Cedric Chauve - LaBRI, PIMS

Cedric Chauve
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Name
Cedric Chauve
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LaBRI, PIMS
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Computer Science - Data Structures and Algorithms (14)
 
Quantitative Biology - Quantitative Methods (7)
 
Computer Science - Discrete Mathematics (5)
 
Quantitative Biology - Genomics (4)
 
Mathematics - Combinatorics (4)
 
Mathematics - Representation Theory (1)
 
Computer Science - Computational Complexity (1)
 
Quantitative Biology - Populations and Evolution (1)
 
Computer Science - Computational Engineering; Finance; and Science (1)

Publications Authored By Cedric Chauve

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

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

Distance-hereditary graphs form an important class of graphs, from the theoretical point of view, due to the fact that they are the totally decomposable graphs for the split-decomposition. The previous best enumerative result for these graphs is from Nakano et al. (J. Read More

The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity multipartite graph. We present a model for constructing a median of three genomes in this family-free setting, based on maximizing an objective function that generalizes the classical breakpoint distance by integrating sequence similarity in the score of a gene adjacency. We show that the corresponding computational problem is MAX SNP-hard and we present a 0-1 linear program for its exact solution. 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

Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different principles. In the present note, we show how it is possible to combine the principles of two of these algorithms in order to design a hybrid dynamic programming algorithm that combines the advantages of both algorithms. Read More

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. Read More

For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order of genes on each chromosome). Modern bulk genome sequencing mixes the signals of tumour clones and contaminating normal cells, complicating inference of genomic content and structure. Read More

The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Read More

The genome of a 650 year old Yersinia pestis bacteria, responsible for the medieval Black Death, was recently sequenced and assembled into 2,105 contigs from the main chromosome. According to the point mutation record, the medieval bacteria could be an ancestor of most Yersinia pestis extant species, which opens the way to reconstructing the organization of these contigs using a comparative approach. We show that recent computational paleogenomics methods, aiming at reconstructing the organization of ancestral genomes from the comparison of extant genomes, can be used to correct, order and complete the contig set of the Black Death agent genome, providing a full chromosome sequence, at the nucleotide scale, of this ancient bacteria. Read More

The Consecutive-Ones Property (C1P) is a classical concept in discrete mathematics that has been used in several genomics applications, from physical mapping of contemporary genomes to the assembly of ancient genomes. A common issue in genome assembly concerns repeats, genomic sequences that appear in several locations of a genome. Handling repeats leads to a variant of the C1P, the C1P with multiplicity (mC1P), that can also be seen as the problem of covering edges of hypergraphs by linear and circular walks. Read More

The Consecutive Ones Property is an important notion for binary matrices, both from a theoretical and applied point of view. Tucker gave in 1972 a characterization of matrices that do not satisfy the Consecutive Ones Property in terms of forbidden submatrices, the Tucker patterns. We describe here a linear time algorithm to find a Tucker pattern in a non-C1P binary matrix, which allows to extract in linear time a certificate for the non-C1P. Read More

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. B\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Read More

The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to be NP-complete. We show here that, if the number of vertices of degree 3 in the breakpoint graph of the three input genomes is fixed, then the problem is tractable Read More

A binary matrix has the consecutive ones property (C1P) if it is possible to order the columns so that all 1s are consecutive in every row. In [McConnell, SODA 2004 768-777] the notion of incompatibility graph of a binary matrix was introduced and it was shown that odd cycles of this graph provide a certificate that a matrix does not have the consecutive ones property. A bound of (k+2) was claimed for the smallest odd cycle of a non-C1P matrix with k columns. Read More

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. Read More

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. Read More

Motivated by problems of comparative genomics and paleogenomics, in [Chauve et al., 2009], the authors introduced the Gapped Consecutive-Ones Property Problem (k,delta)-C1P: given a binary matrix M and two integers k and delta, can the columns of M be permuted such that each row contains at most k blocks of ones and no two consecutive blocks of ones are separated by a gap of more than delta zeros. The classical C1P problem, which is known to be polynomial is equivalent to the (1,0)-C1P problem. Read More

We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this speciation. We call this problem the Minimum Duplication Bipartition Problem. Using a generalization of the Minimum Edge-Cut Problem, known as Submodular Function Minimization, we propose a polynomial time and space 3-approximation algorithm for the Minimum Duplication Bipartition Problem. Read More

A sequence of reversals that takes a signed permutation to the identity is perfect if at no step a common interval is broken. Determining a parsimonious perfect sequence of reversals that sorts a signed permutation is NP-hard. Here we show that, despite this worst-case analysis, with probability one, sorting can be done in polynomial time. Read More

We present combinatorial operators for the expansion of the Kronecker product of irreducible representations of the symmetric group. These combinatorial operators are defined in the ring of symmetric functions and act on the Schur functions basis. This leads to a combinatorial description of the Kronecker powers of the irreducible representations indexed with the partition (n-1,1) which specializes the concept of oscillating tableaux in Young's lattice previously defined by S. Read More