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During the last decade, data on Protein-Protein Interactions (PPI) has increased in a huge manner. Searching for motifs in PPI Network has thus became a crucial problem to interpret this data. A large part of the literature is devoted to the query of motifs with a given topology. However, the biological data are, by now, so noisy (missing and erroneous(More)
Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To(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)
In this paper, we consider the problem of maximizing the spread of influence through a social network. Given a graph with a threshold value thr(v) attached to each vertex v, the spread of influence is modeled as follows: A vertex v becomes " active " (influenced) if at least thr(v) of its neighbors are active. In the corresponding optimization problem the(More)
Finding the longest subsequence present in two different strings is known as the Longest Common Subsequence (LCS) problem. It has been widely used as a measure to compare strings in different fields [2], in particular for the comparison of two (or more) genomes in Bioinformatics. Genomes are usually viewed as strings, where each symbol represents a gene,(More)
The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have(More)
The Minimum Duplication problem is a well-known problem in phylogenetics and comparative genomics. Given a set of gene trees, the Minimum Duplication problem asks for a species tree that induces the minimum number of gene duplications in the input gene trees. More recently, a variant of the Minimum Duplication problem, called Minimum Duplication Bipartite,(More)