Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting (original) (raw)

The Third Annual Meeting of the European Virus Bioinformatics Center

Viruses

The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28–29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers. The meeting was held at the McIntyre Building of the University of Glasgow; a perfect location, as it was originally built to be a place for “rubbing your brains with those of other people”, as Rector Stanley Baldwin described it. The goal of the meeting was to provide a meaningful and interactive scientific envir...

The International Virus Bioinformatics Meeting 2022

Viruses

The International Virus Bioinformatics Meeting 2022 took place online, on 23–25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus–host interactions, viral sequence analysis, virus identification ...

The International Virus Bioinformatics Meeting 2020

Viruses, 2020

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively a...

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Journal of Virology, 2014

The beginning of the second century of research in the field of virology (the first virus 27 was discovered in 1898) was marked with its amalgamation with bioinformatics 28 resulting in the birth of a new domain -viroinformatics. The availability of more than 29 100 web servers and databases embracing all or specific viruses (for example dengue, 30 influenza, hepatitis, HIV, HFV, HPV, West Nile etc.) as well as distinct applications 31 (comparative/diversity analysis, viral recombination, siRNA/shRNA/miRNA studies, 32 RNA folding, protein-protein interaction, structural analysis, phylotyping/genotyping) 33 will definitely aid the development of effective drugs and vaccines. However, the 34 information about their access and utility is not available at any single 35 source/platform. Therefore, a compendium of various computational tools/resources 36 dedicated specifically to virology is presented in this article.

Challenges in RNA virus bioinformatics

Bioinformatics, 2014

Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of 4200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and wellorganized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands. Results: The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses.

Bioinformatics Methods For Studying Intra-Host and Inter-Host Evolution Of Highly Mutable Viruses

2021

Understanding viral disease progression is vital to the detection of outbreaks and subsequent planning for public health actions. Bioinformatics methods are extremely useful for this purpose through a range of applications among which the analysis of viral next-generation sequencing (NGS) data, tracing virus evolution and reconstruction of transmission networks have been explored in this research. The first part of this research focuses on the processing of NGS data where quantification methods are proposed to describe the robustness and reproducibility of the output of bioinformatics tools. This research shows the importance of assessing the reliability of genomic tools. The second part of this study is the application of processed NGS data to investigate the intra-host evolution of Hepatitis C Virus (HCV) to diagnose and detect new and incident HCV cases. A computational method based on Machine Learning algorithms is proposed to solve this problem. This genomic multi feature-based...

Women in the European Virus Bioinformatics Center

Viruses

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure...

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

Nucleic acids research, 2012

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadatadriven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal 'Workbenches' for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

Viral bioinformatics: computational views of host and pathogen

Novartis Foundation symposium, 2003

Wherever cellular life occurs, viruses are also found. As a result, complex organism and cellular antiviral responses co-evolve with virally encoded countermeasures. Since viruses co-opt or interfere with specific cellular pathways during their replication, knowledge of viral genome sequences has helped fundamental understanding of host biology. During viral infection, shifts in the balance between host and viral biological processes result in acute or chronic viral disease pathology accompanied with either active viral replication, viral containment/persistence or viral clearance. Studying host-virus interactions at the level of single gene effects, however, fails to produce a global systems-level understanding. This should now be achievable in the context of complete host and pathogen genome sequences. New experimental methods and computational approaches are rapidly developing, allowing global views of dynamic viral and cellular molecular mechanisms. Systems level virology using ...