Florian Sikora

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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)
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)
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)
In this paper, we consider the Target Set Selection problem: given a graph and a threshold value thr(v) for each vertex v of the graph, find a minimum size vertex-subset to “activate” s.t. all the vertices of the graph are activated at the end of the propagation process. A vertex v is activated during the propagation process if at least thr(v) of its(More)
The Grundy number of a graph is the maximum number of colors used by the greedy coloring algorithm over all vertex orderings. In this paper, we study the computational complexity of Grundy Coloring, the problem of determining whether a given graph has Grundy number at least k. We also study the variants Weak Grundy Coloring (where the coloring is not(More)
In this paper, we consider the problem of maximizing the spread of influence through a social network. Here, we are given a graph G = (V,E), a positive integer k and a threshold value thr(v) attached to each vertex v ∈ V . The objective is then to find a subset of k vertices to “activate” such that the number of activated vertices at the end of a(More)
Recent techniques increase the amount of our knowledge of interactions between proteins. To filter, interpret and organize this data, many authors have provided tools for querying patterns in the shape of paths or trees in Protein-Protein Interaction networks. In this paper, we propose an exact algorithm for querying graphs pattern based on dynamic(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)