Sallam Abualhaija, Tristan Miller, Judith Eckle-Kohler, Iryna Gurevych, Karl-Heinz Zimmermann. Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 1, Long Papers. 2017.

BACKGROUND: A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level. RESULTS: We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in in vitro translation system that a viable protein can be autonomously assembled. CONCLUSION: Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.

We present two new binary codes: a (25,384,9) code and a (49,393216,13) code. These codes are better than the currently known binary codes with the same length and minimum distance.

Adleman's (1994) successful solution of a seven-vertex instance of the NP-complete Hamiltonian directed path problem by a DNA algorithm initiated the field of biomolecular computing. In this correspondence, we describe DNA algorithms based on the sticker model to perform encoding, minimum-distance computation, and maximum-likelihood (ML) decoding of binary linear codes. We also discuss feasibility and limitations of the sticker algorithms.

We present a method for decoding an arbitrary linear code over a Galois ring /spl Rscr/ by a process of lifting decoding algorithms for a family of linear codes over a finite field /spl Kscr/ forming an /spl alpha/-element chain, where /spl Kscr/ is the quotient field of /spl Rscr/ and /spl Rscr/ has characteristic p/sup /spl alpha//. As a new result, this method also works for linear codes over /spl Rscr/ which are nonfree /spl Rscr/-modules.

We first consider repeated-root cyclic codes, i.e., cyclic codes whose block length is divisible by the characteristic of the underlying field. It is well known that the formula for the minimum distance of repeated-root cyclic codes is similar to that for generalized concatenated codes. We show that indecomposable repeated-root cyclic codes are product codes and that the minimum weight of each repeated-root cyclic code is attained by one of its subcodes being equivalent to a product code. We then generalize the coding theoretical results on repeated-root cyclic codes to a larger class of left ideals in group algebra F/sub p/m/spl Gscr/ defined on non-Abelian groups, namely, groups /spl Gscr/ containing a normal cyclic Sylow p-subgroup. We show that a class of these codes compares reasonably to (shortened) generalized Reed-Muller codes over the primes and finally indicate by the special linear group SL/sub 2/(F/sub p/) how a further generalization may in principle be settled.

Indecomposable nonsemisimple Abelian codes are investigated. The author describes all indecomposable Abelian group codes and shows that the minimal distance of such a code M is the product of the minimal distance of a semisimple Abelian group code and the minimal distance of the source module of M. It is illustrated that the minimal distance of every indecomposable Abelian code depends upon its associated vertex.>