Literature DB >> 35594018

Databases, Knowledgebases, and Software Tools for Virus Informatics.

Yuxin Lin1, Yulan Qian2, Xin Qi3, Bairong Shen4.   

Abstract

Virus infection is a common social health issue. In the past decades, serious virus infectious events have caused great loss in people's life and the economics. The nature of rapid widespread and frequent variation increases the difficulty for precision viral prevention and treatment. In the era of big data and artificial intelligence (AI), advances in bioinformatics techniques bring unprecedented opportunities for virus informatics study, which contribute to the systems-level modeling of virus biology. In this chapter, data resources including virus-related databases and knowledgebases are introduced. Bioinformatics models and software tools for multiple sequence alignment, evolutionary analysis, and genome-wide research of viruses are summarized and emphasized. Translational applications of recently developed data-driven and AI-assisted methods to viral cases such as SARS-CoV-2, HBV/HCV, and influenza virus are discussed. Finally, the concept and significance of virus informatics are highlighted for both virus surveillance and health promotion.
© 2022. The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

Entities:  

Keywords:  Bioinformatics tools; Databases and knowledgebases; Precision medicine; Systems health; Virus informatics

Mesh:

Year:  2022        PMID: 35594018     DOI: 10.1007/978-981-16-8969-7_1

Source DB:  PubMed          Journal:  Adv Exp Med Biol        ISSN: 0065-2598            Impact factor:   2.622


  60 in total

Review 1.  A new era of virus bioinformatics.

Authors:  Bashar Ibrahim; Dino P McMahon; Franziska Hufsky; Martin Beer; Li Deng; Philippe Le Mercier; Massimo Palmarini; Volker Thiel; Manja Marz
Journal:  Virus Res       Date:  2018-05-08       Impact factor: 3.303

2.  ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics.

Authors:  Winfried Goettsch; Niko Beerenwinkel; Li Deng; Lars Dölken; Bas E Dutilh; Florian Erhard; Lars Kaderali; Max von Kleist; Roland Marquet; Jelle Matthijnssens; Shawna McCallin; Dino McMahon; Thomas Rattei; Ronald P Van Rij; David L Robertson; Martin Schwemmle; Noam Stern-Ginossar; Manja Marz
Journal:  Viruses       Date:  2021-04-27       Impact factor: 5.818

Review 3.  Middle East Respiratory Syndrome (MERS) Virus-Pathophysiological Axis and the Current Treatment Strategies.

Authors:  Abdullah M Alnuqaydan; Abdulmajeed G Almutary; Arulmalar Sukamaran; Brian Tay Wei Yang; Xiao Ting Lee; Wei Xuan Lim; Yee Min Ng; Rania Ibrahim; Thiviya Darmarajan; Satheeshkumar Nanjappan; Jestin Chellian; Mayuren Candasamy; Thiagarajan Madheswaran; Ankur Sharma; Harish Dureja; Parteek Prasher; Nitin Verma; Deepak Kumar; Kishneth Palaniveloo; Dheeraj Bisht; Gaurav Gupta; Jyotsana R Madan; Sachin Kumar Singh; Niraj Kumar Jha; Kamal Dua; Dinesh Kumar Chellappan
Journal:  AAPS PharmSciTech       Date:  2021-06-08       Impact factor: 3.246

4.  ViPR: an open bioinformatics database and analysis resource for virology research.

Authors:  Brett E Pickett; Eva L Sadat; Yun Zhang; Jyothi M Noronha; R Burke Squires; Victoria Hunt; Mengya Liu; Sanjeev Kumar; Sam Zaremba; Zhiping Gu; Liwei Zhou; Christopher N Larson; Jonathan Dietrich; Edward B Klem; Richard H Scheuermann
Journal:  Nucleic Acids Res       Date:  2011-10-17       Impact factor: 16.971

5.  Virus Variation Resource - improved response to emergent viral outbreaks.

Authors:  Eneida L Hatcher; Sergey A Zhdanov; Yiming Bao; Olga Blinkova; Eric P Nawrocki; Yuri Ostapchuck; Alejandro A Schäffer; J Rodney Brister
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

6.  Bioinformatics resources for SARS-CoV-2 discovery and surveillance.

Authors:  Tao Hu; Juan Li; Hong Zhou; Cixiu Li; Edward C Holmes; Weifeng Shi
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

7.  Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies.

Authors:  G Lizbeth Ramírez-Salinas; Jazmín García-Machorro; Saúl Rojas-Hernández; Rafael Campos-Rodríguez; Arturo Contis-Montes de Oca; Miguel Medina Gomez; Rocío Luciano; Mirko Zimic; José Correa-Basurto
Journal:  Arch Virol       Date:  2020-02-14       Impact factor: 2.574

8.  ViruSurf: an integrated database to investigate viral sequences.

Authors:  Arif Canakoglu; Pietro Pinoli; Anna Bernasconi; Tommaso Alfonsi; Damianos P Melidis; Stefano Ceri
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

Review 9.  Novel corona virus (COVID-19); Global efforts and effective investigational medicines: A review.

Authors:  Madhusudan Goyal; Nisha Tewatia; Hemlata Vashisht; Reena Jain; Sudershan Kumar
Journal:  J Infect Public Health       Date:  2021-05-01       Impact factor: 3.718

Review 10.  Orthobunyaviruses: From Virus Binding to Penetration into Mammalian Host Cells.

Authors:  Stefan Windhaber; Qilin Xin; Pierre-Yves Lozach
Journal:  Viruses       Date:  2021-05-10       Impact factor: 5.048

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