Related papers: Investigating the complexity of the double distanc…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
Given a directed graph D = (N, A) and a sequence of positive integers 1 <= c_1 < c_2 < ... < c_m <= |N|, we consider those path and cycle polytopes that are defined as the convex hulls of simple paths and cycles of D of cardinality c_p for…
The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
We study the problem of comparing a pair of geometric networks that may not be similarly defined, i.e., when they do not have one-to-one correspondences between their nodes and edges. Our motivating application is to compare power…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Whole genome duplication (WGD) is one of the most important events in the molecular evolution of organisms. In fish species, a WGD is considered to have occurred in the ancestral lineage of teleosts. Recent comprehensive ortholog…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
This paper presents the first polynomial time algorithm to compute geodesics in a CAT(0) cubical complex in general dimension. The algorithm is a simple iterative method to update breakpoints of a path joining two points using Miller, Owen…
Point configurations have been widely used as model systems in condensed matter physics, materials science and biology. Statistical descriptors such as the $n$-body distribution function $g_n$ is usually employed to characterize the point…
Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…