Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Optimizing nonadaptive group tests for objects with heterogeneous priors
SIAM Journal on Applied Mathematics
Physical mapping of chromosomes using unique probes
SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
Open Combinatorial Problems in computational Molecular Biology
ISTCS '95 Proceedings of the 3rd Israel Symposium on the Theory of Computing Systems (ISTCS'95)
Finding hidden independent sets in interval graphs
Theoretical Computer Science
European Journal of Combinatorics - Special issue on extremal and probabilistic combinatorics
The Journal of Machine Learning Research
Learning a hidden graph using O( logn) queries per edge
Journal of Computer and System Sciences
Optimal query complexity bounds for finding graphs
STOC '08 Proceedings of the fortieth annual ACM symposium on Theory of computing
Nonadaptive algorithms for threshold group testing
Discrete Applied Mathematics
Finding hidden independent sets in interval graphs
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Optimal query complexity bounds for finding graphs
Artificial Intelligence
Inferring social networks from outbreaks
ALT'10 Proceedings of the 21st international conference on Algorithmic learning theory
Almost tight upper bound for finding Fourier coefficients of bounded pseudo-Boolean functions
Journal of Computer and System Sciences
Reconstruction of hidden graphs and threshold group testing
Journal of Combinatorial Optimization
COLT'05 Proceedings of the 18th annual conference on Learning Theory
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Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure has been used in a number of microbial sequencing projects including Streptococcus pneumoniae and other bacteria. In this paper we describe a theoretical framework for this problem and propose an improved method that guarantees to minimize the number of steps involved in the gap closure procedures. In given particular collection of n/2 DNA fragments we describe a strategy that requires. 0.75 log n work in eight parallel rounds of experiment closely matching a corresponding lower bound 0.5 log of n