Combinatorica
Explicit construction of linear sized tolerant networks
Discrete Mathematics - First Japan Conference on Graph Theory and Applications
Algorithmic number theory
The kth prime is greater than k(lnk + ln lnk - 1) for k ≥ 2
Mathematics of Computation
Universal DNA tag systems: a combinatorial design scheme
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Strand design for biomolecular computation
Theoretical Computer Science - Natural computing
Solution of a Satisfiability Problem on a Gel-Based DNA Computer
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Stochastic Local Search Algorithms for DNA Word Design
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Linear constructions for DNA codes
Theoretical Computer Science
Randomized fast design of short DNA words
ACM Transactions on Algorithms (TALG)
Hybrid randomised neighbourhoods improve stochastic local search for DNA code design
AI'03 Proceedings of the 16th Canadian society for computational studies of intelligence conference on Advances in artificial intelligence
IEEE Transactions on Information Theory - Part 1
Deterministic polynomial-time algorithms for designing short DNA words
Theoretical Computer Science
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Designing short DNA words is a problem of constructing n DNA strings (words) with the minimum length such that the Hamming distance between each pair is at least k and the words satisfy a set of extra constraints This problem has applications in DNA computing, DNA self-assembly, and DNA arrays Previous works include those that extended results from coding theory to obtain bounds on code size for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms In particular, Kao, Sanghi and Schweller developed polynomial-time randomized algorithms to construct n DNA words of length 9· max {logn,k} satisfying a sets of constraints with high probability In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on expander codes, Ramanujan graphs, and derandomization techniques Our algorithms can construct n DNA words of length max {3logn, 4k} or 2.1 logn+6.28 k satisfying the same sets of constraints as the words constructed by the algorithms of Kao et al We have also extended these algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al do not work.