Viruses and Bioinformatics from Virology.uvic.ca
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Genome Biology | The Transcription Factor Encyclopedia

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration.
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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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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
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Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Structure of the immature Zika virus at 9 A resolution : Nature Structural & Molecular Biology : Nature Research

Structure of the immature Zika virus at 9 A resolution : Nature Structural & Molecular Biology : Nature Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The cryo-EM structure of immature Zika virus shows partially ordered capsid proteins and reveals differences between pre-epidemic and epidemic strains at protein interfaces within the trimeric spikes.
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Historical Perspective: What Constitutes Discovery (of a New Virus)? - PubMed - NCBI

Historical Perspective: What Constitutes Discovery (of a New Virus)? - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A historic review of the discovery of new viruses leads to reminders of traditions that have evolved over 118 years. One such tradition gives credit for the discovery of a virus to the investigator(s) who not only carried out the seminal experiments but also correctly interpreted the findings (within the technological context of the day). Early on, ultrafiltration played a unique role in "proving" that an infectious agent was a virus, as did a failure to find any microscopically visible agent, failure to show replication of the agent in the absence of viable cells, thermolability of the agent, and demonstration of a specific immune response to the agent so as to rule out duplicates and close variants. More difficult was "proving" that the new virus was the etiologic agent of the disease ("proof of causation")-for good reasons this matter has been revisited several times over the years as technologies and perspectives have changed. One tradition is that the discoverers get to name their discovery, their new virus (unless some grievous convention has been broken)-the stability of these virus names has been a way to honor the discoverer(s) over the long term. Several vignettes have been chosen to illustrate several difficulties in holding to the traditions (vignettes chosen include vaccinia and variola viruses, yellow fever virus, and influenza viruses. Crimean-Congo hemorrhagic fever virus, Murray Valley encephalitis virus, human immunodeficiency virus 1, Sin Nombre virus, and Ebola virus). Each suggests lessons for the future. One way to assure that discoveries are forever linked with discoverers would be a permanent archive in one of the universal virus databases that have been constructed for other purposes. However, no current database seems ideal-perhaps members of the global community of virologists will have an ideal solution.

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Can we replace curation with information extraction software?

Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are too high to replace professional curation today. Furthermore, current IEP programs extract single narrow slivers of information, such as individual protein interactions; they cannot extract the large breadth of information extracted by professional curators for databases such as EcoCyc. They also cannot arbitrate among conflicting statements in the literature as curators can. Therefore, funding agencies should not hobble the curation efforts of existing databases on the assumption that a problem that has stymied Artificial Intelligence researchers for more than 60 years will be solved tomorrow. Semi-automated extraction techniques appear to have significantly more potential based on a review of recent tools that enhance curator productivity. But a full cost-benefit analysis for these tools is lacking. Without such analysis it is possible to expend significant effort developing information-extraction tools that automate small parts of the overall curation workflow without achieving a significant decrease in curation costs.
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Gilbert C FAURE's curator insight, January 13, 4:05 AM
curation is curation and curation?
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Xenolog classification

Orthology analysis is a fundamental tool in comparative genomics. Sophisticated methods have been developed to distinguish between orthologs and paralogs and to classify paralogs into subtypes depending on the duplication mechanism and timing, relative to speciation. However, no comparable framework exists for xenologs: gene pairs whose history, since their divergence, includes a horizontal transfer. Further, the diversity of gene pairs that meet this broad definition calls for classification of xenologs with similar properties into subtypes.
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A Peek Inside the Strange World of Fake Academia

A Peek Inside the Strange World of Fake Academia | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Sham scholarly publications and academic conferences without rigor reflect a legitimate problem: too many Ph.D.-holders chasing too few credentials.
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Rapid and sensitive point-of-care detection of Orthopoxviruses by ABICAP immunofiltration

Rapid and sensitive point-of-care detection of Orthopoxviruses by ABICAP immunofiltration | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The rapid and reliable detection of infectious agents is one of the most challenging tasks in scenarios lacking well-equipped laboratory infrastructure, like diagnostics in rural areas of developing countries. Commercially available point-of-care diagnostic tests for emerging and rare diseases are particularly scarce. In this work we present a point-of-care test for the detection of Orthopoxviruses (OPV). The OPV ABICAP assay detects down to 1 × 104 plaque forming units/mL of OPV particles within 45 min. It can be applied to clinical material like skin crusts and detects all zoonotic OPV infecting humans, including Vaccinia, Cowpox, Monkeypox, and most importantly Variola virus. Given the high sensitivity and the ease of handling, the novel assay could be highly useful for on-site diagnostics of suspected Monkeypox virus infections in areas lacking proper laboratory infrastructure as well as rapid on-site testing of suspected bioterrorism samples.
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Friday Action Item: Have a science conversation with a non-scientist

Friday Action Item: Have a science conversation with a non-scientist | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
In the wake of the recent U.S. election, we’ve started these “Friday Action Item” posts with ideas about specific things you can do to support science — from calling Congres…
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Calling out fake medical journals that exist to promote acupuncture

Calling out fake medical journals that exist to promote acupuncture | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Comic strip by Rudis Muiznecks, cectic.com Fake news has been in the news a lot lately. Fake news proliferated wildly during the 201
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New tools to analyze overlapping coding regions

New tools to analyze overlapping coding regions | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We generalize the notion of codon preference index (CPI) to overlapping coding regions, and use RNAsampleCDS to generate control sequences required in the computation of CPI for the Gag-Pol overlapping coding region of HIV-1. These applications show that RNAsampleCDS constitutes a unique tool in the software arsenal now available to evolutionary biologists. Source code for the programs and additional data are available at
http://bioinformatics.bc.edu/clotelab/RNAsampleCDS/

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A Multicomponent Animal Virus Isolated from Mosquitoes

A Multicomponent Animal Virus Isolated from Mosquitoes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Multicomponent viruses, which separately package different genome segments, were thought
to be restricted to plant and fungal hosts. Ladner et al. characterize a multicomponent
mosquito virus and describe an evolutionarily related, segmented virus in a nonhuman
primate. These findings provide evidence for multicomponent animal viruses and suggest
relevance to animal health.
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Genetically engineered mosquitos resist dengue fever virus

Genetically engineered mosquitos resist dengue fever virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Dengue has represented a significant public health burden for a number of decades. Given the lack of dengue-specific drugs and limited availability of licensed vaccine, new methods for prevention and control are urgently needed. Researchers investigated whether genetic manipulation of the mosquitoes' native JAK/STAT pathway-mediated anti-DENV defense system could be used to render mosquitoes more…
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Ten Simple Rules for Developing Usable Software in Computational Biology

Ten Simple Rules for Developing Usable Software in Computational Biology | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development. - PubMed - NCBI

Modified Vaccinia Virus Ankara: History, Value in Basic Research, and Current Perspectives for Vaccine Development. - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Safety tested Modified Vaccinia virus Ankara (MVA) is licensed as third-generation vaccine against smallpox and serves as a potent vector system for development of new candidate vaccines against infectious diseases and cancer. Historically, MVA was developed by serial tissue culture passage in primary chicken cells of vaccinia virus strain Ankara, and clinically used to avoid the undesirable side effects of conventional smallpox vaccination. Adapted to growth in avian cells MVA lost the ability to replicate in mammalian hosts and lacks many of the genes orthopoxviruses use to conquer their host (cell) environment. As a biologically well-characterized mutant virus, MVA facilitates fundamental research to elucidate the functions of poxvirus host-interaction factors. As extremely safe viral vectors MVA vaccines have been found immunogenic and protective in various preclinical infection models. Multiple recombinant MVA currently undergo clinical testing for vaccination against human immunodeficiency viruses, Mycobacterium tuberculosis or Plasmodium falciparum. The versatility of the MVA vector vaccine platform is readily demonstrated by the swift development of experimental vaccines for immunization against emerging infections such as the Middle East Respiratory Syndrome. Recent advances include promising results from the clinical testing of recombinant MVA-producing antigens of highly pathogenic avian influenza virus H5N1 or Ebola virus. This review summarizes our current knowledge about MVA as a unique strain of vaccinia virus, and discusses the prospects of exploiting this virus as research tool in poxvirus biology or as safe viral vector vaccine to challenge existing and future bottlenecks in vaccinology.

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Oral Immunization with Recombinant Vaccinia Virus Prime and Intramuscular Protein Boost Provides Protection against Intrarectal Simian-Human Immuno... - PubMed - NCBI

Clin Vaccine Immunol. 2015 Dec 30;23(3):204-12. doi: 10.1128/CVI.00597-15. Research Support, N.I.H., Extramural
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HiSeq move over, here comes Nova! A first look at Illumina NovaSeq

So Illumina has announced the next revolution of sequencers-- the NovaSeq.

Read an opinion here: "Illumina have announced NovaSeq, an entirely new sequencing system that completely disrupts their existing HiSeq user-base.  In my opinion, if you have a HiSeq and you are NOT currently engaged in planning to migrate to NovaSeq, then you will be out of business in 1-2 years time.  It’s not quite the death knell for HiSeqs, but it’s pretty close and moving to NovaSeq over the next couple of years is now the only viable option if you see Illumina as an important part of your offering."

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Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum

Despite the central place held by bioinformatics in modern life sciences and related areas, it has only recently been integrated to a limited extent into high-school teaching and learning programs. Here we describe the assessment of a learning environment entitled ‘Bioinformatics in the Service of Biotechnology’.... Analysis of students’ affective outcomes revealed positive attitudes toward bioinformatics and the learning environment, as well as their perception of the teacher’s role. Insights from this analysis yielded implications and recommendations for curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum.

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The Tweeted Times - personal newspaper generated from your Twitter account

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Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia

Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Biological invasions are a major threat to global biodiversity. Australia has experienced many invasive species, with the common carp (Cyprinus carpio L.) a prominent example. Cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biological control (biocontrol) agent for invasive carp in Australia. Safety and efficacy are critical factors in assessing the suitability of biocontrol agents, and extensive host-specificity testing suggests that CyHV-3 is safe. Efficacy depends on the relationship between virus transmissibility and virulence. Based on observations from natural outbreaks, as well as the biology of virus-host interactions, we hypothesize that (i) close contact between carp provides the most efficient transmission of virus, (ii) transmission occurs at regular aggregations of carp that favour recrudescence of latent virus, and (iii) the initially high virulence of CyHV-3 will decline following its release in Australia. We also suggest that the evolution of carp resistance to CyHV-3 will likely necessitate the future release of progressively more virulent strains of CyHV-3, and/or an additional broad-scale measure(s) to complement the effect of the virus. If the release of CyHV-3 does go ahead, longitudinal studies are required to track the evolution of a virus-host relationship from its inception, and particularly the complex interplay between transmission, virulence and host resistance.
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Prevalence and Genetic Diversity of Avipoxvirus in House Sparrows in Spain

Prevalence and Genetic Diversity of Avipoxvirus in House Sparrows in Spain | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Avipoxvirus (APV) is a fairly common virus affecting birds that causes morbidity and mortality in wild and captive birds. We studied the prevalence of pox-like lesions and genetic diversity of APV in house sparrows (Passer domesticus) in natural, agricultural and urban areas in southern Spain in 2013 and 2014 and in central Spain for 8 months (2012–2013). Overall, 3.2% of 2,341 house sparrows visually examined in southern Spain had cutaneous lesions consistent with avian pox. A similar prevalence (3%) was found in 338 birds from central Spain. Prevalence was higher in hatch-year birds than in adults. We did not detect any clear spatial or temporal patterns of APV distribution. Molecular analyses of poxvirus-like lesions revealed that 63% of the samples were positive. Molecular and phylogenetic analyses of 29 DNA sequences from the fpv167 gene, detected two strains belonging to the canarypox clade (subclades B1 and B2) previously found in Spain. One of them appears predominant in Iberia and North Africa and shares 70% similarity to fowlpox and canarypox virus. This APV strain has been identified in a limited number of species in the Iberian Peninsula, Morocco and Hungary. The second one has a global distribution and has been found in numerous wild bird species around the world. To our knowledge, this represents the largest study of avian poxvirus disease in the broadly distributed house sparrow and strongly supports the findings that Avipox prevalence in this species in South and central Spain is moderate and the genetic diversity low.
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A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses. - PubMed - NCBI

A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses. - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Virus Genes. 2016 Dec 20. doi: 10.1007/s11262-016-1416-9. [Epub ahead of print]
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A serendipitous demonstration of the power of social media in the classroom

A serendipitous demonstration of the power of social media in the classroom | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
“Social media is a waste of time”, “You should be writing grants”, “Spend more time at the bench and less time on Twitter” I don’t really want to wade into…
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Visualize metagenomes in a web browser

Visualize metagenomes in a web browser | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Quick visualization of coverage-GC profiles without installing additional software
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