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Deep Sequencing Data Analysis
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Table of Contents

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 Francois 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

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