Probabilistic construction of deterministic algorithms: approximating packing integer programs
Journal of Computer and System Sciences - 27th IEEE Conference on Foundations of Computer Science October 27-29, 1986
Randomized algorithms
Polynomial time approximation schemes for dense instances of NP-hard problems
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Finding similar regions in many strings
STOC '99 Proceedings of the thirty-first annual ACM symposium on Theory of computing
Distinguishing string selection problems
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Efficient approximation algorithms for the Hamming center problem
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
A Linear-Time Algorithm for the 1-Mismatch Problem
WADS '97 Proceedings of the 5th International Workshop on Algorithms and Data Structures
Banishing Bias from Consensus Sequences
CPM '97 Proceedings of the 8th Annual Symposium on Combinatorial Pattern Matching
Finding similar regions in many sequences
Journal of Computer and System Sciences - STOC 1999
Genetic Algorithm Approach for the Closest String Problem
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Integer programming models for computational biology problems
Journal of Computer Science and Technology - Special issue on bioinformatics
The Closest Substring problem with small distances
FOCS '05 Proceedings of the 46th Annual IEEE Symposium on Foundations of Computer Science
Superiority and complexity of the spaced seeds
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
A polynomial time approximation scheme for embedding a directed hypergraph on a ring
Information Processing Letters
Optimal Solutions for the Closest-String Problem via Integer Programming
INFORMS Journal on Computing
An Exact Data Mining Method for Finding Center Strings and All Their Instances
IEEE Transactions on Knowledge and Data Engineering
On the complexity of the spaced seeds
Journal of Computer and System Sciences
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximation algorithms for labeling hierarchical taxonomies
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
A parallel multistart algorithm for the closest string problem
Computers and Operations Research
An improved lower bound on approximation algorithms for the Closest Substring problem
Information Processing Letters
An effective algorithm of motif finding problem
International Journal of Bioinformatics Research and Applications
Finding Additive Biclusters with Random Background
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Packing multiway cuts in capacitated graphs
SODA '09 Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms
A polynomial-time approximation scheme for embedding hypergraph in a cycle
ACM Transactions on Algorithms (TALG)
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
A data-based coding of candidate strings in the closest string problem
Proceedings of the 11th Annual Conference Companion on Genetic and Evolutionary Computation Conference: Late Breaking Papers
Efficient Algorithms for the Closest String and Distinguishing String Selection Problems
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
Consensus Optimizing Both Distance Sum and Radius
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
A simple algorithm for (l, d) motif search
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Ant-CSP: An Ant Colony Optimization Algorithm for the Closest String Problem
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
A polynomial time approximation scheme for embedding a directed hypergraph on a ring
Information Processing Letters
Complexities of the centre and median string problems
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
A lower bound on approximation algorithms for the closest substring problem
COCOA'07 Proceedings of the 1st international conference on Combinatorial optimization and applications
Efficient algorithms for model-based motif discovery from multiple sequences
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
More efficient algorithms for closest string and substring problems
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Finding optimal alignment and consensus of circular strings
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
AAIM'10 Proceedings of the 6th international conference on Algorithmic aspects in information and management
Improved sublinear time algorithm for width-bounded separators
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Near optimal solutions for maximum quasi-bicliques
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
Constant time approximation scheme for largest well predicted subset
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
A three-string approach to the closest string problem
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
Discovering almost any hidden motif from multiple sequences
ACM Transactions on Algorithms (TALG)
More Efficient Algorithms for Closest String and Substring Problems
SIAM Journal on Computing
Probabilistic Analysis of a Motif Discovery Algorithm for Multiple Sequences
SIAM Journal on Discrete Mathematics
Exact algorithm and heuristic for the Closest String Problem
Computers and Operations Research
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A GRASP algorithm for the Closest String Problem using a probability-based heuristic
Computers and Operations Research
A heuristic algorithm based on Lagrangian relaxation for the closest string problem
Computers and Operations Research
A polynomial time approximation scheme for embedding hypergraph in a weighted cycle
Theoretical Computer Science
Approximations and partial solutions for the consensus sequence problem
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
A three-string approach to the closest string problem
Journal of Computer and System Sciences
Approximation algorithms for bi-clustering problems
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
A linear-time algorithm for studying genetic variation
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Lower bounds and parameterized approach for longest common subsequence
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
Slightly superexponential parameterized problems
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
An approximation algorithm for embedding a directed hypergraph on a ring
AAIM'05 Proceedings of the First international conference on Algorithmic Applications in Management
On the longest common rigid subsequence problem
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Randomized algorithms for motif detection
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Space and time efficient algorithms for planted motif search
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
An improved heuristic for the far from most strings problem
Journal of Heuristics
A dense hierarchy of sublinear time approximation schemes for bin packing
FAW-AAIM'12 Proceedings of the 6th international Frontiers in Algorithmics, and Proceedings of the 8th international conference on Algorithmic Aspects in Information and Management
A polynomial time approximation scheme for embedding a directed hypergraph on a weighted ring
Journal of Combinatorial Optimization
Identification of distinguishing motifs
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Configurations and minority in the string consensus problem
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Finding consensus and optimal alignment of circular strings
Theoretical Computer Science
An efficient two-phase ant colony optimization algorithm for the closest string problem
SEAL'12 Proceedings of the 9th international conference on Simulated Evolution and Learning
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The problem of finding a center string that is "close" to everygiven string arises in computational molecular biology and codingtheory. This problem has two versions: the Closest String problemand the Closest Substring problem. Given a set of strings S= {s1, s2, ...,sn}, each of length m, the Closest Stringproblem is to find the smallest d and a string s of lengthm which is within Hamming distance d to eachsi ε S. This problem comes fromcoding theory when we are looking for a code not too far away froma given set of codes. Closest Substring problem, with an additionalinput integer L, asks for the smallest d and a strings, of length L, which is within Hamming distance daway from a substring, of length L, of each si. This problemis much more elusive than the Closest String problem. The ClosestSubstring problem is formulated from applications in findingconserved regions, identifying genetic drug targets and generatinggenetic probes in molecular biology. Whether there are efficientapproximation algorithms for both problems are major open questionsin this area. We present two polynomial-time approximationalgorithms with approximation ratio 1 + ε for any smallε to settle both questions.