Deep Sequencing Data Analysis

ISBN-13: 9781071611029 / Angielski / Twarda / 2021 / 374 str.

Noam Shomron

Spis treści

1. Detecting Causal Variants in Mendelian Disorders using Whole Genome Sequencing

Abdul Rezzak Hamzeh, T. Daniel Andrews, and Matt A. Field

 

2. Statistical Considerations on NGS Data for Inferring Copy Number Variations

Jie Chen

 

3. Applications of Community Detection Algorithms to Large Biological Datasets

Itamar Kanter, Gur Yaari, and Tomer Kalisky

 

4. Processing and Analysis of RNA-seq data from Public Resources Yazeed Zoabi and Noam Shomron

 

5. Improved Analysis of High-throughput Sequencing Data Using Small Universal k-mer Hitting Sets

Yaron Orenstein

 

6. An Introduction to Whole-metagenome Shotgun Sequencing Studies

Tyler A. Joseph and Itsik Pe'er

 

7. Microbiome Analysis using 16S Amplicon Sequencing: From Samples to ASVs

Amnon Amir

 

8. RNA-Seq in Non-model Organisms

Vered Chalifa-Caspi

 

9. Deep Learning Applied on Next Generation Sequencing Data Analysis

Artem Danilvesky and Noam Shomron

 

10. Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes using ATAC-seq

Georgi K. Marinov and Zohar Shipony

  11. Genome-Wide Noninvasive Prenatal Diagnosis of SNPs and Indels Tom Rabinowitz and Noam Shomron

 

12. Genome-wide Noninvasive Prenatal Diagnosis of De Novo Mutations Ravit Peretz Machluf, Tom Rabinowitz, and Noam Shomron

 

13. Accurate Imputation of Untyped Variants from Deep Sequencing Data

Davoud Torkamaneh and François Belzile

 

14. Multi-region Sequence Analysis to Predict Intratumor Heterogeneity and Clonal Evolution

Soyeon Ahn and Haiyan Huang

 

15. Overcoming Interpretability in Deep Learning Cancer Classification

Yueyang Teo, Artem Danilevsky, and Noam Shomron

16. Single-cell Transcriptome Profiling

Guy Shapira and Noam Shomron

 

17. Biological Perspectives of RNA-sequencing Experimental Design

Metsada Pasmanik-Chor

 

18. Analysis of microRNA Regulation in Single Cells

Wendao Liu and Noam Shomron

 

19. DNA Data Collection and Analysis in the Forensic Arena

Sydnie Grabell and Noam Shomron

 

 

Blurb

This second edition provides new and updated chapters from expert researchers in the field detailing methods used to study the multi-facet deep sequencing data field. Chapters guide readers through techniques for processing RNA-seq data, microbiome analysis, deep learning methodologies, and various approaches for the identification of sequence variants. 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, Deep Sequencing Data Analysis: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.