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
Biography
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
“Virology is progressing under the comfortable simplifications or reductionism and the disturbing recognition of complexity. Viruses are ubiquitous and diverse, and individual viral populations are exceedingly complex and dynamic, both genetically and phenotypically. As intracellular infection events are scrutinized at the single cell level of analysis, we are learning that virus-cell-organism interactions are multifaceted and intricate. Bioinformatics emerges to rescue virology amid a turmoil of new information in need of order. This book, edited by Manja Marz and Dimitrij Frishman, with outstanding contributing authors, will play the role of a lighthouse in a stormy ocean, to guide virologists on possible paths to follow.”
-- Esteban Domingo, Professor of Research at the Spanish National Research Council (CSIC), Madrid, Winter 2021
