Viruses, Immunology & Bioinformatics from 4Virology.net at UVic
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Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative
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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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What we can learn from the Swedish paradox

What we can learn from the Swedish paradox | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
There's nothing libertarian about this country. So why the laissez-faire response to Covid-19?
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Functional analysis of a novel βV1 gene identified in a geminivirus betasatellite

Functional analysis of a novel βV1 gene identified in a geminivirus betasatellite | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Betasatellites (DNA β) are circular ssDNA molecules that are associated with monopartite geminiviruses and exert a positive effect on the viral infection. Betasatellites encode one protein, named βC1, on the complementary strand; βC1 functions as a pathogenicity factor and RNA silencing suppressor.
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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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Why we aren't wearing masks in Sweden

Why we aren't wearing masks in Sweden | Viruses, Immunology & Bioinformatics from 4Virology.net at UVic | Scoop.it
Anders Tegnell, architect of a unique response to the pandemic, defends his approach
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MetaviralSPAdes: assembly of viruses from metagenomic data

"We describe a METAVIRALSPADES tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked METAVIRALSPADES on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines."
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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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