Related papers: Gene tree species tree reconciliation with gene co…
Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
Over the past decade, random forest models have become widely used as a robust method for high-dimensional data regression tasks. In part, the popularity of these models arises from the fact that they require little hyperparameter tuning…
The ancestral sequence reconstruction problem is the inference, back in time, of the properties of common sequence ancestors from measured properties of contemporary populations. Standard algorithms for this problem assume independent…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
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…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…
The main goal of this paper is to provide an algorithm for the random sampling of Butcher trees and the probabilistic numerical solution of ordinary differential equations (ODEs). This approach complements and simplifies a recent approach…
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…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
We consider the genealogy tree for a critical branching process conditioned on non-extinction. We enumerate vertices in each generation of the tree so that for each two generations one can define a monotone map describing the…
Industrial robots can solve very complex tasks in controlled environments, but modern applications require robots able to operate in unpredictable surroundings as well. An increasingly popular reactive policy architecture in robotics is…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Death has long been overlooked in evolutionary algorithms. Recent research has shown that death (when applied properly) can benefit the overall fitness of a population and can outperform sub-sections of a population that are "immortal" when…