Related papers: Closing the complexity gap of the double distance …
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…
In real-world, many problems can be formulated as the alignment between two geometric patterns. Previously, a great amount of research focus on the alignment of 2D or 3D patterns, especially in the field of computer vision. Recently, the…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
We show that computing the interleaving distance between two multi-graded persistence modules is NP-hard. More precisely, we show that deciding whether two modules are $1$-interleaved is NP-complete, already for bigraded, interval…
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…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
In the well-known complexity class NP are combinatorial problems, whose optimization counterparts are important for many practical settings. These problems typically consider full knowledge about the input. In practical settings, however,…
In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
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…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…