Guillaume Fertin

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All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher. Combinatorics of genome rearrangements / Guillaume Fertin. .. [et al.]. p. cm. — (Computational molecular biology) Includes(More)
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogenetic tree. A large number of such measures has been proposed in the recent past: number of reversals, number of breakpoints, number of common or conserved intervals, SAD etc. In their initial definitions, all(More)
A star coloring of an undirected graph G is a proper vertex coloring of G (i.e., no two neighbors are assigned the same color) such that any path of length 3 in G is not bicolored. The star chromatic number of an undirected graph G, denoted by χs(G), is the smallest integer k for which G admits a star coloring with k colors. In this paper, we give the exact(More)
In this paper, we deal with the notion of star coloring of graphs. A star coloring of an undirected graph G is a proper vertex coloring of G (i.e., no two neighbors are assigned the same color) such that any path of length 3 in G is not bicolored. We give the exact value of the star chromatic number of different families of graphs such as trees, cycles,(More)
A promising and active field of comparative genomics consists in comparing two genomes by establishing a one-to-one correspondence (i.e., a matching) between their genes. This correspondence is usually chosen in order to optimize a predefined measure. One such problem is the Exemplar Breakpoint Distance problem (or EBD, for short), which asks, given two(More)
Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permutation), when the only allowed operation is to insert a spatula anywhere in the stack and to flip the pancakes above it (that is, to perform a prefix reversal). In the burnt variant, one side of each pancake is marked as burnt, and it is required to finish(More)
An acyclic coloring of a graph G is a coloring of its vertices such that: (i) no two neighbors in G are assigned the same color and (ii) no bicolored cycle can exist in G. The acyclic chromatic number of G is the least number of colors necessary to acyclically color G. In this paper, we show that any graph of maximum degree 5 has acyclic chromatic number at(More)
Given two comparative maps, that is two sequences of markers each representing a genome, the Maximal Strip Recovery problem (MSR) asks to extract a largest sequence of markers from each map such that the two extracted sequences are decomposable into non-intersecting strips (or synteny blocks). This aims at defining a robust set of synteny blocks between(More)
We study the problem of finding occurrences of motifs in vertex-colored graphs, where a motif is a multiset of colors, and an occurrence of a motif is a subset of connected vertices with a bijection between its colors and the colors of the motif. This problem has applications in metabolic network analysis, an important area in bioinformatics. We give two(More)