Virus Bioinformatics

Viruses are the most numerous and deadliest biological entities on the planet, infecting all types of living organisms—from bacteria to human beings. The constantly expanding repertoire of experimental approaches available to study viruses includes both low-throughput techniques, such as imaging and 3D structure determination, and modern OMICS technologies, such as genome sequencing, ribosomal profiling, and RNA structure probing. Bioinformatics of viruses faces significant challenges due to their seemingly unlimited diversity, unusual lifestyle, great variety of replication strategies, compact genome organization, and rapid rate of evolution. At the same time, it also has the potential to deliver decisive clues for developing vaccines and medications against dangerous viral outbreaks, such as the recent coronavirus pandemics. Virus Bioinformatics reviews state-of-the-art bioinformatics algorithms and recent advances in data analysis in virology. FEATURES Contributions from leading international experts in the field Discusses open questions and urgent needs Covers a broad spectrum of topics, including evolution, structure, and function of viruses, including coronaviruses The book will be of great interest to computational biologists wishing to venture into the rapidly advancing field of virus bioinformatics as well as to virologists interested in acquiring basic bioinformatics skills to support their wet lab work.

Chapter 1 ? Comparative Genomics of Viruses Thomas Rattei Chapter 2 ? Current Techniques and Approaches for Metagenomic Exploration of Phage Diversity Simon Roux and Mark Borodovsky Chapter 3 ? Direct RNA Sequencing for Complete Viral Genomes Sebastian Krautwurst, Ronald Dijkman, Volker Thiel, Andi Krumbholz, and Manja Marz Chapter 4 ? Computational Methods for Viral Quasispecies Assembly Kim Philipp Jablonski and Niko Beerenwinkel Chapter 5 ? Functional RNA Structures in the 3' UTR of Mosquito-Borne Flaviviruses Michael T. Wolfinger, Roman Ochsenreiter, and Ivo L. Hofacker vi ? Contents Chapter 6 ? Structural Bioinformatics of Influenza Virus RNA Genomes Alexander P. Gultyaev, René C.L. Olsthoorn, Monique I. Spronken, and Mathilde Richard Chapter 7 ? Structural Genomics and Interactomics of SARS-COV2: Decoding Basic Building Blocks of the Coronavirus Ziyang Gao, Senbao Lu, Oleksandr Narykov, Suhas Srinivasan, and Dmitry Korkin Chapter 8 ? Computational Tools for Discovery of CD8 T cell Epitopes and CTL Immune Escape in Viruses Causing Persistent Infections Hadi Karimzadeh, Daniel Habermann, Daniel Hoffmann, and Michael Roggendorf Chapter 9 ? Virus-Host Transcriptomics Caroline C. Friedel Chapter 10 ? Sequence Classification with Machine Learning at the Example of Viral Host Prediction Florian Mock and Manja Marz Chapter 11 ? Master Regulators of Host Response to SARS-CoV-2 as Promising Targets for Drug Repurposing Manasa KP , Kamilya Altynbekova, and Alexander Kel Chapter 12 ? The Potential of Computational Genomics in the Design of Oncolytic Viruses Henni Zommer and Tamir Tuller Chapter 13 ? Sharing Knowledge in Virology Edouard De Castro, Chantal Hulo, Patrick Masson, and Philippe Le Mercier

Dmitrij Frishman is Professor for Bioinformatics at Munich Technical University (TUM) Manja Marz is Professor for High-Throughput Sequencing Analysis at Friedrich Schiller University Jena