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Scaffolding and validation of bacterial genome assemblies using optical restriction maps
 Bioinformatics
, 2008
"... Motivation: New, highthroughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing techno ..."
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Motivation: New, highthroughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of matepair information. In this paper we propose methods to overcome such limitations by incorportating information from optical restriction maps. Results: We demonstrate the robustness of our methods to sequencing and assemby errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a costeffective framework for the assembly of genomes. Availability: The tools described here are available as an opensource package at
An Algorithm for Computing the Restriction Scaffold Assignment Problem in Computational Biology
 in computational biology. Information Processing Letters, 95(Issue 4):466–471
, 2005
"... Let S and T be two finite sets of points on the real line with S + T  = n and S > T . The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every e ..."
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Cited by 8 (5 self)
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Let S and T be two finite sets of points on the real line with S + T  = n and S > T . The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element s i of S to an element t j of T is s i  t j , i.e., the distance between s i and t j . In 2003 BenDor, Karp, Schwikowski and Shamir [2] published an O(n logn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n ) time, improving the best previous complexity of O(n ).
An O(n log n)time algorithm for the restriction scaffold assignment problem
 Journal of Computational Biology
"... The assignment problem takes as input two finite point sets S and T and establishes a correspondence between points in S and points in T, such that each point in S maps to exactly one point in T, and each point in T maps to at least one point in S. In this paper we show that this problem has an O(n ..."
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Cited by 5 (3 self)
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The assignment problem takes as input two finite point sets S and T and establishes a correspondence between points in S and points in T, such that each point in S maps to exactly one point in T, and each point in T maps to at least one point in S. In this paper we show that this problem has an O(n log n)time solution, provided that the points in S and T are restricted to lie on a line (linear time, if S and T are presorted). 1
Efficient ManyToMany Point Matching in One Dimension
"... Abstract. Let S and T be two sets of points with total cardinality n. The minimumcost manytomany matching problem matches each point in S to at least one point in T and each point in T to at least one point in S, such that sum of the matching costs is minimized. Here we examine the special case w ..."
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Abstract. Let S and T be two sets of points with total cardinality n. The minimumcost manytomany matching problem matches each point in S to at least one point in T and each point in T to at least one point in S, such that sum of the matching costs is minimized. Here we examine the special case where both S and T lie on the line and the cost of matching s ∈ S to t ∈ T is equal to the distance between s and t. In this context, we provide an algorithm that determines a minimumcost manytomany matching in O(n log n) time, improving the previous best time complexity of O(n 2) for the same problem. 1.
Faster Algorithms for Computing Distances between OneDimensional Point Sets
 PROCEEDINGS OF THE XI ENCUENTROS DE GEOMETRIA COMPUTACIONAL
, 2005
"... Let S and T be two finite sets of points on the real line with S + T = n and S > T. We consider two distance measures between S and T that have applications in music information retrieval and computational biology: the surjection distance and the link distance. The former is called the ..."
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Cited by 3 (2 self)
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Let S and T be two finite sets of points on the real line with S + T = n and S > T. We consider two distance measures between S and T that have applications in music information retrieval and computational biology: the surjection distance and the link distance. The former is called the restriction scaffold assignment problem in computational biology, and assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element s i of S to an element t j of T is s i  t j , i.e., the distance between s i and t j . In 2003 BenDor, Karp, Schwikowski and Shamir [2] published an O(n log n) time algorithm for this problem. Here we
Computational Geometric Aspects of Rhythm, Melody, and VoiceLeading
, 2009
"... Many problems concerning the theory and technology of rhythm, melody, and voiceleading are fundamentally geometric in nature. It is therefore not surprising that the field of computational geometry can contribute greatly to these problems. The interaction between computational geometry and music yi ..."
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Many problems concerning the theory and technology of rhythm, melody, and voiceleading are fundamentally geometric in nature. It is therefore not surprising that the field of computational geometry can contribute greatly to these problems. The interaction between computational geometry and music yields new insights into the theories of rhythm, melody, and voiceleading, as well as new problems for research in several areas, ranging from mathematics and computer science to music theory, music perception, and musicology. Recent results on the geometric and computational aspects of rhythm, melody, and voiceleading are reviewed, connections to established areas of computer science, mathematics, statistics, computational biology, and crystallography are pointed out, and new open problems are proposed.
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm420
"... Effect of the mutation rate and background size on the quality of pathogen identification ..."
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Effect of the mutation rate and background size on the quality of pathogen identification
Vol. 24 no. 10 2008, pages 1229–1235 BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btn102
"... Scaffolding and validation of bacterial genome assemblies using optical restriction maps ..."
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Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Minimum ManytoMany Matchings for Computing the Distance Between Two Sequences
"... Motivated by a problem in music theory of measuring the distance between chords and scales we consider algorithms for obtaining a minimumweight manytomany matching between two sets of points on the real line. Given sets A and B, we want to find the best rigid translation of B and a manytomany m ..."
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Motivated by a problem in music theory of measuring the distance between chords and scales we consider algorithms for obtaining a minimumweight manytomany matching between two sets of points on the real line. Given sets A and B, we want to find the best rigid translation of B and a manytomany matching that minimizes the sum of the squares of the distances between matched points. We provide a discrete algorithm that solves this continuous optimization problem, and discuss other related matters. 1