Special Issue "Tools for Population and Evolutionary Genetics"
Deadline for manuscript submissions: 31 July 2019
In recent years, the development of next generation sequencing techniques has fueled an explosion in the pace at which genomic data sets are generated, while dramatically decreasing the costs of genome sequencing. Comparison of these datasets can uncover remarkable information about the evolution of organisms. The availability of datasets of ever-increasing size and complexity has resulted in a growing need for computational tools that allow their effective and efficient analysis.
This special issue focuses on tools for population and evolutionary genetics, including, but not limited to, bioinformatics approaches, and computational tools, algorithms and resources. We welcome submissions of reviews, research articles, and short communications. We also encourage the submission of manuscripts describing new tools, in the form of “concept papers”.
Dr. David Alvarez-Ponce
Dr. Julie M. Allen
Dr. Won C. Yim
Dr. Marco Fondi
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 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. 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 1600 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.
- Comparative Genomics
- Population genomics
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
1) Tentative Title: R package for data mining and analysis of the GWAS catalog
Tentative Abstract: An R script will be provided to extract useful information from the GWAS catalog and carry out analyses such as obtaining distributions of SNP frequencies and effects, contributions to heritability, ascertaining the level of pleiotropy of variants, analysis of the genomic position of SNPs and correlation between traits for SNP positions and effects.
Authors: Eugenio López-Cortegano and Armando Caballero*
2) Tentative Title: Bayesian inference for agent-based epidemiological population simulations
Tentative Abstract: Computer simulation is a generally used tool in modeling infectious diseases, offering extensive exibility by avoiding the limitations of analytical tractability. For example, common factors such as heterogenous mixing and population structure can be efficiently taken into account by using agent-based simulations. The trade-off arising from eschewing analytically tractable models is the increased difficulty in parameter estimation. Approximate Bayesian Computation (ABC) provides a principled approach to inferring model parameters from computer simulations, however, due to its computational complexity it has not yet been widely applied to agent-based simulators. Using the latest advances in ABC inference utilizing Bayesian optimization and automated parallelization, we develop a Python software module embedded in ELFI for inferring parameters in models implemented in the generic epidemiological population modeling platform EMOD. Analysing emerging infectious disease outbreaks presents a particularly challenging statistical problem due to the limited amount of observational data and the complex relationships between key epidemiological parameters and latent variables, such as the basic reproduction number, growth rate, incubation times and case fatality rates. To demonstrate the usefulness of our software we present a case study of using EMOD and ELFI to analyze the 2014-2015 Ebola outbreak.
Authors: Kusti Skytén, Jukka Corander*
3) Tentative Title: PanGloss a tool for Pan-genome analysis of microbial Eukaryotes
Tentative Abstract: The concept of the species “pan-genome”, the union of “core” conserved genes and all “accessory” non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously-published prokaryote methodology based on sequence homology and conserved microsynteny we have developed a bespoke pipelines to investigate the the pan-genomes of a number of fungal species. Our initial analyses show that between 80-90% of gene models per strain in each species are core genes that are highly-conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species the remaining “accessory” gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance.
Authors: Charley McCarthy, David Fitzpatrick*