Virus Bioinformatics Chapman & Hall/CRC Computational Biology Series

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