Special Issue "Genomes and Evolution: Computational Approaches"


A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: 31 July 2014

Special Issue Editors

Guest Editor
Prof. Dr. Rainer Breitling
Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
Website: http://www.ls.manchester.ac.uk/research/researchgroups/computationalandevolutionarybiology/people/?alias=breitlingr
E-Mail: rainer.breitling@manchester.ac.uk
Phone: +44 (0)141 306 5117
Interests: computational systems biology; bioinformatics; metabolomics; dynamic modelling; synthetic biology

Guest Editor
Dr. Marnix Medema
MPI for Marine Microbiology, Celciusstraße 1, 28359 Bremen, Germany
E-Mail: mhmedema@mpi-bremen.de
Phone: +49 421 202 8984

Special Issue Information

Dear Colleagues,

The computational analysis of gene and genome sequences has become a key methodology for understanding the function and evolution of biological systems. Often, descriptions of specific computational methods that have led to exciting research results are discussed only briefly, or relegated to the supplementary information of the papers describing them. Yet, many of these methods merit a more thorough discussion of the key concepts on which they are based, and of the possible further opportunities for exploiting these methods in other contexts. This Special Issue aims to offer a platform for explaining, discussing and contextualizing important computational methods and algorithms. Such methods can assist other scientists researching the evolutionary history of gene and genome sequences and such genes’ biological functions.

Specific topics include, but are not limited to:

  • Methods for tracing the evolutionary history of genome sequences, including, for example, the dynamics of introns and transposons, as well as duplication, recombination, and horizontal transfer events
  • Methods for improving (meta)genome assembly by employing evolutionary information
  • Phylogenetic methods for evaluating evolutionary relationships between genes and genomes
  • Algorithms for studying patterns in amino acid sequences and/or protein structure evolution
  • Tools for automating the annotation of genomes or genomic regions according to function
  • Algorithms or pipelines for identifying mutations from high-throughput sequencing experiments
  • Pipelines for evaluating the outcome of next-generation sequence assemblies
  • Methods for evaluating the evolutionary similarity of genes, gene clusters, genomes, pan-genomes or metagenomes
  • Models and tools for simulating, predicting or otherwise evaluating the evolution of genome-based metabolic or regulatory networks from a systems biology perspective

Prof. Dr. Rainer Breitling
Dr. Marnix Medema
Guest Editors


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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Computation is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


  • bioinformatics
  • computational biology
  • evolution
  • systems biology
  • algorithms
  • comparative genomics
  • phylogeny
  • sequence analysis
  • metagenomics

Published Papers

No papers have been published in this special issue yet.

Last update: 10 December 2013

Computation EISSN 2079-3197 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert