Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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A Review of “Bioinformatics Algorithms – An Active Learning ...

A Review of “Bioinformatics Algorithms – An Active Learning ... | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Each chapter attempts to answer a biological/bioinformatics question, but also has multiple sub-themes for students from different backgrounds. The chapters are so elegantly planned that readers from different backgrounds ...
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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, 12:46 PM
Thank You.
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Poxviruses: Slipping and sliding through transcription and translation

Poxviruses: Slipping and sliding through transcription and translation | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Efficient comparative phylogenetics on large trees | Bioinformatics | Oxford Academic

Efficient comparative phylogenetics on large trees | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over
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The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. - PubMed - NCBI

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. - PubMed - NCBI | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Nat Commun. 2017 Nov 13;8(1):1455. doi: 10.1038/s41467-017-01542-z.
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JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.
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Migrating into the Tumor: a Roadmap for T Cells

Migrating into the Tumor: a Roadmap for T Cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Tumors can be divided into ‘hot’ (T cell inflamed) or ‘cold’ (T cell noninflamed)
according to the presence of immune cells. In this review, we discuss variables that
influence T cell migration into the tumor microenvironment. Chemokines can attract
T cells to the tumor site and tumor intrinsic pathways can influence the composition
of local chemokines. Tumor-induced vasculature can hamper T cell migration. Other
immune cells and tumor-derived molecules can block T cell proliferation and survival.

Via Krishan Maggon
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Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review

Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Poxviridae family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely observed because this viral family has been more heavily investigated. However, relative to each member of the Poxviridae family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes. Would it be possible to extrapolate the restriction of viral replication in a specific cell lineage to an animal, a far more complex organism? In this study, we compare and discuss the relationship between the host range of poxvirus species and the abundance/diversity of host range genes. We analyzed the sequences of 38 previously identified and putative homologs of poxvirus host range genes, and updated these data with deposited sequences of new poxvirus genomes. Overall, the term host range genes might not be the most appropriate for these genes, since no correlation between them and the viruses’ host spectrum was observed, and a change in nomenclature should be considered. Finally, we analyzed the evolutionary history of these genes, and reaffirmed the occurrence of horizontal gene transfer (HGT) for certain elements, as previously suggested. Considering the data presented in this study, it is not possible to associate the diversity of host range factors with the amount of hosts of known poxviruses, and this traditional nomenclature creates misunderstandings.
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The evolution of seasonal influenza viruses

The evolution of seasonal influenza viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Despite decades of surveillance and pharmaceutical and non-pharmaceutical interventions, seasonal influenza viruses continue to cause epidemics around the world each year. The key process underlying these recurrent epidemics is the evolution of the viruses to escape the immunity that is induced by prior infection or vaccination. Although we are beginning to understand the processes that underlie the evolutionary dynamics of seasonal influenza viruses, the timing and nature of emergence of new virus strains remain mostly unpredictable. In this Review, we discuss recent advances in understanding the molecular determinants of influenza virus immune escape, sources of evolutionary selection pressure, population dynamics of influenza viruses and prospects for better influenza virus control.
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Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization

Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary We determined the binding sites of six novel human norovirus specific Nanobodies (Nano-4, Nano-14, Nano-26, Nano-27, Nano-32, and Nano-42) using X-ray crystallography. The unique Nanobody recognition epitopes were correlated with their potential neutralizing capacities. We showed that one Nanobody (Nano-26) bound numerous genogroup II genotypes and interacted with highly conserved capsid residues. Four Nanobodies (Nano-4, Nano-26, Nano-27, and Nano-42) bound to occluded regions on the intact particles and impaired normal capsid morphology and particle integrity. One Nanobody (Nano-14) bound contiguous to the HBGA pocket and interacted with several residues involved in binding HBGAs. We found that the Nanobodies delivered multiple inhibition mechanisms, which included steric obstruction, allosteric interference, and disruption of the capsid stability. Our data suggested that the HBGA pocket might not be an ideal target for drug development, since the surrounding region is highly variable and inherently suffers from lack of conservation among the genetically diverse genotypes. Instead, we showed that the capsid contained other highly susceptible regions that could be targeted for virus inhibition.
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CGDV: a webtool for circular visualization of genomics and transcriptomics data

CGDV: a webtool for circular visualization of genomics and transcriptomics data | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along with user defined karyotypes. Circular plot provides holistic visualization of high throughput large scale data but it is very complex and challenging to generate as most of the available tools need informatics expertise to install and run them. We have developed CGDV (Circos for Genomics and Transcriptomics Data Visualization), a webtool based on Circos, for seamless and automated visualization of a variety of large scale genomics and transcriptomics data. CGDV takes output of analyzed genomics or transcriptomics data of different formats, such as vcf, bed, xls, tab limited matrix text file, CNVnator raw output and Gene fusion raw output, to plot circular view of the sample data. CGDV take cares of generating intermediate files required for circos. CGDV is freely available at
https://cgdv-upload.persistent.co.in/cgdv/

. The circular plot for each data type is tailored to gain best biological insights into the data. The inter-relationship between data points, homologous sequences, genes involved in fusion events, differential expression pattern, sequencing depth, types and size of variations and enrichment of DNA binding proteins can be seen using CGDV. CGDV thus helps biologists and bioinformaticians to visualize a variety of genomics and transcriptomics data seamlessly.
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Ten simple rules for writing a response to reviewers

Ten simple rules for writing a response to reviewers | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Advice for publishing research papers
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A Method for the Acute and Rapid Degradation of Endogenous Proteins

A Method for the Acute and Rapid Degradation of Endogenous Proteins | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Methods for the targeted disruption of protein function have revolutionized science and greatly expedited the systematic characterization of genes. Two main approaches are currently used to disrupt protein function: DNA knockout and RNA interference, which act at the genome and mRNA level, respectively. A method that directly alters endogenous protein levels is currently not available. Here, we present Trim-Away, a technique to degrade endogenous proteins acutely in mammalian cells without prior modification of the genome or mRNA. Trim-Away harnesses the cellular protein degradation machinery to remove unmodified native proteins within minutes of application. This rapidity minimizes the risk that phenotypes are compensated and that secondary, non-specific defects accumulate over time. Because Trim-Away utilizes antibodies, it can be applied to a wide range of target proteins using off-the-shelf reagents. Trim-Away allows the study of protein function in diverse cell types, including non-dividing primary cells where genome- and RNA-targeting methods are limited.
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Reference-guided de novo assembly approach improves genome reconstruction for related species

Reference-guided de novo assembly approach improves genome reconstruction for related species | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.
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Namibia Gets Over U.S. $30 Million War Chest to Fight HIV

Namibia Gets Over U.S. $30 Million War Chest to Fight HIV | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Namibia has signed an amendment to the 2007 bilateral grant agreement with the USA to add N$435 million of funding under the US government's President's Emergency Plan for AIDS Relief (PEPFAR), to help fight against the HIV/AIDS pandemic.

Via Ed Rybicki
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The enigmatic archaeal virosphere

The enigmatic archaeal virosphere | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus–host interactions, including interactions with archaeal CRISPR–Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.


Via Ed Rybicki
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A Next-Generation Sequencing Approach Uncovers Viral Transcripts Incorporated in Poxvirus Virions

A Next-Generation Sequencing Approach Uncovers Viral Transcripts Incorporated in Poxvirus Virions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus. Our results revealed the incorporation of 19 viral transcripts, while host identifications were restricted to ribosomal and mitochondrial RNA. Most viral transcripts had an unknown and immunomodulatory function, suggesting that transcript incorporation may be beneficial for poxvirus immune evasion. Notably, the most abundant transcript originated from the D5L/I1R gene that encodes a viral inhibitor of the host cytoplasmic DNA sensing machinery.
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ViraPipe: Scalable Parallel Pipeline for Viral Metagenome Analysis from Next Generation Sequencing Reads.

ViraPipe is Apache Spark based pipeline for performing metagenome analysis from NGS read data in a computing cluster. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De Novo assembler, and BLAST and HMMER3 sequence search tools.
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Ten simple rules for structuring papers

Ten simple rules for structuring papers | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper’s contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and are typically untrained in paper writing. Focusing on how readers consume information, we present a set of ten simple rules to help you communicate the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.
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Life’s First Molecule Was Protein, Not RNA, New Model Suggests 

Life’s First Molecule Was Protein, Not RNA, New Model Suggests  | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Which mattered first at the dawn of life: proteins or nucleic acids? Proteins may have had the edge if a theorized process let them grow long enough to become self-replicating catalysts. 


Via Integrated DNA Technologies, Kenzibit
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Detecting positive selection in the genome

Detecting positive selection in the genome | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Population geneticists have long sought to understand the contribution of natural selection to molecular evolution. A variety of approaches have been proposed that use population genetics theory to quantify the rate and strength of positive selection acting in a species’ genome. In this review we discuss methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data. We also discuss recently proposed methods to detect positive selection from a population’s haplotype structure. The application of these tests has resulted in the detection of pervasive adaptive molecular evolution in multiple species.
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The future of DNA sequencing

The future of DNA sequencing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Eric D. Green, Edward M. Rubin and Maynard V. Olson speculate on the next forty years of the applications, from policing to data storage.
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Evolution of drug-resistant bacteria never exposed to antibiotics

Evolution of drug-resistant bacteria never exposed to antibiotics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Antibiotic-resistant microbes are a huge problem in human and global health. One of the microbial characteristics that allows development o
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Key challenges in bringing CRISPR-mediated somatic cell therapy into the clinic

Genome editing using clustered regularly interspersed short palindromic repeats (CRISPR) and CRISPR-associated proteins offers the potential to facilitate safe and effective treatment of genetic diseases refractory to other types of intervention. Here, we identify some of the major challenges for clinicians, regulators, and human research ethics committees in the clinical translation of CRISPR-mediated somatic cell therapy.
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