Viruses, Immunology & Bioinformatics from 4Virology.net at UVic
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Newly discovered insect virus could combat invasive ants

Newly discovered insect virus could combat invasive ants | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it

Like colonial Europeans carrying smallpox to the Americas, the tiny brown Argentine ant may be harboring a dangerous virus that’s killing the world’s already vulnerable honey bees. That’s the conclusion of a new study, which also finds that the ants have their own disease to worry about—one that scientists could target to limit the spread of this invasive species.

 

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Viruses, Immunology & Bioinformatics from 4Virology.net at UVic
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it

get in touch if you want to help curate this topic

Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
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Sweden: The One Chart that Matters, by Mike Whitney

Sweden: The One Chart that Matters, by Mike Whitney | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
While the Covid-19 epidemic continues to drag on in the United States, it's largely over in Sweden where fatalities have dropped to no more than 2 deaths per day for the last week. Sweden has been harshly criticized in the media for not imposing draconian lockdowns like the United States and the other European countries.  Instead, Sweden implemented a policy that was both conventional and sensible. They recommended that people maintain a safe distance between each other and they banned gatherings of 50 people or more. They also asked their elderly citizens to isolate themselves and to avoid interacting with
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A contrarian view on the COVID-19 lockdown
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Sunetra Gupta: Covid-19 is on the way out

Sunetra Gupta: Covid-19 is on the way out | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
The author of the Oxford model defends her view that the virus has passed through the UK's population
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GTO: A toolkit to unify pipelines in genomic and proteomic research - ScienceDirect

GTO: A toolkit to unify pipelines in genomic and proteomic research - ScienceDirect | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These…
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https://www.youtube.com/channel/UClB9Np8SoxXaA4sVsm3Ea3A

 Great set of #Bioinformatics videos by David #Tabb
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Emergence of SARS-CoV-2 through recombination and strong purifying selection | Science Advances

Emergence of SARS-CoV-2 through recombination and strong purifying selection | Science Advances | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
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Eight practical Google advanced search tips for students

Eight practical Google advanced search tips for students | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it

"Here is a handy visual you can use with your students in class to help them become better Google searchers ..."


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Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research[v1] | Preprints

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research[v1] | Preprints | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding, and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are freely available online, either through web applications or public code repositories.
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Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements | Oxford Academic

Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
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MichelaNglo: sculpting protein views on web pages without coding | Bioinformatics | Oxford Academic

MichelaNglo: sculpting protein views on web pages without coding | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
AbstractMotivation. The sharing of macromolecular structural information online by scientists is predominantly performed via 2D static images, since the embedd
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metaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic

metaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
AbstractMotivation. Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth’s virome has been sequenced so f
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Five things to tell someone who insists coronavirus is just a bad flu - The Boston Globe

Five things to tell someone who insists coronavirus is just a bad flu - The Boston Globe | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Here are a few reasons why those suggesting the novel coronavirus is no worse than the flu have got it all wrong.

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Genomic characterization of Canine circovirus detected in a dog with intermittent hemorrhagic gastroenteritis in Brazil

Genomic characterization of Canine circovirus detected in a dog with intermittent hemorrhagic gastroenteritis in Brazil | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it

 Because Canine circovirus (CanineCV) is a new species of the genus Circovirus, several issues related to its epidemiology, pathogenesis and clinical disease remain unknown. Thus, this study aimed to perform the characterization of the first complete genome sequence of CanineCV detected in a dog with diarrhea in Brazil. A stool sample was collected of a ten-month-old female German Shepherd dog which had signs of intermittent hemorrhagic gastroenteritis, vomiting, and a history of eating raw pork. The complete CanineCV genome was sequenced by Next-Generation Sequencing. The sequence had 2,063 nucleotides, showed a typical genomic organization for circovirus, and was grouped with strain 214 described in the United States by phylogenetic analysis. One amino acid change was found in the replicase protein, and because of that it was considered unique to CanineCV. Therefore, the characterization of the complete genome of Brazilian CanineCV can be used in future studies of molecular epidemiology, pathogenesis and development of diagnostic tools for the prevention and control of this disease. 

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Clinical trials of monoclonal antibodies to prevent COVID-19 now enrolling

Clinical trials of monoclonal antibodies to prevent COVID-19 now enrolling | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Phase 3 trials conducted in the NIAID COVID-19 Prevention Network.
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Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses—the viral subgenus containing SARS-CoV and SARS-CoV-2—undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades. In this manuscript, the authors address evolutionary questions on the emergence of SARS-CoV-2. They find that SARS-CoV-2 is not a recombinant of any sarbecoviruses detected to date, and that the bat and pangolin sequences most closely related to SARS-CoV-2 probably diverged several decades ago or possibly earlier from human SARS-CoV-2 samples.
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LogoJS: a Javascript package for creating sequence logos and embedding them in web applications | Bioinformatics | Oxford Academic

LogoJS: a Javascript package for creating sequence logos and embedding them in web applications | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
AbstractSummary. Sequence logos were introduced nearly 30 years ago as a human-readable format for representing consensus sequences, and they remain widely use
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CRAMER: A Lightweight, Highly Customizable Web-Based Genome Browser Supporting Multiple Visualization Instances

Supplementary data are available at Bioinformatics online.
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Publications on SARS-CoV-2 and coronaviruses in general –

Publications on SARS-CoV-2 and coronaviruses in general – | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
[bibfilter file= group=year group_order=desc allow=article,incollection author=”A. B. Abecasis|E. M. Adriaenssens|A. C. Andeweg|R. Backofen|A. T. Baker|A. Bataille|S. C. Becker|S. Becker|M. B…
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Should We Purposely Infect Healthy Volunteers With Covid-19? | WIRED

Should We Purposely Infect Healthy Volunteers With Covid-19? | WIRED | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Such studies could speed up the development of a vaccine—but would mean deliberately giving people a disease that could kill them.
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MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments - Pablo Mier, Miguel A Andrade-Navarro, 2020

MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments - Pablo Mier, Miguel A Andrade-Navarro, 2020 | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at position
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Scientists Explore Molecular Connections Between Genetics, Gut Microbiome, and Memory – SciTechDaily

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Feature-Viewer: a visualization tool for positional annotations on a sequence | Bioinformatics | Oxford Academic

Feature-Viewer: a visualization tool for positional annotations on a sequence | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
AbstractSummary. The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designe
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Ideas for how informaticians can get involved with COVID-19 research | BioData Mining | Full Text

Ideas for how informaticians can get involved with COVID-19 research | BioData Mining | Full Text | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on population health and wellbeing. Biomedical informatics is central to COVID-19 research efforts and for the delivery of healthcare for COVID-19 patients. Critical to this effort is the participation of informaticians who typically work on other basic science or clinical problems. The goal of this editorial is to highlight some examples of COVID-19 research areas that could benefit from informatics expertise. Each research idea summarizes the COVID-19 application area, followed by an informatics methodology, approach, or technology that could make a contribution. It is our hope that this piece will motivate and make it easy for some informaticians to adopt COVID-19 research projects.
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researchseminars.org - Browse talks

researchseminars.org - Browse talks | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Welcome to researchseminars.org, a listing of research seminars and conferences!
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The TLR4 Antagonist, Eritoran, Protects Mice from Lethal Influenza Infection

The TLR4 Antagonist, Eritoran, Protects Mice from Lethal Influenza Infection | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
There is pressing need to develop alternatives to annual influenza vaccines and antiviral agents licensed for mitigating influenza infection. Previous studies reported that acute lung injury (ALI) caused by chemical or microbial insults is secondary to ...
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