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Viral Metagenomics

Overview of attention for book
Cover of 'Viral Metagenomics'

Table of Contents

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    Book Overview
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    Chapter 1 Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics
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    Chapter 2 Small RNA Isolation from Tissues of Grapevine and Woody Plants
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    Chapter 3 Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
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    Chapter 4 Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing
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    Chapter 5 Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
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    Chapter 6 Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples
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    Chapter 7 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities
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    Chapter 8 Different Approaches to Discover Mycovirus Associated to Marine Organisms
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    Chapter 9 Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections
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    Chapter 10 The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
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    Chapter 11 High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing
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    Chapter 12 Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
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    Chapter 13 DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method
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    Chapter 14 From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
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    Chapter 15 Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
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    Chapter 16 Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches
Attention for Chapter 15: Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (75th percentile)
  • Average Attention Score compared to outputs of the same age and source

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11 tweeters

Citations

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Chapter title
Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
Chapter number 15
Book title
Viral Metagenomics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7683-6_15
Pubmed ID
Book ISBNs
978-1-4939-7682-9, 978-1-4939-7683-6
Authors

Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Masoud Shams-bakhsh, Walter Pirovano, Vitantonio Pantaleo

Abstract

Next-generation sequencing has opened the door to the reconstruction of viral populations and examination of the composition of mutant spectra in infected cells, tissues, and host organisms. In this chapter we present details on the use of the Shannon entropy method to estimate the site-specific nucleotide relative variability of turnip crinkle virus, a positive (+) stranded RNA plant virus, in a large dataset of short RNAs of Cicer arietinum L., a natural reservoir of the virus. We propose this method as a viral metagenomics tool to provide a more detailed description of the viral quasispecies in infected plant tissue. Viral replicative fitness relates to an optimal composition of variants that provide the molecular basis of virus behavior in the complex environment of natural infections. A complete description of viral quasispecies may have implications in determining fitness landscapes for host-virus coexistence and help to design specific diagnostic protocols and antiviral strategies.

Twitter Demographics

The data shown below were collected from the profiles of 11 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 12 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 42%
Student > Ph. D. Student 3 25%
Professor > Associate Professor 2 17%
Professor 1 8%
Unknown 1 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 42%
Biochemistry, Genetics and Molecular Biology 2 17%
Environmental Science 1 8%
Veterinary Science and Veterinary Medicine 1 8%
Immunology and Microbiology 1 8%
Other 0 0%
Unknown 2 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 8. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 February 2019.
All research outputs
#3,647,682
of 21,190,873 outputs
Outputs from Methods in molecular biology
#908
of 11,951 outputs
Outputs of similar age
#71,433
of 294,198 outputs
Outputs of similar age from Methods in molecular biology
#4
of 5 outputs
Altmetric has tracked 21,190,873 research outputs across all sources so far. Compared to these this one has done well and is in the 82nd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 11,951 research outputs from this source. They receive a mean Attention Score of 3.3. This one has done particularly well, scoring higher than 92% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 294,198 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 75% of its contemporaries.
We're also able to compare this research output to 5 others from the same source and published within six weeks on either side of this one.