arXiv subjects

Hendrik Jan Hoogeboom

Publications and source records attributed to Hendrik Jan Hoogeboom.

22 records · Page 2Linked to original sources

arXiv2007

The Fibers and Range of Reduction Graphs in Ciliates

The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the notion of breakpoint graph in the theory of sorting by reversal, for legal strings provide valuable insights into the gene assembly process. We characterize which legal strings obtain the same reduction graph (up to isomorphism), and moreover we characterize which graphs are (isomorphic to) reduction graphs.

cs.LO↗

arXiv2006

Strategies of Loop Recombination in Ciliates

Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) can possibly be applied in the transformation of a given gene from its micronuclear form to its macronuclear form. We also characterize in which order these loop recombination operations are applicable. This is done in the abstract and more general setting of so-called legal strings.

cs.LO↗

arXiv2006

Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the development of the theoretical models of gene assembly, and in particular we demonstrate the use of the concept of the breakpoint graph, known from another branch of DNA transformation research. More specifically: (1) we characterize the intermediate gene patterns that can occur during the transformation of a given micronuclear gene pattern to its macronuclear form; (2) we determine the number of applications of the loop recombination operation (the most basic of the three molecular operations that accomplish gene assembly) needed in this transformation; (3) we generalize previous results (and give elegant alternatives for some proofs) concerning characterizations of the micronuclear gene patterns that can be assembled using a specific subset of the three molecular operations.

cs.LO↗

arXiv1999

MSO definable string transductions and two-way finite state transducers

String transductions that are definable in monadic second-order (mso) logic (without the use of parameters) are exactly those realized by deterministic two-way finite state transducers. Nondeterministic mso definable string transductions (i.e., those definable with the use of parameters) correspond to compositions of two nondeterministic two-way finite state transducers that have the finite visit property. Both families of mso definable string transductions are characterized in terms of Hennie machines, i.e., two-way finite state transducers with the finite visit property that are allowed to rewrite their input tape.

cs.LO↗