Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence - Arch Virol. 2014

Abstract

Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.

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Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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 Virology.uvic.ca | 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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low-complexity add-on score for protein remote homology search with COMER | Bioinformatics | Oxford Academic

low-complexity add-on score for protein remote homology search with COMER | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Protein sequence alignment forms the basis for comparative modeling, the most reliable approach to protein structure prediction, among many
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BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach | Bioinformatics | Oxford Academic

BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuit
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Porcine Circovirus Type 2 Suppresses IL-12p40 Induction via Capsid/gC1qR-Mediated MicroRNAs and Signalings. - 

J Immunol. 2018 Jun 1. pii: ji1800250. doi: 10.4049/jimmunol.1800250.[Epub ahead of print]...
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Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution

Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Cloud computing applications for biomedical science: A perspective

Cloud computing applications for biomedical science: A perspective | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Biomedical research has become a digital data–intensive endeavor, relying on secure and scalable computing, storage, and network infrastructure, which has traditionally been purchased, supported, and maintained locally. For certain types of biomedical applications, cloud computing has emerged as an alternative to locally maintained traditional computing approaches. Cloud computing offers users pay-as-you-go access to services such as hardware infrastructure, platforms, and software for solving common biomedical computational problems. Cloud computing services offer secure on-demand storage and analysis and are differentiated from traditional high-performance computing by their rapid availability and scalability of services. As such, cloud services are engineered to address big data problems and enhance the likelihood of data and analytics sharing, reproducibility, and reuse. Here, we provide an introductory perspective on cloud computing to help the reader determine its value to their own research.
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NGL Viewer: Web-based molecular graphics for large complexes | Bioinformatics | Oxford Academic

NGL Viewer: Web-based molecular graphics for large complexes | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental technique
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Featured Projects - Teb’s Lab

Featured Projects - Teb’s Lab | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Teb’s Lab is a place to learn about computer science, programming, genetics, genomics, bioinformatics, math, artificial intelligence, machine learning and more. I create mixed media educational materials that includes writing, code projects, websites, videos, and more.
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The cytosolic sensor STING is required for intestinal homeostasis and control of inflammation

The cytosolic sensor STING is required for intestinal homeostasis and control of inflammation | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Article Report

Via Gilbert C FAURE
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Giant pandoraviruses create their own genes.

Giant pandoraviruses create their own genes. | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Giant viruses overlapping in size and genome complexity with unicellular organisms are among the most unexpected discoveries of the last 15 years in virology. Yet they are in turn considered evolutionary freak by some, or precious living fossils of ancestral life forms by others. Our comparative analysis of 6 strains of the spectacular Pandoraviridae family now suggests that their giant genomes may be actively breeding new proteins and functions.
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Next-generation sequencing tests to become routine

Cancer patients in the US and UK will soon access next-generation sequencing (NGS) as part of routine clinical care.
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Live neighbor-joining | BMC Bioinformatics | Full Text

Live neighbor-joining | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa. We also applied Live Neighbor-Joining on a set of bacterial genomes and to sets of images and texts. Non-biological data may be better explored visually when their relationship in terms of content similarity is represented by means of a phylogeny. Our experiments have shown interesting alternative phylogenetic hypothesis for RNA virus genomes, bacterial genomes and alternative relationships among images and texts, illustrating a wide range of scenarios where Live Neighbor-Joining may be used.
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Some science journals that claim to peer review papers do not do so - Publish and don’t be damned

Some science journals that claim to peer review papers do not do so - Publish and don’t be damned | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
WHETHER to get a promotion or merely a foot in the door, academics have long known that they must publish papers, typically the more the better. Tallying scholarly publications to evaluate their authors has been common since the invention of scientific journals in the 17th century.
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Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” - ScienceDirect

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. Th…
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HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA | Bioinformatics | Oxford Academic

HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods
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Purifying and positive selection in the evolution of stop codons

Purifying and positive selection in the evolution of stop codons | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Modes of evolution of stop codons in protein-coding genes, especially the conservation of UAA, have been debated for many years. We reconstructed the evolution of stop codons in 40 groups of closely related prokaryotic and eukaryotic genomes. The results indicate that the UAA codons are maintained by purifying selection in all domains of life. In contrast, positive selection appears to drive switches from UAG to other stop codons in prokaryotes but not in eukaryotes. Changes in stop codons are significantly associated with increased substitution frequency immediately downstream of the stop. These positions are otherwise more strongly conserved in evolution compared to sites farther downstream, suggesting that such substitutions are compensatory. Although GC content has a major impact on stop codon frequencies, its contribution to the decreased frequency of UAA differs between bacteria and archaea, presumably, due to differences in their translation termination mechanisms.
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We can make academia more family friendly |

We can make academia more family friendly | | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
This one tickled me for too long. It became a serious itch and I feel I have to say something. Two weeks ago, Rebecca Calisi Rodríguez and a Working Group of Mothers in Science published an opinion…
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5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more

5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
5 new videos on YouTube: Get the most out of BLAST, MedGen, PubChem and more
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Minimap2: pairwise alignment for nucleotide sequences | Bioinformatics | Oxford Academic

Minimap2: pairwise alignment for nucleotide sequences | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughpu
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New insights into the immunomodulatory properties of poxvirus cytokine decoy receptors at the cell surface - F1000Research

New insights into the immunomodulatory properties of poxvirus cytokine decoy receptors at the cell surface - F1000Research | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract
Poxviruses encode a set of secreted proteins that bind cytokines and chemokines as a strategy to modulate host defense mechanisms. These viral proteins mimic the activity of host cytokine decoy receptors but have unique properties that may enhance their activity. Here, we describe the ability of poxvirus cytokine receptors to attach to the cell surface after secretion from infected cells, and we discuss the advantages that this property may confer to these viral immunomodulatory proteins.
Keywords
Poxvirus, Immune evasion, cytokine receptor, interferon, chemokine, glycosaminoglycan

Via Krishan Maggon
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Statisticians issue warning over misuse of P values

Statisticians issue warning over misuse of P values | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Misuse of the P value — a common test for judging the strength of scientific evidence — is contributing to the number of research findings that cannot be reproduced, the American Statistical Association (ASA) warns in a statement released today1. The group has taken the unusual step of issuing principles to guide use of the P value, which it says cannot determine whether a hypothesis is true or whether results are important.
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Ten simple rules for writing a cover letter to accompany a job application for an academic position

Ten simple rules for writing a cover letter to accompany a job application for an academic position | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Influenza’s signature move

Influenza’s signature move | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Fig. 1: The gene-expression pattern in influenza virus–infected patients reflects the severity of disease and time since infection.
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An introduction to part-of-speech tagging and the Hidden Markov Model

Let’s go back into the times when we had no language to communicate. The only way we had was sign language. That’s how we usually communicate with our dog at home, right? When we tell him, “We love…
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HMM is employed in many bioinformatics tools. This blog post explain the basic concept of the (Hidden) Markov Model.
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