16 papers · ranked by Valyu relevance
Ekaterina Noskova, Vladimir Ulyantsev, Stephen J. O’Brien, Pavel Dobrynin
During the last few years more and more genomic analysis of individuals of closely related species has appeared. The history of evolution and development of populations, so-called demographic history, is embedded into their genome and we can try to pull it out. Allele frequency spectrum or AFS, the distribution of…
Edith Invernizzi, Graeme D Ruxton
The metaphor of fitness landscapes is common in evolutionary biology, as a way to visualise the change in allele or phenotypic frequencies of a population under selection. Understanding how different factors in the evolutionary process affect the trajectory of the population across the landscape is of interest to both…
Syed Islam, Dewan M. Sarwar
Computation and visualization of connectivity among the brain regions is vital for tasks such as disease identification and drug discovery. An effective visualization can aid clinicians and biologists to perform these tasks addressing a genuine research and industrial need. In this paper, we present…
Melania Nowicka, Heike Siebert
Cell classifiers are decision-making synthetic circuits that allow in vivo cell-type classification. Their design is based on finding a relationship between differential expression of miRNAs and the cell condition. Such biological devices have shown potential to become a valuable tool in cancer treatment as a new…
Deniz Akdemir
Optimal subset selection is an important task that has numerous algorithms designed for it and has many application areas. STPGA contains a special genetic algorithm supplemented with a tabu memory property (that keeps track of previously tried solutions and their fitness for a number of iterations), and with a…
Dogan Corus, Duc-Cuong Dang, Anton V. Eremeev, Per Kristian Lehre
Understanding how the time-complexity of evolutionary algorithms (EAs) depend on their parameter settings and characteristics of fitness landscapes is a fundamental problem in evolutionary computation. Most rigorous results were derived using a handful of key analytic techniques, including drift analysis. However…
Biswanath Chowdhury, Arnav Garai, Gautam Garai
Detection of important functional and/or structural elements and identifying their positions in a large eukaryotic genome is an active research area. Gene is an important functional and structural unit of DNA. The computation of gene prediction is essential for detailed genome annotation. In this paper, we propose a…
André L. L. Moreira, César Rennó-Costa
Evolution optimizes cellular behavior throughout sequential generations by selecting the successful individual cells in a given context. As gene regulatory networks (GRNs) determine the behavior of single cells by ruling the activation of different processes - such as cell differentiation and death - how GRNs change…
Alexander Lalejini, Emily Dolson, Anya E. Vostinar, Luis Zaman
Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a…
Donal A. Hickey, G. Brian Golding
Recombination allows a finite population to resample the genotype pool, i.e., the universe of all possible genotypic combinations. This is important in populations that contain abundant genetic variation because, in such populations, the number of potential genotypes is much larger than the number of individuals in the…
Nicolas Heslot, Vitaliy Feoktistov
Calibration population design for genomic prediction has attracted a lot of interest in the plant and animal breeding literature. In this article we present an efficient optimization method to select a subset of preexisting individuals to phenotype. Application to the choice of maize hybrids to create and phenotype, to…
Oliver Attie, Brian Sulkow, Chong Di, Wei-Gang Qiu
Learning algorithms have been proposed as a non-selective mechanism capable of creating complex adaptive systems in life. Evolutionary learning however has not been demonstrated to be a plausible cause for the origin of a specific molecular system. Here we show that genetic codes as optimal as the Standard Genetic Code…
Kenji Okubo, Kunihiko Kaneko
Mendelian inheritance is a fundamental law of genetics. Considering two alleles in a diploid, a phenotype of a heterotype is dominated by a particular homotype according to the law of dominance. This picture is usually based on simple genotype-phenotype mapping in which one gene regulates one phenotype. However, in…
Padavinangady Nakul Bhat, Debnath Pal
This study introduces a formal framework for modeling inheritance patterns based on an algebraic representation of genotype distributions. The approach defines genotypes as probability measures rather than discrete states, enabling the computation of genetic expectations, a probabilistic analogue that captures the…
Kangbien Park
Humans have long employed directed evolution (DE) to engineer desired biological traits. In this paper, I introduce an algebraic framework that provides a quantitative representation of the general phenotypic traits of asexual populations, enabling the systematic modeling of DE processes. Within this framework, key…
Andreina I. Castillo, Ben H. Roos, Michael S. Rosenberg, Reed A. Cartwright + 1 more
Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is specially challenging. Here we present Genie, a browser-based educational tool that facilitates demonstration of concepts such as genetic drift, population isolation, gene flow, and genetic mutation.…