Related papers: Detecting gene innovations for phenotypic diversit…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
Both evolution and ecology have long been concerned with the impact of variable environmental conditions on observed levels of genetic diversity within and between species. We model the evolution of a quantitative trait under selection that…
In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally…
Feature selection is one of the most challenging issues in machine learning, especially while working with high dimensional data. In this paper, we address the problem of feature selection and propose a new approach called Evolving Fast and…
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…
A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different…
Non-genetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype confers a fitness advantage, selection may promote its genetic stabilization. Non-genetic perturbations can…
In this work, an evolutionary art project is presented where images are approximated by transparent, overlapping and geometric shapes of different types, e.g., polygons, circles, lines. Genotypes representing features and order of the…
The ability of a classifier to recognize unknown inputs is important for many classification-based systems. We discuss the problem of simultaneous classification and novelty detection, i.e. determining whether an input is from the known set…
Research increasingly relies on computational methods to analyze experimental data and predict molecular properties. Current approaches often require researchers to use a variety of tools for statistical analysis and machine learning,…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabad\'an in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an…
Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…
This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…