Manuel Lafond

Manuel Lafond
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Manuel Lafond
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Computer Science - Data Structures and Algorithms (7)
 
Mathematics - Combinatorics (2)
 
Computer Science - Discrete Mathematics (2)
 
Quantitative Biology - Quantitative Methods (1)
 
Quantitative Biology - Genomics (1)
 
Quantitative Biology - Populations and Evolution (1)
 
Physics - Physics and Society (1)
 
Mathematics - Optimization and Control (1)
 
Computer Science - Distributed; Parallel; and Cluster Computing (1)

Publications Authored By Manuel Lafond

Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of genes or species, and aims at finding a single tree that minimizes the leaf-removal distance to the input trees. This problem is a specific instance of the general consensus/supertree problem, widely used to combine or summarize discordant evolutionary trees. Read More

Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree $S$. This idea of detecting errors through inconsistency with a species tree has mostly been studied in the presence of speciation and duplication events only. Read More

A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a threshold k such that uv is an edge if and only if the distance between u and v in T is at most k. Characterizing leaf powers is a challenging open problem, along with determining the complexity of their recognition. Read More

Assume n wireless mobile sensors are initially dispersed in an ad hoc manner in a rectangular region. They are required to move to final locations so that they can detect any intruder crossing the region in a direction parallel to the sides of the rectangle, and thus provide weak barrier coverage of the region. We study three optimization problems related to the movement of sensors to achieve weak barrier coverage: minimizing the number of sensors moved (MinNum), minimizing the average distance moved by the sensors (MinSum), and minimizing the maximum distance moved by the sensors (MinMax). Read More

Alice wants to join a new social network, and influence its members to adopt a new product or idea. Each person $v$ in the network has a certain threshold $t(v)$ for {\em activation}, i.e adoption of the product or idea. Read More

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on alternative protein isoforms. These methods often lead to inaccurate gene tree reconstructions that require to be corrected before being used in phylogenetic tree reconciliation analyses or gene products phylogeny reconstructions. Read More

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a set of input gene trees on partial data. In this perspective, the phylogenetic tree for the species containing the genes of interest can be used to choose among the many possible compatible "supergenetrees", the most natural criteria being to minimize a reconciliation cost. Read More

In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on the Weighted Quartet Consensus problem, a problem with unknown complexity status so far. Here we prove that the Weighted Quartet Consensus problem is NP-hard and we give a 1/2-factor approximation for this problem. Read More

Traders buy and sell financial instruments in hopes of making profit, and brokers are responsible for the transaction. Some brokers, known as market-makers, take the position opposite to the trader's. If the trader buys, they sell; if the trader sells, they buy. Read More

Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a single ancestral genome, use a scaffolding approach to select a subset of ancestral gene adjacencies, generally aiming at reducing the fragmentation of the reconstructed ancestral genome. In this paper, we describe an exact algorithm for the Small Parsimony Problem that combines both approaches. Read More

In 1990, Hendry conjectured that every Hamiltonian chordal graph is cycle extendible; that is, the vertices of any non-Hamiltonian cycle are contained in a cycle of length one greater. We disprove this conjecture by constructing counterexamples on $n$ vertices for any $n \geq 15$. Furthermore, we show that there exist counterexamples where the ratio of the length of a non-extendible cycle to the total number of vertices can be made arbitrarily small. Read More