Strategic directions in research in theory of computing
ACM Computing Surveys (CSUR) - Special ACM 50th-anniversary issue: strategic directions in computing research
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Optimal sequencing by hybridization in rounds
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
ESA '02 Proceedings of the 10th Annual European Symposium on Algorithms
Partial words and the critical factorization theorem
Journal of Combinatorial Theory Series A
Periodicity and unbordered words: A proof of the extended duval conjecture
Journal of the ACM (JACM)
International Journal of Bioinformatics Research and Applications
Discrete Applied Mathematics
Algorithm note: Multistage isothermic sequencing by hybridization
Computational Biology and Chemistry
Generalized framework for selectors with applications in optimal group testing
ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
Watson-Crick conjugate and commutative words
DNA13'07 Proceedings of the 13th international conference on DNA computing
Sequencing by hybridization in few rounds
Journal of Computer and System Sciences
Optimal probing patterns for sequencing by hybridization
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Tight bounds for string reconstruction using substring queries
APPROX'05/RANDOM'05 Proceedings of the 8th international workshop on Approximation, Randomization and Combinatorial Optimization Problems, and Proceedings of the 9th international conference on Randamization and Computation: algorithms and techniques
Linear computation of unbordered conjugate on unordered alphabet
Theoretical Computer Science
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We establish a variety of combinatorial bounds on the tradeoffs inherent in reconstructing strings using few rounds of a given number of substring queries per round. These results lead us to propose a new approach to sequencing by hybridization (SBH), which uses interaction to dramatically reduce the number of oligonucleotides used for de novo sequencing of large DNA fragments, while preserving the parallelism which is the primary advantage of SBH.