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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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Shedding poliovirus for 28 years

An immunodeficient individual has been excreting poliovirus in his stool for 28 years. Such chronic excreters pose a threat to the poliovirus eradication program.

Via Mel Melendrez-Vallard
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Development of high-yield influenza A virus vaccine viruses.

Development of high-yield influenza A virus vaccine viruses. | Virology and Bioinformatics from Virology.ca | Scoop.it
Nat Commun. 2015 Sep 2;6:8148. doi: 10.1038/ncomms9148.
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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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Rescooped by Chris Upton + helpers from Emerging Viruses, Virus Discovery and Virus Characterization
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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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Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints

by October M. Sessions, Andreas Wilm, Uma Sangumathi Kamaraj, Milly M. Choy, Angelia Chow, Yuwen Chong, Xin Mei Ong, Niranjan Nagarajan, Alex R.

Via Mel Melendrez-Vallard
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Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification http://t.co/Q6w9k48F9N

Via Mel Melendrez-Vallard
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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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Rakesh Yashroy's curator insight, Today, 11:49 AM

Every living organism has an enemy threatening its existence. What is  the threat to bacteriophages? Any reply!#@?

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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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