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In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: a b s t r a c t We investigate the power of (1-reversal) counter machines (finite(More)
Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density(More)
Insertions and deletions of small circular DNA strands into long linear DNA strands are phenomena that happen frequently in nature and thus constitute an attractive paradigm for biomolecular computing. This paper presents a new model for DNA-based computation that involves circular as well as linear molecules, and that uses the operations of insertion and(More)
The process of gene unscrambling in ciliates (a type of unicellular protozoa), which accomplishes the diicult task of rearranging gene segments in the correct order and deleting non-coding sequences from an " encrypted " version of a DNA strand, has been modeled and studied so far from the point of view of the computational power of the DNA bio-operations(More)
As the fabrication of integrated circuits continues to take place on increasingly smaller scales, we grow closer to several fundamental limitations on electronic computers. For many classes of problems, computing devices based on biochemical reactions present an attractive alternative to conventional computing paradigms. We present here a survey of the(More)
The process of gene unscrambling in ciliates (a type of unicel-lular protozoa), which accomplishes the difficult task of rearranging gene segments in the correct order and deleting non-coding sequences from an " encrypted " version of a DNA strand, has been modeled and studied so far from the point of view of the computational power of the DNA(More)
We investigate families of languages defined by closure under operations generalized from models of gene descrambling in stichotrichous ciliates. We specifically consider languages that are closed under the synchronized insertion and deletion operations as well as languages closed under the hi (hairpin inversion) operation. Biologically, this studies sets(More)