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15
A unifying view of genome rearrangements
 WABI 2006. LNCS (LNBI
, 2006
"... Abstract. Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifyi ..."
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Cited by 92 (12 self)
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Abstract. Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifying the algorithms. In this paper we show a simple way to apply this operation to the most general type of genomes with a mixed collection of linear and circular chromosomes. We also describe a graph structure that allows simplifying the theory and distance computation considerably, as neither capping nor concatenation of the linear chromosomes are necessary. 1
Reversal distance without hurdles and fortresses
 Lecture Notes in Computer Science
, 2004
"... Abstract. This paper presents an elementary proof of the HannenhalliPevzner theorem on the reversal distance of two signed permutations. It uses a single PQtree to encode the various features of a permutation. The parameters called hurdles and fortress are replaced by a single one, whose value is ..."
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Cited by 38 (4 self)
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Abstract. This paper presents an elementary proof of the HannenhalliPevzner theorem on the reversal distance of two signed permutations. It uses a single PQtree to encode the various features of a permutation. The parameters called hurdles and fortress are replaced by a single one, whose value is computed by a simple and efficient algorithm. 1
On computing the breakpoint reuse rate in rearrangement scenarios
 IN PROCEEDINGS OF RECOMBCG 2008, VOLUME 5267 OF LNBI
, 2008
"... In the past years, many combinatorial arguments have been made to support the theory that mammalian genome rearrangement scenarios rely heavily on breakpoint reuse. Different models of genome rearrangements have been suggested, from the classical set of operations that include inversions, transloca ..."
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Cited by 6 (1 self)
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In the past years, many combinatorial arguments have been made to support the theory that mammalian genome rearrangement scenarios rely heavily on breakpoint reuse. Different models of genome rearrangements have been suggested, from the classical set of operations that include inversions, translocations, fusions and fissions, to more elaborate models that include transpositions. Here we show that the current definition of breakpoint reuse rate is based on assumptions that are seldom true for mammalian genomes, and propose a new approach to compute this parameter. We explore the formal properties of this new measure and apply these results to the humanmouse genome comparison. We show that the reuse rate is intimately linked to a particular rearrangement scenario, and that the reuse rate can vary from 0.89 to 1.51 for scenarios of the same length that transform the mouse genome into the human genome, where a rate of 1 indicates no reuse at all.
On sorting by translocations
 J. Comput. Biol
"... The study of genome rearrangements is an important tool in comparative genomics. This paper revisits the problem of sorting a multichromosomal genome by translocations, i.e., exchanges of chromosome ends. We give an elementary proof of the formula for computing the translocation distance in linear ..."
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Cited by 23 (2 self)
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The study of genome rearrangements is an important tool in comparative genomics. This paper revisits the problem of sorting a multichromosomal genome by translocations, i.e., exchanges of chromosome ends. We give an elementary proof of the formula for computing the translocation distance in linear time, and we give a new algorithm for sorting by translocations, correcting an error in a previous algorithm by Hannenhalli. Key words: comparative genomics, genome rearrangement, translocation distance, sorting by translocations. 1.
Computation of Median Gene Clusters
, 2009
"... Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e., sets of genes that occur colocalized in several genomes. For most applications, it is preferable to extend this definition to a ..."
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Cited by 18 (8 self)
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Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e., sets of genes that occur colocalized in several genomes. For most applications, it is preferable to extend this definition to allow for small deviations in the gene content of the cluster occurrences. However, relaxing the equality constraint increases the computational complexity of gene cluster detection drastically. Existing approaches deal with this problem by using simplifying constraints on the cluster definition and/or allowing only pairwise genome comparison. In this article, we introduce a cluster concept named median gene clusters that improves over existing models, present efficient algorithms for their computation and show experimental results on the detection of approximate gene clusters in multiple genomes.
GENOME HALVING WITH DOUBLE CUT AND JOIN
, 2007
"... The genome halving problem, previously solved by ElMabrouk for inversions and reciprocal translocations, is here solved in a more general context allowing transpositions and block interchange as well, for genomes including multiple linear and circular chromosomes. We apply this to several data sets ..."
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Cited by 10 (3 self)
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The genome halving problem, previously solved by ElMabrouk for inversions and reciprocal translocations, is here solved in a more general context allowing transpositions and block interchange as well, for genomes including multiple linear and circular chromosomes. We apply this to several data sets and compare the results to the previous algorithm.
HP distance via Double Cut and Join distance
 IN PROCEEDINGS OF CPM 2008, VOLUME 5029 OF LNCS
, 2008
"... The genomic distance problem in the HannenhalliPevzner theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of inversions and translocations that transform one genome into the other. This paper presents a new distance formula based on a simple tre ..."
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Cited by 3 (2 self)
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The genomic distance problem in the HannenhalliPevzner theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of inversions and translocations that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way.
On Common Intervals with Errors
, 2006
"... The information that groups of genes cooccur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene clusters, has led to various models of increasing generality. A central feature to enhance the biological re ..."
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The information that groups of genes cooccur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene clusters, has led to various models of increasing generality. A central feature to enhance the biological relevance of their definition when applied to real genomic data is to allow for slight differences in the gene content within a cluster, thus not only considering groups of exact equality. We contribute a model defining gene clusters as common intervals with errors and discuss different representations and the corresponding problems resulting for the search procedure. 1
Madrid Melbourne Mexico City Nairobi New Delhi Taipei Toronto
"... It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in ..."
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It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in
The genesis of the DCJ formula
"... Abstract. The formula N−(C+I/2) to compute the number of DoubleCutandJoin operations needed to transform one genome into another is both simple and easy to prove. When it was published, in 2006, we omitted all details on how it was constructed. In this chapter, we will give an elementary treatmen ..."
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Abstract. The formula N−(C+I/2) to compute the number of DoubleCutandJoin operations needed to transform one genome into another is both simple and easy to prove. When it was published, in 2006, we omitted all details on how it was constructed. In this chapter, we will give an elementary treatment on the intuitions and methods underlying the formula, showing that simplicity is sometimes difficult to achieve. We will also prove that this formula is one among an infinite number of candidates, and that the techniques can be applied to other genomic distances. 1
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