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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.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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Virology and Bioinformatics from Virology.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: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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LayerCake: a tool for the visual comparison of viral deep sequencing data

LayerCake: a tool for the visual comparison of viral deep sequencing data | Virology and Bioinformatics from Virology.ca | Scoop.it
#bioinformatics LayerCake: a tool for the visual comparison of viral deep sequencing data http://t.co/UwqNy7B4Zq
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University of Pennsylvania: The Role of Bioinformatics in Precision Medicine

University of Pennsylvania: The Role of Bioinformatics in Precision Medicine | Virology and Bioinformatics from Virology.ca | Scoop.it
In this video, Jason Moore, PhD, outlines the role of bioinformatics as a component of precision medicine and its valuable part in the diagnosis and treatment choices for patients with serious disease.
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From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data | Virology and Bioinformatics from Virology.ca | Scoop.it
RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS).
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Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features.

BMC Bioinformatics. 2014 Dec 10;15:363. doi: 10.1186/s12859-014-0363-5. Comparative Study; Research Support, Non-U.S. Gov't
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A virus that made us sick that we don't even know about

A virus that made us sick that we don't even know about | Virology and Bioinformatics from Virology.ca | Scoop.it
Many infections are never diagnosed. We never know which virus or bacteria caused the illness - especially with colds and coughs. Thing is, until 2001, we didn't even know we all came down with Metapneumovirus.
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Sierra Leone News : Ebola Breaks Out in a Remote Tonko Limba Village: Sierra Leone News


Via Ian M Mackay, PhD
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How Methods Videos Are Making Science Smarter

How Methods Videos Are Making Science Smarter | Virology and Bioinformatics from Virology.ca | Scoop.it
For some researchers, the most significant obstacle to the successful replication of experiments is the outdated text format of traditional journals.
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Ed Rybicki's curator insight, August 31, 12:40 PM

Yup, something I've been thinking about quite a lot - now just to DO it!!

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40 reasons why you should blog about your research

40 reasons why you should blog about your research | Virology and Bioinformatics from Virology.ca | Scoop.it
It helps you become more clear about your ideas. It gives you practice at presenting your ideas for a non-specialist audience. It increases your visibility within academia. It increases your visibi...
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Performance of the Xpert HPV assay in women attending for cervical screening

Performance of the Xpert HPV assay in women attending for cervical screening | Virology and Bioinformatics from Virology.ca | Scoop.it

This is the first study to report on the performance of the Xpert HPV Assay in a screening population.

 

Xpert HPV Assay׳s performance in detecting HPV is comparable to two clinically validated HPV tests.

 

Xpert HPV Assay showed a relative sensitivity of 98.73% for CIN 2 or higher and 100% for CIN3 or higher.

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Deep sequencing of HPV16 genomes

Deep sequencing of HPV16 genomes | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract

For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current “gold standard” of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%.

Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3–222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis.

  

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An Enhanced Synthetic Multiclade DNA Prime Induces Improved Cross-Clade-Reactive Functional Antibodies when Combined with an Adjuvanted Protein Boost in Nonhuman Primates

The search for an efficacious human immunodeficiency virus type 1 (HIV-1) vaccine remains a pressing need. The moderate success of the RV144 Thai clinical vaccine trial suggested that vaccine-induced HIV-1-specific antibodies can reduce the risk of HIV-1 infection. We have made several improvements to the DNA platform and have previously shown that improved DNA vaccines alone are capable of inducing both binding and neutralizing antibodies in small-animal models. In this study, we explored how an improved DNA prime and recombinant protein boost would impact HIV-specific vaccine immunogenicity in rhesus macaques (RhM). After DNA immunization with either a single HIV Env consensus sequence or multiple constructs expressing HIV subtype-specific Env consensus sequences, we detected both CD4+ and CD8+ T-cell responses to all vaccine immunogens. These T-cell responses were further increased after protein boosting to levels exceeding those of DNA-only or protein-only immunization. In addition, we observed antibodies that exhibited robust cross-clade binding and neutralizing and antibody-dependent cellular cytotoxicity (ADCC) activity after immunization with the DNA prime-protein boost regimen, with the multiple-Env formulation inducing a more robust and broader response than the single-Env formulation. The magnitude and functionality of these responses emphasize the strong priming effect improved DNA immunogens can induce, which are further expanded upon protein boost. These results support further study of an improved synthetic DNA prime together with a protein boost for enhancing anti-HIV immune responses.

 
Ed Rybicki's insight:

You have to get to the abstract to find out it's for HIV...B-)

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Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus

The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus.

 
Ed Rybicki's insight:

My babies...B-) Refers both to the viruses - I helped name all of the original genera and the family - and two of the authors.

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Scientists Unearth a Trove of New Bacteria-Killing Viruses

Scientists Unearth a Trove of New Bacteria-Killing Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Bacteria prey on humans, but the bugs have to beware of their own predators, too: a special class of viruses called phages.
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BMC Bioinformatics | Breaking the computational barriers of pairwise genome comparison

Conventional pairwise sequence comparison software algorithms are being used to process much larger datasets than they were originally designed for.
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BMC Bioinformatics | Full text | A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples

Detecting and quantifying isoforms from RNA-seq data is an important but challenging task. The problem is often ill-posed, particularly at low coverage. One promising direction is to exploit several samples simultaneously.
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Evolutionary Relationship Between Existing Virus Families Mapped Out in a New Study

Evolutionary Relationship Between Existing Virus Families Mapped Out in a New Study | Virology and Bioinformatics from Virology.ca | Scoop.it
Oak Ridge, TN (Scicasts) — An Oak Ridge National Laboratory team of comparative genomics and computational science researchers compared approximately 4,000 complete virus genomes downloaded from a public database known as GenBank.
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A virus that made us sick that we don't even know about

A virus that made us sick that we don't even know about | Virology and Bioinformatics from Virology.ca | Scoop.it
Many infections are never diagnosed. We never know which virus or bacteria caused the illness - especially with colds and coughs. Thing is, until 2001, we didn't even know we all came down with Metapneumovirus.

Via Ed Rybicki
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50-plus years of fungal viruses

50-plus years of fungal viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Highlights
• Historical perspective of fungal virus research.
• Description, classification and diversity of fungal virus families.
• Structural features of fungal virus particles.
• Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.


Via Steve Marek, Niklaus Grunwald
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New microscope techniques give deepest view yet of living cells

New microscope techniques give deepest view yet of living cells | Virology and Bioinformatics from Virology.ca | Scoop.it
Two new microscopy techniques are helping scientists see smaller structures in living cells than ever glimpsed before.
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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Pathway-based visualization is particularly powerful since it enables one to analyze complex datasets within the context of actual biological processes and to elucidate how each change in a cell effects related processes. To facilitate such approaches, we present Escher, a web application that can be used to rapidly build pathway maps. On Escher maps, diverse datasets related to genes, reactions, and metabolites can be quickly contextualized within metabolism and, increasingly, beyond metabolism. Escher is available now for free use (under the MIT license) at https://escher.github.io .
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Potential additional benefit of a nine-valent second generation HPV vaccine

Potential additional benefit of a nine-valent second generation HPV vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
AbstractIntroduction

A second generation HPV vaccine has been developed for the prevention of anogenital cancers and precancerous lesions of the cervix, vulva, vagina, anus and of genital warts due to nine HPV types.

We estimated the annual burden of these diseases attributable to the nine HPV types compared to HPV types from first generation vaccines in women and men in Europe.

Material and methods

Incidence rates from the IARC database, cancer registries, the literature and Eurostat population data were used.

The burden attributable to the HPV types targeted by both vaccines was estimated by applying the relative contribution of the respective HPV types from epidemiological studies.

Results

In 2013, the number of new anogenital HPV-attributable cancers was 44,480 with 39,494 of these cases related to second vs. 33,285 to first generation vaccine types.

Among the 284,373 to 541,621 new HPV-attributable anogenital precancerous lesions 235,364–448,423 and 135,025–256,830 were estimated to be related to second and first generation vaccine types, respectively.

The annual number of new genital warts was 753,608–935,318, with 90% related to HPV6/11.

Conclusions

These data demonstrate how the large public health impact that was achieved by the first generation HPV vaccines could be further increased by second generation vaccines.

  
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Cloak and Dagger: Alternative Immune Evasion and Modulation Strategies of Poxviruses

Cloak and Dagger: Alternative Immune Evasion and Modulation Strategies of Poxviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
As all viruses rely on cellular factors throughout their replication cycle, to be successful they must evolve strategies to evade and/or manipulate the defence mechanisms employed by the host cell. In addition to their expression of a wide array of host modulatory factors, several recent studies have suggested that poxviruses may have evolved unique mechanisms to shunt or evade host detection. These potential mechanisms include mimicry of apoptotic bodies by mature virions (MVs), the use of viral sub-structures termed lateral bodies for the packaging and delivery of host modulators, and the formation of a second, “cloaked” form of infectious extracellular virus (EVs). Here we discuss these various strategies and how they may facilitate poxvirus immune evasion. Finally we propose a model for the exploitation of the cellular exosome pathway for the formation of EVs.
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Double-Stranded RNA Is Detected by Immunofluorescence Analysis

Early biochemical studies of viral replication suggested that most viruses produce double-stranded RNA (dsRNA), which is essential for the induction of the host immune response. However, it was reported in 2006 that dsRNA could be detected by immunofluorescence antibody staining in double-stranded DNA and positive-strand RNA virus infections but not in negative-strand RNA virus infections. Other reports in the literature seemed to support these observations. This suggested that negative-strand RNA viruses produce little, if any, dsRNA or that more efficient viral countermeasures to mask dsRNA are mounted. Because of our interest in the use of dsRNA antibodies for virus discovery, particularly in pathological specimens, we wanted to determine how universal immunostaining for dsRNA might be in animal virus infections. We have detected the in situ formation of dsRNA in cells infected with vesicular stomatitis virus, measles virus, influenza A virus, and Nyamanini virus, which represent viruses from different negative-strand RNA virus families. dsRNA was also detected in cells infected with lymphocytic choriomeningitis virus, an ambisense RNA virus, and minute virus of mice (MVM), a single-stranded DNA (ssDNA) parvovirus, but not hepatitis B virus. Although dsRNA staining was primarily observed in the cytoplasm, it was also seen in the nucleus of cells infected with influenza A virus, Nyamanini virus, and MVM. Thus, it is likely that most animal virus infections produce dsRNA species that can be detected by immunofluorescence staining. The apoptosis induced in several uninfected cell lines failed to upregulate dsRNA formation.

 
Ed Rybicki's insight:

I love it when an old technique comes back: I remember hearing about use of Abs to dsRNA as far back as the early 1980s, and here it is back again - largely because of the improvement in microscopes and techniques for detecting immunoflourescence.  Nice one!  It'll have to find its way into my textbook....

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The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus

The multiplicity of cellular infection (MOI) is the number of virus genomes of a given virus species that infect individual cells. This parameter chiefly impacts the severity of within-host population bottlenecks as well as the intensity of genetic exchange, competition, and complementation among viral genotypes. Only a few formal estimations of the MOI currently are available, and most theoretical reports have considered this parameter as constant within the infected host. Nevertheless, the colonization of a multicellular host is a complex process during which the MOI may dramatically change in different organs and at different stages of the infection. We have used both qualitative and quantitative approaches to analyze the MOI during the colonization of turnip plants by Turnip mosaic virus. Remarkably, different MOIs were observed at two phases of the systemic infection of a leaf. The MOI was very low in primary infections from virus circulating within the vasculature, generally leading to primary foci founded by a single genome. Each lineage then moved from cell to cell at a very high MOI. Despite this elevated MOI during cell-to-cell progression, coinfection of cells by lineages originating in different primary foci is severely limited by the rapid onset of a mechanism inhibiting secondary infection. Thus, our results unveil an intriguing colonization pattern where individual viral genomes initiate distinct lineages within a leaf. Kin genomes then massively coinfect cells, but coinfection by two distinct lineages is strictly limited.

 
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Rabenstein, Frank's curator insight, September 1, 2:59 AM

A paper is of general interest.