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Life
Special Issues
Open Science Phyloinformatics: Resources, Methods, and Analyses 2021
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Open Science Phyloinformatics: Resources, Methods, and Analyses 2021

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 2852

Special Issue Editors

Dr. William H Piel

E-Mail Website
Guest Editor
Yale NUS College, Singapore City, Singapore
Interests: arachnology; phyloinformatics; phylogeny
Special Issues, Collections and Topics in MDPI journals
Dr. Rutger Vos

E-Mail Website
Guest Editor
Naturalis Biodiversity Center, Endless Forms group, Leiden, The Netherlands
Interests: comparative genomics; big data; computational biology; open source; emergent characters; phyloinformatics; comparative analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

Phylogenetic research, today, is increasingly complex and data-intensive, placing increased demands on effective data sharing, analytical reproducibility, and knowledge synthesis. Large trees, vast datasets, and long multi-step analysis pipelines demand that biologists follow best practices in open access, sharing, and data integration.

This Special Issue aims to assemble articles on phyloinformatic resources, tools, and research reports that exemplify best practices supporting open science reproducibility and/or demonstrate inference of broad-scale patterns through the integration of large datasets in phylogenetics.

Dr. William H Piel
Dr. Rutger Vos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phyloinformatics
  • phylogenomics
  • phylogenetics
  • open science
  • data integration
  • assembling the Tree of Life (AToL)

Published Papers (1 paper)

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Research

15 pages, 3896 KiB  
Article
Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus
by Kevin Nicolas Calderon, Johan Fabian Galindo and Clara Isabel Bermudez-Santana
Life 2021, 11(4), 344; https://doi.org/10.3390/life11040344 - 14 Apr 2021
Cited by 1 | Viewed by 2441
Abstract
Zika virus (ZIKV), without a vaccine or an effective treatment approved to date, has globally spread in the last century. The infection caused by ZIKV in humans has changed progressively from mild to subclinical in recent years, causing epidemics with greater infectivity, tropism [...] Read more.
Zika virus (ZIKV), without a vaccine or an effective treatment approved to date, has globally spread in the last century. The infection caused by ZIKV in humans has changed progressively from mild to subclinical in recent years, causing epidemics with greater infectivity, tropism towards new tissues and other related symptoms as a product of various emergent ZIKV–host cell interactions. However, it is still unknown why or how the RNA genome structure impacts those interactions in differential evolutionary origin strains. Moreover, the genomic comparison of ZIKV strains from the sequence-based phylogenetic analysis is well known, but differences from RNA structure comparisons have barely been studied. Thus, in order to understand the RNA genome variability of lineages of various geographic distributions better, 410 complete genomes in a phylogenomic scanning were used to study the conservation of structured RNAs. Our results show the contemporary landscape of conserved structured regions with unique conserved structured regions in clades or in lineages within circulating ZIKV strains. We propose these structures as candidates for further experimental validation to establish their potential role in vital functions of the viral cycle of ZIKV and their possible associations with the singularities of different outbreaks that lead to ZIKV populations to acquire nucleotide substitutions, which is evidence of the local structure genome differentiation. Full article
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses 2021)
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