for Metabolite Profile Exploration
Jing Cheng, Wenxian Lan, Guangyong Zheng, and Xianfu Gao
17. Single-Cell Protein Assays--A Review
Beiyuan Fan, Junbo Wang, Ying Xu, and Jian Chen
18. Data Analysis in Single-cell Transcriptome Sequencing
19. Applications of Single-cell Sequencing for Multi-omics
20. Progress on Diagnosis of Tuberculous Meningitis
Yi-yi Wang and Bing-di Xie
Heng Xu and Yang Shu
Show more
This volume introduces the reader to the latest experimental and bioinformatics methods for DNA sequencing, RNA sequencing, cell-free tumour DNA sequencing, single cell sequencing, single-cell proteomics and metabolomics. Chapters detail advanced analysis methods, such as Genome-Wide Association Studies (GWAS), machine learning, reconstruction and analysis of gene regulatory networks and differential coexpression network analysis, and gave a practical guide for how to choose and use the right algorithm or software to handle specific high throughput data or multi-omics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Computational Systems Biology: Methods and Protocols aims to ensure successful results in the further study of this vital field.
1. DNA Sequencing Data Analysis
Keyi Long, Lei Cai, and Lin He
2. Transcriptome Sequencing: RNA-seq
Hong Zhang, Lin He, and Lei Cai
3. Capture Hybridization of Long-range DNA Fragments for High-throughput Sequencing
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
Jun Li, Renzhong Liu, Cuihong Huang, and Mingyan Xu
Shifu Chen, Ming Liu, and Yanqing Zhou
6. An Overview of Genome-Wide Association Studies
7. Integrative Analysis of Omics Big Data
Xiang-tian Yu, Tao Zeng
8. The Reconstruction and Analysis of Gene Regulatory Networks
Guangyong Zheng and Tao Huang
10. iSeq: Web-based RNA-seq Data Analysis and Visualization
Xiang-tian Yu, Lu Wang, and Tao Zeng
12. Identifying Interactions Between Long Non-coding RNAs and Diseases Based on Computational Methods
Wei Lan , Liyu Huang, Dehuan Lai, and Qingfeng Chen
13. Survey Of Computational Approaches For Prediction of DNA-binding Residues on Protein Surfaces
Yi Xiong, Xiaolei Zhu, Hao Dai, and Dong-Qing Wei
14. Computational Prediction of Protein O-GlcNAc Modification
Cangzhi Jia and Yun Zuo
15. Machine Learning Based Modeling of Drug Toxicity
Jing Lu, Dong Lu, Zunyun Fu, Mingyue Zheng, and Xiaomin Luo
16. Metabolomics: A High-throughput Platform for Metabolite Profile Exploration
Jing Cheng, Wenxian Lan, Guangyong Zheng, and Xianfu Gao
17. Single-Cell Protein Assays--A Review
Beiyuan Fan, Junbo Wang, Ying Xu, and Jian Chen
18. Data Analysis in Single-cell Transcriptome Sequencing
19. Applications of Single-cell Sequencing for Multi-omics
20. Progress on Diagnosis of Tuberculous Meningitis
Yi-yi Wang and Bing-di Xie
Heng Xu and Yang Shu
Show more
DNA Sequencing Data Analysis.- Transcriptome Sequencing: RNA-seq.- Capture Hybridization of Long-range DNA Fragments for High-throughput Sequencing.- The Introduction and Clinical Application of Cell-free Tumour DNA.- Bioinformatics Analysis for Cell-free Tumor DNA Sequencing Data.- An Overview of Genome-Wide Association Studies.- Integrative Analysis of Omics Big Data.- The Reconstruction and Analysis of Gene Regulatory Networks.- Differential Coexpression Network Analysis for Gene Expression Data.- iSeq: Web-based RNA-seq Data Analysis and Visualization.- Revisit of Machine Learning Supported Biological and Biomedical Studies.- Identifying Interactions Between Long Non-coding RNAs and Diseases Based on Computational Methods.- Survey Of Computational Approaches For Prediction of DNA-binding Residues on Protein Surfaces.- Computational Prediction of Protein O-GlcNAc Modification.- Machine Learning Based Modeling of Drug Toxicity.- Metabolomics: A High-throughput Platform for Metabolite Profile Exploration.- Single-Cell Protein Assays--A Review.- Data Analysis in Single-cell Transcriptome Sequencing.- Applications of Single-cell Sequencing For Multi-omics.- Progress on Diagnosis of Tuberculous Meningitis.- Insights of Acute Lymphoblastic Leukemia with Development of Genomic Investigation.
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