Parallelism in gene assemby (bibtex)
by Harju, Tero, Li, Chang, Petre, Ion and Rozenberg, Grzegorz
Abstract:
The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked lists data structure. Three molecular operations ($mld,mhi$, and $mdlad$) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern; or how many steps are needed to assemble (in parallel) a micronuclear gene. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.
Reference:
Parallelism in gene assemby (Harju, Tero, Li, Chang, Petre, Ion and Rozenberg, Grzegorz), In Natural Computing, Springer, volume 5, 2006.
Bibtex Entry:
@Article{j17,
  author    = {Harju, Tero AND Li, Chang AND Petre, Ion AND Rozenberg, Grzegorz},
  title     = {Parallelism in gene assemby},
  journal   = {Natural Computing},
  year      = {2006},
  volume    = {5},
  number    = {2},
  pages     = {203-223},
  abstract  = {The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked lists data structure. Three molecular operations ($mld,mhi$, and $mdlad$) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern; or how many steps are needed to assemble (in parallel) a micronuclear gene. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.},
  pdf       = {pdfs/HLPR2006b.pdf},
  publisher = {Springer},
}
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