Viruses and Bioinformatics from Virology.uvic.ca
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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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Viruses and 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 and 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, 12:46 PM
Thank You.
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Prediction of virus-host protein-protein interactions mediated by short linear motifs

Prediction of virus-host protein-protein interactions mediated by short linear motifs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1). We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins (C), 2) located in disordered regions (D) and 3) rare or scarce in a set of randomized viral sequences (R). The sets C,D,R are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them – with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID). The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them: D∪R and C. The ordering of the sets is descending on the probability of capturing functional interactions. With respect to HIV-1, the sets C∪R, D∪R, C∪D∪R infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions. We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.
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Hydrophobic proteins on virus surfaces can help purify vaccines

Hydrophobic proteins on virus surfaces can help purify vaccines | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Through experimental and computational tests, new research expands on the theory of virus surface hydrophobicity. By being slightly water-repellent, the outer layers of proteins in virus capsids affect how it interacts with cells and the environment. Understanding this more can improve vaccine production and virus detection.
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HiLive: real-time mapping of illumina reads while sequencing | Bioinformatics | Oxford Academic

HiLive: real-time mapping of illumina reads while sequencing | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Ross River Virus: Many Vectors and Unusual Hosts Make for an Unpredictable Pathogen

Ross River Virus: Many Vectors and Unusual Hosts Make for an Unpredictable Pathogen | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
@GertrudRey #ZIKA Ross River Virus, another MBV, can be transmitted from animals to humans.

https://t.co/1X2HmZO7PP
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The sense behind retroviral anti-sense transcription

Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.

Via Ed Rybicki
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The blood DNA virome in 8,000 humans

The blood DNA virome in 8,000 humans | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Dramatic evolution within human genome may have been caused by malaria parasite

Dramatic evolution within human genome may have been caused by malaria parasite | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A genetic mutation that protects people from a common form of malaria spread like wildfire in sub-Saharan Africa about 42,000 years ago, according to a new study. Today, it’s nearly impossible to find somebody from this region who doesn’t have it. That makes the mutation one of the swiftest, strongest changes to the human genome yet seen—though it remains a mystery why this particular disease sparked such a dramatic evolutionary response.


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Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The transmembrane envelope (TM) protein gp41 of the human immunodeficiency virus-1 (HIV-1) plays an important role during virus infection inducing the fusio
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Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research

Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The accidental discovery of the giant virus of amoeba — Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) — in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.


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The blood DNA virome in 8,000 humans

The blood DNA virome in 8,000 humans | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Discovery of an HIV reservoir marker: A new avenue toward eliminating the virus

Discovery of an HIV reservoir marker: A new avenue toward eliminating the virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
French researchers have identified a marker that makes it possible to differentiate 'dormant' HIV-infected cells from healthy cells.
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Interleukin-18 Reduces Blood Glucose and Modulates Plasma Co... : Shock

Background: Dysregulation of glucose metabolism, including hyperglycemia with insulin resistance, is
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From crescent to mature virion: vaccinia virus assembly and maturation. - PubMed - NCBI


Abstract Vaccinia virus (VACV) has achieved unprecedented success as a live viral vaccine for smallpox which mitigated eradication of the disease. Vaccinia virus has a complex virion morphology and recent advances have been made to answer some of the key outstanding questions, in particular, the origin and biogenesis of the virion membrane, the transformation from immature virion (IV) to mature virus (MV), and the role of several novel genes, which were previously uncharacterized, but have now been shown to be essential for VACV virion formation. This new knowledge will undoubtedly contribute to the rational design of safe, immunogenic vaccine candidates, or effective antivirals in the future. This review endeavors to provide an update on our current knowledge of the VACV maturation processes with a specific focus on the initiation of VACV replication through to the formation of mature virions.

Viruses. 2014 Oct 7;6(10):3787-808. doi: 10.3390/v6103787. Research Support, Non-U.S. Gov't; Review

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UniProt Protein Feature Viewer, a BioJS component

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations.

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node.dating: dating ancestors in phylogenetic trees in R | Bioinformatics | Oxford Academic

node.dating: dating ancestors in phylogenetic trees in R | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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The sense behind retroviral anti-sense transcription

Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.

Via Ed Rybicki
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Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author Summary Dengue is a globally important viral disease. Despite this, there is still much unknown about the immunology, virology and epidemiology of dengue. As for all viral infections, the interaction between virus and immune response is a complex one. Using data collected from patients, we model how the virus replicates in an infected individual and how the human antibody response acts to control that replication. We show that the timing and magnitude of the growth and decline of virus and antibody levels in dengue-infected patients are consistent with antibody playing a key role in controlling infection. Our results are of use in the evaluation of potential antiviral drugs and vaccines.
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Scientists assemble Zika virus mosquito genome from scratch

Scientists assemble Zika virus mosquito genome from scratch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A multi-institutional team has developed a new way to sequence genomes, which can assemble the genome of an organism, entirely from scratch, dramatically cheaper and faster.


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The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes | American Council on Science and Health

The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes | American Council on Science and Health | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes https://t.co/WaSpyzyHuy
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New report shares details about the anti-plagiarism software market 2016 global analysis and forecast to 2020 - WhaTech

Sandler Research, Global Anti-Plagiarism Software Market, Anti-Plagiarism Software Industry, Anti-Plagiarism Software Market Outlook, Anti-Plagiarism Software Market Research, Anti-Plagiarism Software Market Growth, Anti-Plagiarism Software Market...
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Sustained fecal-oral human-to-human transmission following a zoonotic event

Sustained fecal-oral human-to-human transmission following a zoonotic event | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.


Via Ed Rybicki
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Co-circulation of multiple genotypes of African swine fever viruses among domestic pigs in Zambia (2013-2015). - PubMed - NCBI

Co-circulation of multiple genotypes of African swine fever viruses among domestic pigs in Zambia (2013-2015). - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Transbound Emerg Dis. 2017 Mar 15. doi: 10.1111/tbed.12635. [Epub ahead of print]
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GMO - Common Science Space

GMO - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
It’s a good idea to look critically at any powerful new technology, and the creation of genetically-modified organisms, GMOs, is no exception. Like any new technology, it might have unanticipated, deleterious consequences that outweigh any benefit. Many criticisms of GMO have of course been raised, as a brief interrogation of the internet will show. But unfortunately,... Continue Reading
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PISCES – alignment free RNA-seq quantiation and QC pipeline | RNA-Seq Blog

Matt Shirley -- PISCES: alignment free RNA-seq quantiation and QC pipeline
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