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This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
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.…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
If one goes backward in time, the number of ancestors of an individual doubles at each generation. This exponential growth very quickly exceeds the population size, when this size is finite. As a consequence, the ancestors of a given…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Family history is a major risk factor for many types of cancer. Mendelian risk prediction models translate family histories into cancer risk predictions based on knowledge of cancer susceptibility genes. These models are widely used in…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
In this paper we look at the problem of adjacency labeling of graphs. Given a family of undirected graphs the problem is to determine an encoding-decoding scheme for each member of the family such that we can decode the adjacency…
We study the problems of counting copies and induced copies of a small pattern graph $H$ in a large host graph $G$. Recent work fully classified the complexity of those problems according to structural restrictions on the patterns $H$. In…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…