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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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This topic is a collaborative effort:

This topic is a collaborative effort: | Virology and Bioinformatics from Virology.ca | Scoop.it
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An Apple a Day, and Other Myths

An Apple a Day, and Other Myths | Virology and Bioinformatics from Virology.ca | Scoop.it
The gap grows between food folklore and science on cancer.
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Ten Simple Rules for Making Good Oral Presentations

Ten Simple Rules for Making Good Oral Presentations | Virology and Bioinformatics from Virology.ca | Scoop.it

Continuing our “Ten Simple Rules” series [1–5], we consider here what it takes to make a good oral presentation. While the rules apply broadly across disciplines, they are certainly important from the perspective of this readership. Clear and logical delivery of your ideas and scientific results is an important component of a successful scientific career. Presentations encourage broader dissemination of your work and highlight work that may not receive attention in written form.

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H5N1: Vietnam sees vaccination rush as measles deaths hit 123

Via Thanh Nien Daily: Vietnam sees vaccination rush as measles deaths hit 123. Excerpt: Adults and children have been flocking the Pasteur Institute in Ho Chi Minh City to seek measles vaccination as the fatalities on infected children have reached...
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How r u? Is it worth my time to appeal my grade?

How r u? Is it worth my time to appeal my grade? | Virology and Bioinformatics from Virology.ca | Scoop.it
Steve Caplan: Are today's biomedical research graduate students lacking in professionalism as well as skill?
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Essential Collection: HIV reviews issue - Virology - Elsevier

Essential Collection: HIV reviews issue - Virology - Elsevier | Virology and Bioinformatics from Virology.ca | Scoop.it
We are proud to present five HIV Reviews in the April issue of Virology written by experts in the field. Three of these reviews describe the...
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Naturopath Education: Still Replete With Bollocks « Alternative Medicine « Health « Skeptic North

Naturopath Education: Still Replete With Bollocks « Alternative Medicine « Health « Skeptic North | Virology and Bioinformatics from Virology.ca | Scoop.it

#Naturopaths are allowed to call themselves doctors in Ontario, placing them alongside Physicians, Dentists, Psychologists, Optometrists, and (regrettably)…

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The contribution of epistasis to the architecture of fitness in an RNA virus

The contribution of epistasis to the architecture of fitness in an RNA virus | Virology and Bioinformatics from Virology.ca | Scoop.it
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A Possible Cure for Ebola Virus Infection? | RCScience

A Possible Cure for Ebola Virus Infection? | RCScience | Virology and Bioinformatics from Virology.ca | Scoop.it
Ken Yaw Agyeman-Badu's insight:

The molecule, named BCX4430, resembles the famous "A" found in DNA: adenosine. (Recall that DNA is made of Adenosine, Thymidine, Cytidine and Guanosine.) The RNA-based filoviruses also use "A" in their genomes. BCX4430, because it resembles "A", can be accidentally used by the virus when it is trying to grow inside of our cells. For the virus, this is a fatal mistake. BCX4430 blocks further growth and reproduction.

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The Hallmarks of Cancer 8: Tumor-Promoting Inflammation | Guest Blog, Scientific American Blog Network

The Hallmarks of Cancer 8: Tumor-Promoting Inflammation | Guest Blog, Scientific American Blog Network | Virology and Bioinformatics from Virology.ca | Scoop.it
The Hallmarks of Cancer are ten underlying principles shared by all cancers. You can read the first seven Hallmarks of Cancer articles here. The eighth Hallmark ...
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DNA looping damage tied to HPV cancer, researcher discovers

DNA looping damage tied to HPV cancer, researcher discovers | Virology and Bioinformatics from Virology.ca | Scoop.it
Certain strains of human papillomavirus (HPV) are known to cause about five percent of all cancer cases, yet all the mechanisms aren't completely understood. Now, researchers have leveraged Ohio Supercomputer Center resources and whole-genome sequencing to identify a new way that HPV might spark cancer development -- by disrupting the human DNA sequence with repeating loops when HPV is inserted into host-cell DNA as it replicates.
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Warnings of 'catastrophic' Chikungunya epidemic; fears it could spread during the World Cup

Warnings of 'catastrophic' Chikungunya epidemic; fears it could spread during the World Cup | Virology and Bioinformatics from Virology.ca | Scoop.it
A team of French and Brazilian researchers warn that chikungunya virus is poised to invade, and become epidemic in the Americas according to research published ahead of print in the Journal of Virology.
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Now researchers can explore genomic data across space and time

Now researchers can explore genomic data across space and time | Virology and Bioinformatics from Virology.ca | Scoop.it
The figure above is part of a four-step procedure for the multiscale segmentation of genomic signals.

Via Pedro Fernandes
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Why is N50 used as an assembly metric

Why N50?

Maybe it is worth remembering why we even have N50 as a statistic. The final assembly for any genome project, i.e. the one that is described in a paper or uploaded to a database, is not necessarily the biggest assembly that was generated.

 
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From ACGT blog
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The running of Taverna Workflows within an IPython Notebook

The running of Taverna Workflows within an IPython Notebook | Virology and Bioinformatics from Virology.ca | Scoop.it
biodiversity, data mobilization, data, publishing, data, acquisition, data, curation
data, synthesis, data, interoperability, linked, data, flora, fauna, taxon, treatment, legacy, literature, prospective, publishing, semantic, interoperability,
taxonomy, coordination, policy, development, European Open Biodiversity Knowledge Management System, dissemination, mark up, persistent, identifiers
Chris Upton + helpers's insight:

During the recent pro-iBiosphere Data Enrichment Hackathon, a prototype Taverna Player Client Python package was developed for IPython Notebook. The package allows the listing of workflows available on a Taverna Portal, selection of a workflow and the running of the workflow within the Notebook. Data from the Python environment can be used as inputs to the workflow, and the results of the workflow run are available for further manipulation in the notebook.  User can interact with the running of the workflow using the Taverna Player and interaction services.

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Viruses101 | Learn Science at Scitable

Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses 101 will delve into the world of microscopic killers. Each post will explore a new virus ? its components, effects on victims, and its impact on the global community.
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Are groundbreaking new hepatitis C drugs too expensive?

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Iceland – a hotbed for bird flu viruses

Iceland – a hotbed for bird flu viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists at the University of Iceland, in collaboration with American and Icelandic colleagues, demonstrated that bird flu viruses from both continental Europe and North-America, as well as mixed virus strains are found in wild birds in Iceland.
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Researchers identify a new variant of Ebola virus in Guinea

Researchers identify a new variant of Ebola virus in Guinea | Virology and Bioinformatics from Virology.ca | Scoop.it
In a new article, researchers have published their initial findings on the characteristics of the Ebola virus discovered in Guinea. Initial virological investigations enabled them to identify Zaire ebolavirus as the pathogen responsible for this epidemic.
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Health Canada – It’s Far Past Time to Put a Stop to the NHPD Farce « Alt-Med Or Alt-Menace? « Health « Skeptic North

Health Canada – It’s Far Past Time to Put a Stop to the NHPD Farce « Alt-Med Or Alt-Menace? « Health « Skeptic North | Virology and Bioinformatics from Virology.ca | Scoop.it
Another foreign government report has been released concluding that homeopathy is worthless. The UK governmentconcluded that homeopathy was no better than…
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Homeopaths are not Medical Experts « Canada « Skeptic North

Homeopaths are not Medical Experts « Canada « Skeptic North | Virology and Bioinformatics from Virology.ca | Scoop.it
The CBC recently aired a “National Check Up” health panel segment ostensibly to discuss the current state of medical research. The panel, led by Peter…
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HIV-1 Vpu antagonism of tetherin inhibits antibody-dependent cellular cytotoxic responses by natural killer cells

HIV-1 Vpu antagonism of tetherin inhibits antibody-dependent cellular cytotoxic responses by natural killer cells | Virology and Bioinformatics from Virology.ca | Scoop.it
Ken Yaw Agyeman-Badu's insight:

The type I IFN inducible factor tetherin retains virus particles on the surface of cells infected with vpu-deficient HIV-1. While this mechanism inhibits cell-free viral spread, the immunological implications of tethered virus have not been investigated. We found that surface tetherin expression increased the antibody opsonization of vpu-deficient HIV-infected cells.

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France Lost Thousands of Vials Containing the SARS Virus

France Lost Thousands of Vials Containing the SARS Virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Somebody's definitely getting fired, after over 2,300 vials containing fragments of the deadly SARS virus went missing from the Pasteur Institute in France earlier this week. Not one or two vials, mind you. Thousands of them.
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SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes | Virology and Bioinformatics from Virology.ca | Scoop.it

Motivation: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.

Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.

 
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What the Tamiflu saga tells us about drug trials and big pharma

What the Tamiflu saga tells us about drug trials and big pharma | Virology and Bioinformatics from Virology.ca | Scoop.it
Ben Goldacre: We now know the government's Tamiflu stockpile wouldn't have done us much good in the event of a flu epidemic. But the secrecy surrounding clinical trials means there's a lot we don't know about other medicines we take
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It's sad that this causes distrust that spills over to vaccines -  which WORK!

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Drawing a Ring Around Antiviral Immunity | HMS

Drawing a Ring Around Antiviral Immunity | HMS | Virology and Bioinformatics from Virology.ca | Scoop.it
@harvardmed & @BostonChildrens: Drawing a Ring Around Antiviral Immunity http://t.co/OF3EUh4WBr #Ubiquitin #cancer #Immunology

Via Gilbert Faure au nom de l'ASSIM
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How Harmless Bacteria Quickly Turned Into a Flesh-Eating Monster

How Harmless Bacteria Quickly Turned Into a Flesh-Eating Monster | Virology and Bioinformatics from Virology.ca | Scoop.it
Genetic study reveals that just four changes gave Streptococcus the ability to cause deadly disease.
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