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We investigate the power of (1-reversal) counter machines (finite automata with multiple counters, where each counter can ‘‘reverse’’ only once, i.e., once a counter decrements, it can no longer increment) and one-way multihead finite automata (finite automata with multiple one-way input heads) as a language acceptor. They can be non-deterministic as well(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)
We investigate families of languages de%ned by closure under operations generalized from models of gene descrambling in stichotrichous ciliates. We speci%cally consider languages that are closed under the synchronized insertion and deletion operations as well as languages closed under the hairpin inversion (hi) operation. Biologically, this studies sets of(More)
SUMMARY Copy number variants (CNVs) are a major source of genetic variation. Comparing CNVs between samples is important in elucidating their potential effects in a wide variety of biological contexts. HD-CNV (hotspot detector for copy number variants) is a tool for downstream analysis of previously identified CNV regions from multiple samples, and it(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)
Cancer treatment is a fragmented and varied process, as “cancer” is really hundreds of different diseases. The “hallmarks of cancer” proposed by Hanahan and Weinberg (Cell 100(1):57–70, 2000) are a framework for viewing cancer within a common set of underlying principles—ten properties that are common to almost all cancers, allowing them to grow(More)
The process of gene unscrambling in ciliates (a type of unicellular protozoa), which accomplishes the difficult task of re-arranging 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)