Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Whooping cough bounces back | Science News

Whooping cough bounces back | Science News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A new type of pertussis vaccine introduced in the late 1990s may have led to the return of a disease that was nearly eradicated 40 years ago. Public opposition to vaccination hasn’t helped matters.
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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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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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Acupuncture and the placebo problem

Acupuncture and the placebo problem | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Holding out acupuncture as an exemplar for alternative medicine demonstrates the poor state of evidence surrounding most alternative therapies.
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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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Bioinformatics core competencies for undergraduate life sciences education

Bioinformatics core competencies for undergraduate life sciences education | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent’s degree of training, time since degree earned, and/or the Carnegie Classification of the respondent’s institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.
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Bioinformatics in Research

Bioinformatics in Research | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Bioinformatics is the application of information techniques for the storage, retrieval, and analysis of large quantities of biological data.
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