---
res:
  bibo_abstract:
  - "Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous mechanisms
    including horizontal gene transfer and recombination via numerous flanking repeats.
    Genome rearrangements such as inversions, deletions, insertions and duplications
    may independently occur in different strains, providing parallel adaptation or
    phenotypic diversity. Specifically, such rearrangements might be responsible for
    virulence, antibiotic resistance and antigenic variation. However, identification
    of such events requires laborious manual inspection and verification of phyletic
    pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’
    as events that occur independently in phylogenetically distant bacterial strains
    and present a formalization of the problem of parallel rearrangements calling.
    We implement an algorithmic solution for the identification of parallel rearrangements
    in bacterial populations as a tool PaReBrick. The tool takes a collection of strains
    represented as a sequence of oriented synteny blocks and a phylogenetic tree as
    input data. It identifies rearrangements, tests them for consistency with a tree,
    and sorts the events by their parallelism score. The tool provides diagrams of
    the neighbors for each block of interest, allowing the detection of horizontally
    transferred blocks or their extra copies and the inversions in which copied blocks
    are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its
    potential to detect genome rearrangements responsible for pathogenicity and adaptation
    in bacterial genomes.@eng"
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Alexey
      foaf_name: Zabelkin, Alexey
      foaf_surname: Zabelkin
  - foaf_Person:
      foaf_givenName: Yulia
      foaf_name: Yakovleva, Yulia
      foaf_surname: Yakovleva
  - foaf_Person:
      foaf_givenName: Olga
      foaf_name: Bochkareva, Olga
      foaf_surname: Bochkareva
      foaf_workInfoHomepage: http://www.librecat.org/personId=C4558D3C-6102-11E9-A62E-F418E6697425
    orcid: 0000-0003-1006-6639
  - foaf_Person:
      foaf_givenName: Nikita
      foaf_name: Alexeev, Nikita
      foaf_surname: Alexeev
  bibo_doi: 10.1093/bioinformatics/btab691
  bibo_issue: '2'
  bibo_volume: 38
  dct_date: 2022^xs_gYear
  dct_identifier:
  - UT:000743380100008
  dct_isPartOf:
  - http://id.crossref.org/issn/1367-4803
  - http://id.crossref.org/issn/1460-2059
  dct_language: eng
  dct_publisher: Oxford University Press@
  dct_title: 'PaReBrick: PArallel REarrangements and BReaks identification toolkit@'
...