Cancer Bioinformatics

1. An Access Primer to Repositories of Cancer-related Genomic Big Data

John Torcivia-Rodriguez, Hayley Dingerdissen, Ting-Chia Chang, and Raja Mazumder

2. Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study

Gaurav Kaushik and Brandi Davis-Dusenbery

3. Computational Analysis of Structural Variation in Cancer Genomes

4. CORE: A Software Tool for Delineating Regions of Recurrent DNA Copy Number Alteration in Cancer

Guoli Sun and Alexander Krasnitz

5. Identification of Mutated Cancer Driver Genes on Unpaired RNA-Seq Samples

David Mosen-Ansorena

6. A Computational Protocol for Detecting Somatic Mutations by Integrating DNA and RNA Sequencing

Matthew D. Wilkerson

7. Allele-specific Expression Analysis in Cancer Using Next Generation Sequencing Data

Alessandro Romanel

8. Computational Analysis of lncRNA Function in Cancer

Xu Zhang and Tsui-Ting Ho

9. Computational Methods for Identification of T Cell Neoepitopes in Tumors

Vanessa Isabell Jurtz and Lars R nn Olsen

10. Computational and Statistical Analysis of Array-based DNA Methylation Data

Jessica Nordlund, Christofer B?cklin, and Amanda Rain

11. Computational Methods for Subtyping Of Tumors and their Applications for Deciphering Tumor Heterogeneity

Shihua Zhang

12. Statistically Supported Identification of Tumor Subtypes

Guoli Sun and Alexander Krasnitz

13. Computational Methods for Analysis of Tumor Clonality and Evolutionary History

Gerald Goh, Nicholas McGranahan and Gareth A. Wilson

14. Predictive Modeling of Anti-cancer Drug Sensitivity from Genetic Characterizations

Raziur Rahman and Ranadip Pal

15. In silico Oncology Drug Repositioning and Polypharmacology

Feixiong Cheng

Bertin Hoffmann, Thorsten Frenzel, R?diger Schmitz, Udo Schumacher , and Gero Wedemann