Viruses, Immunology & Bioinformatics from 4Virology.net
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Viruses, Immunology & Bioinformatics from 4Virology.net
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 | Scoop.it

get in touch if you want to help curate this topic

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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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CDC’s Redfield: It could take another year to control Ebola in DRC

CDC’s Redfield: It could take another year to control Ebola in DRC | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
CDC Director Robert Redfield offered a bleaker projection than one issued earlier by the director-general of the World Health Organization.
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svist4get: a simple visualization tool for genomic tracks from sequencing experiments | BMC Bioinformatics | Full Text

svist4get: a simple visualization tool for genomic tracks from sequencing experiments | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track constructed by short read mapping to a particular genome assembly. There are many software tools to visualize genomic tracks in a web browser or with a stand-alone graphical user interface. However, there are only few command-line applications suitable for automated usage or production of publication-ready visualizations. Here we present svist4get, a command-line tool for customizable generation of publication-quality figures based on data from genomic signal tracks. Similarly to generic genome browser software, svist4get visualizes signal tracks at a given genomic location and is able to aggregate data from several tracks on a single plot along with the transcriptome annotation. The resulting plots can be saved as the vector or high-resolution bitmap images. We demonstrate practical use cases of svist4get for Ribo-Seq and RNA-Seq data. svist4get is implemented in Python 3 and runs on Linux. The command-line interface of svist4get allows for easy integration into bioinformatics pipelines in a console environment. Extra customization is possible through configuration files and Python API. For convenience, svist4get is provided as pypi package. The source code is available at
https://bitbucket.org/artegorov/svist4get/

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Discovery upturns understanding of how some viruses multiply

Discovery upturns understanding of how some viruses multiply | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Scientists have shown that different segments of a virus genome can exist in distinct cells but work together to cause an infection.
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The web meets genomics: a DNA search engine for microbes

The web meets genomics: a DNA search engine for microbes | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Researchers at EMBL's European Bioinformatics Institute (EMBL-EBI) have combined their knowledge of bacterial genetics and web search algorithms to build a DNA search engine for microbial data. The search engine, described ...
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Ebola treatment center in Congo is attacked again; 1 dead | PBS NewsHour Weekend

Ebola treatment center in Congo is attacked again; 1 dead | PBS NewsHour Weekend | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Armed assailants again attacked an Ebola treatment center in the heart of eastern Congo’s deadly outbreak on Saturday, with one police officer killed and health workers injured.
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Unknown Attackers Threaten to Worsen Ebola Epidemic in Congo

Unknown Attackers Threaten to Worsen Ebola Epidemic in Congo | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Aid workers say they are facing a spike in attacks and threats, slowing their work and potentially triggering a surge of new cases...
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Third patient cured of HIV in history

Third patient cured of HIV in history | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
After the Berlin patient and the London patient, the Düsseldorf patient appears to be the third in history to be cured of HIV. The treatment relies on a rare genetic mutation that may be the path forward for curing the deadly disease.
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mathbionerd: Changing your name after divorce in academia

mathbionerd: Changing your name after divorce in academia | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
I've tried to write this so many times, and I keep putting it off. I have a grant to finish. I have grading. I have emails to respond to
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Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?

Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved? | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The high degree of conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow for the development of T cell-inducing vaccines that provide protection across different strains and subtypes. This conservation is not fully explained by functional constraint, since an additional mutation(s) can compensate for the replicative fitness loss of IAV escape variants. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may have only a modest effect on transmission. Second, polymorphism of the human major histocompatibility complex class I (MHC-I) gene restricts the advantage of an escape variant to only a small fraction of the human population who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell escape variants may result in a compensatory increase in the responses to other epitopes of IAV. We use a combination of population genetics and epidemiological models to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape variants. We conclude that for a wide range of biologically reasonable parameters, the invasion of an escape variant virus will be slow, with a timescale of a decade or more. The results suggest T cell-inducing vaccines do not engender the rapid evolution of IAV. Finally, we identify key parameters whose measurement will allow for more accurate quantification of the long-term effectiveness and impact of universal T cell-inducing influenza vaccines.
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Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences | Bioinformatics | Oxford Academic

Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractMotivation. Function annotation of proteins is fundamental in contemporary biology across fields including genomics, molecular biology, biochemistry, s
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The Giant Medusavirus Turns Victims to ‘Stone’

The Giant Medusavirus Turns Victims to ‘Stone’ | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
A newly discovered giant virus turns its victims to “stone.”
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GToTree: a user-friendly workflow for phylogenomics | Bioinformatics

Genome-level evolutionary inference (i.e., phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required – such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together, etc. – can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files, and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. While GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12,000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.
Cindy's insight:
I tested it out on poxvirus dataset, and after overcoming the customized HMM creation (helpful scripts provided by author here: https://github.com/AstrobioMike/GToTree/wiki/SCG-sets#code), creates a beautiful tree in 1 minute!
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Ebola is Still Stalking Africa. Who's Supporting Front-line Work to Stop More Outbreaks? —

Ebola is Still Stalking Africa. Who's Supporting Front-line Work to Stop More Outbreaks? — | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
One of the deadliest outbreaks of Ebola yet happened just seven months ago in eastern Congo, claiming 600 lives. In response, the foundation of the late Microsoft co-founder Paul G. Allen is making rapid-reaction grants to organizations on the ground.
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Phylogenetic Clustering by Linear Integer Programming (PhyCLIP) | Molecular Biology and Evolution | Oxford Academic

Abstract. Sub-species nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between
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Ebola cases in the Congo rises to more than 900 breaking record

Ebola cases in the Congo rises to more than 900 breaking record | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The second largest Ebola outbreak in history with 900 new cases is currently taking place in the Democratic Republic of Congo in Africa.
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My 7 Takeaways from the 2019 International Center for Academic Integrity Conference

My 7 Takeaways from the 2019 International Center for Academic Integrity Conference | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
The 2019 International ICAI conference is in the books. Here are my 7 biggest takeaways from the three-day event on academic integrity.
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NASH liver disease drug development Gilead Intercept Genfit

NASH liver disease drug development Gilead Intercept Genfit | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Drugmakers are trying to figure out how to treat the liver disease NASH, but one of the first late stage medical studies just fell short of its goal.
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DOH wants Philippines rabies-free by 2030

DOH wants Philippines rabies-free by 2030 | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Rabies is considered a public health problem in the Philippines as the highly fatal infection causes at least 200 deaths every year...
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How Facebook's anti-vaccination movement is kept in check by these Aussie volunteers - Science News

How Facebook's anti-vaccination movement is kept in check by these Aussie volunteers - Science News | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Armed with little more than a healthy respect for science and some memes, Australians go online each day to take on the anti-vaccination movement.
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Scientists Resume Efforts To Create Deadly Flu Virus, With US Government's Blessing

Scientists Resume Efforts To Create Deadly Flu Virus, With US Government's Blessing | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
NIH has just approved two projects that aim to turn avian influenza into a potentially deadly human pathogen. The research was "paused" by the US in 2014, but the pause was quietly lifted last year, despite the warnings of hundreds of distinguished scientists from around the world.
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New portal of entry for influenza viruses

New portal of entry for influenza viruses | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
Researchers from the Medical Center -- University of Freiburg and the University of Zurich have discovered an entirely new infection route for influenza A viruses. While all previously known influenza A viruses bind sialic acid moieties on the host cell surface, the recently discovered bat-derived influenza A virus subtypes infect human and animal cells by utilizing MHC class II proteins. The immunologically relevant MHC class II molecules are ubiquitously found in many animal species, which is why the discovery will play an important role in assessing the risk of spill-over infections to other species than bats. The study, published on 20 February 2019 in the journal Nature, also provides new approaches to the evolutionary genesis of influenza viruses.
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Genome Detective: an automated system for virus identification from high-throughput sequencing data | Bioinformatics | Oxford Academic

Genome Detective: an automated system for virus identification from high-throughput sequencing data | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from 4Virology.net | Scoop.it
AbstractSummary. Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The applicatio
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