Manuel Lafond

Université de Sherbrooke | UdeS · Department of Computer Science

Background Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of...

A graph G is a k -leaf power if there exists a tree T whose leaf set is V ( G ), and such that uv ∈ E ( G ) if and only if the distance between u and v in T is at most k (and u ≠ v ). The graph classes of k -leaf powers have several applications in computational biology, but recognizing them has remained a challenging algorithmic problem for the pa...

Gene duplication is one of the main drivers of evolution. It is well-known that copies arising from duplication can undergo multiple evolutionary fates, but little is known on their relative frequency, and on how environmental conditions affect it. In this paper we provide a general framework to characterize the fate of duplicated genes and formall...

The recombination problem is inspired by genome rearrangement events that occur in bacteriophage populations. Its goal is to explain the transformation of one bacteriophage population into another using the minimum number of recombinations. Here we show that the combinatorial problem is NP-Complete, both when the target population contains only one...

Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry red...

For a graph class $\mathcal{G}$, we define the $\mathcal{G}$-modular cardinality of a graph $G$ as the minimum size of a vertex partition of $G$ into modules that each induces a graph in $\mathcal{G}$. This generalizes other module-based graph parameters such as neighborhood diversity and iterated type partition. Moreover, if $\mathcal{G}$ has boun...

Several classical combinatorial problems have been considered and analysed on temporal graphs. Recently, a variant of Vertex Cover on temporal graphs, called MinTimelineCover, has been introduced to summarize timeline activities in social networks. The problem asks to cover every temporal edge while minimizing the total span of the vertices (where...

Structural graph parameters play an important role in parameterized complexity, including in kernelization. Notably, vertex cover, neighborhood diversity, twin-cover, and modular-width have been studied extensively in the last few years. However, there are many fundamental problems whose preprocessing complexity is not fully understood under these...

Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry red...

Several NP-hard problems are solved exactly using exponential-time branching strategies, whether it be branch-and-bound algorithms, or bounded search trees in fixed-parameter algorithms. The number of tractable instances that can be handled by sequential algorithms is usually small, whereas massive parallelization has been shown to significantly in...

Background: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves o...

In this paper, we start with a variation of the star cover problem called the Two-Squirrel problem. Given a set $P$ of $2n$ points in the plane, and two sites $c_1$ and $c_2$, compute two $n$-stars $S_1$ and $S_2$ centered at $c_1$ and $c_2$ respectively such that the maximum weight of $S_1$ and $S_2$ is minimized. This problem is strongly NP-hard...

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common ancestors of two extant genes (leaves of $T$) and the last common ancestors of the two species (leaves of $S$)...

Covering a graph with cohesive subgraphs is a classical problem in theoretical computer science, for example when the cohesive subgraph model considered is a clique. In this paper, we consider as a model of cohesive subgraph the 2-clubs, which are induced subgraphs of diameter at most 2. We prove new complexity results on the $$\mathsf {Min~2\text...

Recently, a conjecture due to Hendry was disproved which stated that every Hamiltonian chordal graph is cycle extendible. Here we further explore the conjecture, showing that it fails to hold even when a number of extra conditions are imposed. In particular, we show that Hendry's Conjecture fails for strongly chordal graphs, graphs with high connec...

In phylogenetic networks, picking a cherry consists of removing a leaf that shares a parent with another leaf, or removing a reticulate edge whose endpoints are parents of leaves. Cherry-picking operations were recently shown to have several structural and algorithmic applications in the study of networks, for instance in determining their reconstr...

Partitioning genomes into syntenic blocks has many uses in comparative genomics, such as inferring phylogenies or ancestral gene order. These blocks are usually required to contain enough genes to be qualified as syntenic. This leads to the problem of finding a common partition of the genomes in which the size of the blocks are above a certain thre...

A graph $G$ is a $k$-leaf power if there exists a tree $T$ whose leaf set is $V(G)$, and such that $uv \in E(G)$ if and only if the distance between $u$ and $v$ in $T$ is at most $k$. The graph classes of $k$-leaf powers have several applications in computational biology, but recognizing them has remained a challenging algorithmic problem for the p...

Clustering genes in similarity graphs is a popular approach for orthology prediction. Most algorithms group genes without considering their species, which results in clusters that contain several paralogous genes. Moreover, clustering is known to be problematic when in-paralogs arise from ancient duplications. Recently, we proposed a two-step proc...

We introduce and study a new combinatorial problem based on the famous Minimum Common String Partition (MCSP) problem, which we call Permutation-constrained Common String Partition (PCSP for short). In PCSP, we are given two sequences/genomes s and t with the same length and a permutation \(\pi \) on [k], the question is to decide whether it is pos...

Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitoc...

Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these g...

In phylogenetic networks, picking a cherry consists of removing a leaf that shares a parent with another leaf, or removing a reticulate edge whose endpoints are parents of leaves. Cherry-picking operations were recently shown to have several structural and algorithmic applications in the study of networks, for instance in determining their reconstr...

Assembly is a fundamental task in genome sequencing, and many assemblers have been made available in the last decade. Because of the wide range of possible choices, it can be hard to determine which tool or parameter to use for a specific genome sequencing project. In this paper, we propose a consensus approach that takes the best parts of several...

The edge clique cover number ecc ( G ) of a graph G is the size of the smallest collection of complete subgraphs whose union covers all edges of G . Chen, Jacobson, Kézdy, Lehel, Scheinerman, and Wang conjectured in 2000 that if G is claw‐free, then ecc ( G ) is bounded above by its order (denoted n ). Recently, Javadi and Hajebi verified this conj...

Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these g...

Background The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the t...

Two robots stand at the origin of the infinite line and are tasked with searching collaboratively for an exit at an unknown location on the line. They can travel at maximum speed b and can change speed or direction at any time. The two robots can communicate with each other at any distance and at any time. The task is completed when the last robot...

Given a bipartite graph G, the BICLUSTER EDITING problem asks for the minimum number of edges to insert or delete in G so that every connected component is a bicluster, i.e. a complete bipartite graph. This has applications in various areas such as social network analysis and bioinformatics. We study the parameterized complexity of the problem, the...

The history of gene families-which are equivalent to event-labeled gene trees-can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of ortholo-gous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the cas...

Recently, a conjecture due to Hendry was disproved which stated that every Hamiltonian chordal graph is cycle extendible. Here we further explore the conjecture, showing that it fails to hold even when a number of extra conditions are imposed. In particular, we show that Hendry's Conjecture fails for strongly chordal graphs, graphs with high connec...

The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more...

Background: In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involvin...

Background: During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of genes in a genome. Our aim is to compute the evolutionary distance between two cells for which o...

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...

During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of genes in a genome. Our aim is to compute the evolutionary distance between two cells for which only CNPs are...

Background: In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, it is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more tha...

Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a non-negative integer representing the number of copies of a specific gene or segment of interest. In this paper, we prese...

Background: The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible"...

Two robots stand at the origin of the infinite line and are tasked with searching collaboratively for an exit at an unknown location on the line. They can travel at maximum speed b and can change speed or direction at any time. The two robots can communicate with each other at any distance and at any time. The task is completed when the last robot...

Motivated by concerns about diversity in social networks, we consider the following pattern formation problems in rings. Assume n mobile agents are located at the nodes of an n-node ring network. Each agent is assigned a colour from the set \(\{c_1, c_2, \ldots , c_q \}\). The ring is divided into k contiguous blocks or neighbourhoods of length p....

Covering a graph with cohesive subgraphs is a classical problem in theoretical computer science. In this paper, we prove new complexity results on the problem, a variant recently introduced in the literature which asks to cover the vertices of a graph with a minimum number of 2-clubs (which are induced subgraphs of diameter at most 2). First, we an...

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this can be represented as the string operation $AXB \Rightarrow AXXB$. For example, Tandem exon duplications have...

Motivated by concerns about diversity in social networks, we consider the following pattern formation problems in rings. Assume $n$ mobile agents are located at the nodes of an $n$-node ring network. Each agent is assigned a colour from the set $\{c_1, c_2, \ldots, c_q \}$. The ring is divided into $k$ contiguous {\em blocks} or neighbourhoods of l...

Two robots stand at the origin of the infinite line and are tasked with searching collaboratively for an exit at an unknown location on the line. They can travel at maximum speed $b$ and can change speed or direction at any time. The two robots can communicate with each other at any distance and at any time. The task is completed when the last robo...

Consider two robots that start at the origin of the infinite line in search of an exit at an unknown location on the line. The robots can only communicate if they arrive at the same location at exactly the same time, i.e. they use the so-called face-to-face communication model. The group search time is defined as the worst-case time as a function o...

Abstract Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees wit...

Classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is clearly not suited for genes grouped in syntenic blocks, which are more pla...

The median problem is a classical problem in genome rearrangements. It aims to compute a gene order that minimizes the sum of the genomic distances to given gene orders. This problem is intractable except in the related Single-Cut-or-Join and breakpoint rearrangement models. Here we consider the rooted median problem, where we assume one of the giv...

Motivation: When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace. This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function. In this work, we make the...

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a speci...

Motivation When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace. This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function. In this work, we make the di...

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in biogeographical studies, to study the evolution of gene families, and also within approaches to construct phylogenet...

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 \(uv \in E\) if and only if the distance between u and v in T is at most k. Characteriz...

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 corre...

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. T...

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based princi...

Supporting information: Proofs omitted from the main text. This document provides the proofs of Lemmas 2, 3, 5, Theorem 4, and Proposition 2. It ends with a few remarks on the size of rNNI neighborhoods. (PDF)

We consider a problem of routing on directed paths and trees to a single destination, with rate-limited, adversarial traffic. In particular, we focus on local buffer management algorithms that ensure no packet loss, while minimizing the size of the required buffers. While a centralized algorithm for the problem that uses constant-sized buffers has...

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....

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...

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...

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...

Background Given a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and “missing” edges represent paralogs. While a gene tree directly induces a relation graph, the converse is not always true. Indeed, a relation graph is not necessarily “satisfiable”,...

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, focusin...

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. If $v$ has at least $t(v)$ activated neighbors, then $v$ will also become activated. If Alice wants to activate the entire social...

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 containin...

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, whose complexity status has remained open since it was posed in 2008. He...

A relation graph for a gene family is a graph with vertices representing the genes, edges connecting pairs of orthologous genes and “missing” edges representing paralogs. While a gene tree directly leads to a set of orthology and paralogy relations, the converse is not always true. Indeed a relation graph cannot necessarily be inferred from any tre...

Motivations: Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, oft...

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 activation, i.e. adoption of the product or idea. If v has at least t(v) activated neighbors, then v will also become activated. If Alice wants to activate the entire social network, whom...

Background: While tree-oriented methods for inferring orthology and paralogy relations between genes are based on reconciling a gene tree with a species tree, many tree-free methods are also available (usually based on sequence similarity). Recently, the link between orthology relations and gene trees has been formally considered from the perspect...

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. Said differently, brokers make money whenever their traders lose money. From this somew...