41 citations · 224 across the 20 of their papers we have counts for
7 papers · 1 filter
Extending the Overlap Graph for Gene Assembly in Ciliates
Robert Brijder, Hendrik Jan Hoogeboom
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intr…
Automata with Nested Pebbles Capture First-Order Logic with Transitive Closure
Joost Engelfriet, Hendrik Jan Hoogeboom
String languages recognizable in (deterministic) log-space are characterized either by two-way (deterministic) multi-head automata, or following Immerman, by first-order logic with…
How Overlap Determines the Macronuclear Genes in Ciliates
Robert Brijder, Hendrik Jan Hoogeboom, Grzegorz Rozenberg
Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reducti…
The Fibers and Range of Reduction Graphs in Ciliates
Robert Brijder, Hendrik Jan Hoogeboom
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 bee…
Strategies of Loop Recombination in Ciliates
Robert Brijder, Hendrik Jan Hoogeboom, Michael Muskulus
Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronuc…
Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph
Robert Brijder, Hendrik Jan Hoogeboom, Grzegorz Rozenberg
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 dif…