Using simulated annealing to design good codes
IEEE Transactions on Information Theory
Universal DNA tag systems: a combinatorial design scheme
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Solving Combinatorial Auctions Using Stochastic Local Search
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on Innovative Applications of Artificial Intelligence
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
Evidence for invariants in local search
AAAI'97/IAAI'97 Proceedings of the fourteenth national conference on artificial intelligence and ninth conference on Innovative applications of artificial intelligence
Evaluating las vegas algorithms: pitfalls and remedies
UAI'98 Proceedings of the Fourteenth conference on Uncertainty in artificial intelligence
Linear constructions for DNA codes
Theoretical Computer Science
Hardware acceleration of multi-deme genetic algorithm for the application of DNA codeword searching
Proceedings of the 9th annual conference on Genetic and evolutionary computation
Large-scale DNA memory based on the nested PCR
Natural Computing: an international journal
A hybrid quantum chaotic swarm evolutionary algorithm for DNA encoding
Computers & Mathematics with Applications
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
Evolutionary model for sequence generation
ICIC'07 Proceedings of the intelligent computing 3rd international conference on Advanced intelligent computing theories and applications
DNA memory with 16.8M addresses
DNA13'07 Proceedings of the 13th international conference on DNA computing
Dynamic neighborhood searches for thermodynamically designing DNA sequence
DNA13'07 Proceedings of the 13th international conference on DNA computing
Watson---Crick palindromes in DNA computing
Natural Computing: an international journal
DNA computing: a research snapshot
Algorithms and theory of computation handbook
Efficient algorithm for testing structure freeness of finite set of biomolecular sequences
DNA'05 Proceedings of the 11th international conference on DNA Computing
Specificity of hybridization between DNA sequences based on free energy
DNA'05 Proceedings of the 11th international conference on DNA Computing
Randomized fast design of short DNA words
ICALP'05 Proceedings of the 32nd international conference on Automata, Languages and Programming
DNA sequence design by dynamic neighborhood searches
DNA'06 Proceedings of the 12th international conference on DNA Computing
ICIC'06 Proceedings of the 2006 international conference on Computational Intelligence and Bioinformatics - Volume Part III
Deterministic polynomial-time algorithms for designing short DNA words
TAMC'10 Proceedings of the 7th annual conference on Theory and Applications of Models of Computation
Bond-free languages: formalizations, maximality and construction methods
DNA'04 Proceedings of the 10th international conference on DNA computing
Deterministic polynomial-time algorithms for designing short DNA words
Theoretical Computer Science
Improving the design of sequences for DNA computing: A multiobjective evolutionary approach
Applied Soft Computing
| Hi-index | 0.00 |
We present results on the performance of a stochastic local search algorithm for the design of DNA codes, namely sets of equallength words over the nucleotides alphabet {A,C,G, T} that satisfy certain combinatorial constraints. Using empirical analysis of the algorithm, we gain insight on goodd esign principles. We report several cases in which our algorithm finds word sets that match or exceed the best previously known constructions.