Anthony Labarre

Combinatorics of Genome Rearrangements

From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers the first comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. This book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information. Computational Molecular Biology series

Locating a Tree in a Phylogenetic Network in Quadratic Time

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in the number of taxa.

The distribution of cycles in breakpoint graphs of signed permutations

Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of those cycles is therefore critical to gaining insight on the distributions of the genomic distances that rely on it. We extend here the work initiated by Doignon and Labarre [6], who enumerated unsigned permutations whose breakpoint graph contains k cycles, to signed permutations, and prove explicit formulae for computing the expected value and the variance of the corresponding distributions, both in the unsigned case and in the signed case. We also show how our results can be used to derive simpler proofs of other previously known results.

Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time

A phylogenetic network is a rooted acyclic digraph whose leaves are labeled with a set of taxa. The tree containment problem is a fundamental problem arising from model validation in the study of phylogenetic networks. It asks to determine whether or not a given network displays a given phylogenetic tree over the same leaf set. It is known to be NP-complete in general. Whether or not it remains NP-complete for stable networks is an open problem. We make progress towards answering that question by presenting a quadratic time algorithm to solve the tree containment problem for a new class of networks that we call genetically stable networks, which include tree-child networks and comprise a subclass of stable networks.

Solving the tree containment problem in linear time for nearly stable phylogenetic networks

Abstract A phylogenetic network is a rooted acyclic digraph whose leaves are uniquely labeled with a set of taxa. The tree containment problem asks whether or not a phylogenetic network displays a phylogenetic tree over the same set of labeled leaves. It is a fundamental problem arising from validation of phylogenetic network models. The tree containment problem is NP -complete in general. To identify network classes on which the problem is polynomial time solvable, we introduce two classes of networks by generalizations of tree-child networks through vertex stability, namely nearly stable networks and genetically stable networks. Here, we study the combinatorial properties of these two classes of phylogenetic networks. We also develop a linear-time algorithm for solving the tree containment problem on binary nearly stable networks.

Asymptotic normality and combinatorial aspects of the prefix exchange distance distribution

The prefix exchange distance of a permutation is the minimum number of exchanges involving the leftmost element that sorts the permutation. We give new combinatorial proofs of known results on the distribution of the prefix exchange distance for a random uniform permutation. We also obtain expressions for the mean and the variance of this distribution, and finally, we show that the normalised prefix exchange distribution converges in distribution to the standard normal distribution.

The Clever Shopper Problem

We investigate a variant of the so-called Internet Shopping problem introduced by Blazewicz et al. (2010), where a customer wants to buy a list of products at the lowest possible total cost from shops which offer discounts when purchases exceed a certain threshold. Although the problem is NP-hard, we provide exact algorithms for several cases, e.g. when each shop sells only two items, and an FPT algorithm for the number of items, or for the number of shops when all prices are equal. We complement each result with hardness proofs in order to draw a tight boundary between tractable and intractable cases. Finally, we give an approximation algorithm and hardness results for the problem of maximising the sum of discounts.

Sorting with Forbidden Intermediates

A wide range of applications, most notably in comparative genomics, involve the computation of a shortest sorting sequence of operations for a given permutation, where the set of allowed operations is fixed beforehand. Such sequences are useful for instance when reconstructing potential scenarios of evolution between species, or when trying to assess their similarity. We revisit those problems by adding a new constraint on the sequences to be computed: they must avoid a given set of forbidden intermediates, which correspond to species that cannot exist because the mutations that would be involved in their creation are lethal. We initiate this study by focusing on the case where the only mutations that can occur are exchanges of any two elements in the permutations, and give a polynomial time algorithm for solving that problem when the permutation to sort is an involution.