Campo Grande, October 19, 2017
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Jens Stoye

Bielefeld University, Germany

 

 

 

 

 

 

Jens Stoye is a professor for Genome Informatics at the Faculty of Technology, Bielefeld University, Germany. His research interest is the development of algorithms and software for the analysis of genomic and post-genomic data in molecular biology and evolution, from the low level of DNA sequence comparison up to the higher levels of comparative genomics, metagenomics and phylogenetics. Dr. Stoye is an Associate Editor for the IEEE/ACM Transactions on Computational Biology and Bioinformatics and for BMC Bioinformatics. He has been a member of many conference program committees, including co-chairing the German Conference on Bioinformatics (GCB 2004) and the Annual Symposium on Combinatorial Pattern Matching (CPM 2012).
 

Title

Genome Rearrangement by Double Cut and Join

Abstract

Genome evolution on the basis of gene order has been modeled by a variety of rearrangement operations such as inversions, translocations, transpositions, block interchanges, fusions and fissions. The double cut and join (DCJ) operation, introduced by Yancopoulos et al. (2005), allows to model all these classical operations while allowing for very simple algorithms, compared to earlier ones for more restricted models.

We will present several of our results related to genome rearrangement based on the DCJ model: calculation of the distance between two genomes, construction of an optimal scenario transforming one genome into another one, and counting and sampling from the set of all optimal rearrangement scenarios. We will also show how, by small adaptations, other rearrangement distances can be computed easily based on the DCJ model. Finally, we will discuss generalizations for cases where the genomes under study do not have the same gene content. This setting also raises some interesting mathematical modeling questions about the weight of insertions and deletions in genomic distances.

This is joint work with Anne Bergeron, Marília D. V. Braga, Paul Medvedev, Julia Mixtacki, and Eyla Willing.

 

Organization

  • Faculdade de Computação - UFMS
  • UFMS
  • Embrapa Gado de Corte
  • Fundect
  • Museu das Culturas Dom Bosco

Promotion

  • SBC