Topical Collection "Genomic Databases"

Editor

Dr. Aureliano Bombarely
E-Mail Website
Guest Editor
Department of Biosciences, University of Milan (UNIMI), 20122 Milano MI, Italy
Interests: plant genomics; evolutionary genomics; polyploidy; bioinformatics; databases; sequence assembly; solanacea; domestication
Special Issues and Collections in MDPI journals

Topical Collection Information

The development of next-generation sequencing (NGS) at the beginning of 21st century has produced an incredible amount of sequencing data. The data have been used in a wide range of scientific studies, from the development of reference genomes to expression profiling of thousands of genes. Due to the data volume as well as the complexity of the data, they need special platforms in order to be efficiently managed and made accessible to the community.

There are different types of platforms, from gigantic genomic data repositories with little data curation such as GenBank, ENA or the Genome Sequence Archive to project-specific genomic databases with variable levels of data curation. The levels of data curation are one of the determining factors not only in the usability of these platforms, but also in how they meet the needs of the specific communities that they target. Most of these databases have associated popular tools with graphical interfaces, such as BLAST, Gbrowser and JBrowser. Others may have developed their specific set of tools to present data specifically linked to a project.

The goal of this collection is to present to the scientific community some genomic databases that have been developed in recent years.

In order to maximize the usability of the publications associated with the databases, we propose a “concept paper” format.

Dr. Aureliano Bombarely
Guest Editor

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 papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection 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. Genes 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 2000 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

  • genomics
  • databases
  • data curation
  • genomic data analysis

Published Papers (1 paper)

2020

Article
DetR DB: A Database of Ionizing Radiation Resistance Determinants
Genes 2020, 11(12), 1477; https://doi.org/10.3390/genes11121477 - 09 Dec 2020
Viewed by 869
Abstract
Nuclear pollution is an urgent environmental issue and is a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and [...] Read more.
Nuclear pollution is an urgent environmental issue and is a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and cost-saving way. At the same time, the number of known bacterial and archaeal species able to withstand extremely high doses of ionizing radiation (IR) is steadily growing every year, together with growing knowledge about mechanisms of radioresistance that opens up opportunities for developing new biotechnological solutions. However, these data are often not systemized, and can be difficult to access. Here, we present the Determinants of Radioresistance Database, or DetR DB, gathering a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced IR tolerance. The database provides search tools, including taxonomy, common gene name, and BLAST. DetR DB will be a useful tool for the research community by facilitating the extraction of the necessary information to help further analysis of radiation-resistant mechanisms. Full article
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