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Virus Bioinformatics
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Virus Bioinformatics
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Book Description
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.
Key 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.
Table of Contents
Preface
Comparative genomics of viruses
Thomas Rattei
Current techniques and approaches for metagenomic exploration of phage diversity
Simon Roux, Mark Borodovsky
Direct RNA sequencing for complete viral genomes
Sebastian Krautwurst,Ronald Dijkman, Volker Thiel, Andi Krumbholz, Manja Marz
Computational methods for viral quasispecies assembly
Kim Philipp Jablonski, Niko Beerenwinkel
Functional RNA Structures in the 3’UTR of Mosquito-Borne Flaviviruses
Michael T. Wolfinger, Roman Ochsenreiter and Ivo L. Hofacker
Structural bioinformatics of influenza virus RNA genomes
Alexander P. Gultyaev, René C.L. Olsthoorn, Monique I. Spronken, and Mathilde Richard
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
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.
Virus-host transcriptomics
Caroline C. Friedel
Sequence classication with machine learning at the example of viral host prediction
Florian Mock and Manja Marz
Master-regulators of host response to SARS-CoV-2 as promising targets for drug repurposing
Manasa KP, Kamilya Altynbekova, Alexander Kel
The potential of computational genomics in the design of oncolytic viruses
Henni Zommer and Tamir Tuller
Sharing knowledge in Virology
Edouard De Castro, Chantal Hulo, Patrick Masson and Philippe Le Mercier
Editor(s)
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
Reviews
“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