Related papers: On the Fourier transform of a quantitative trait: …
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the…
The resources required to characterise the dynamics of engineered quantum systems-such as quantum computers and quantum sensors-grow exponentially with system size. Here we adapt techniques from compressive sensing to exponentially reduce…
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites,…
Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
Sparse latent multi-factor models have been used in many exploratory and predictive problems with high-dimensional multivariate observations. Because of concerns with identifiability, the latent factors are almost always assumed to be…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in…
The primary goal of this work is to review the importance of data compression and present a fast Fourier-based method for generating the deterministic compression matrix in the area of deterministic compressed sensing. The principle…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
We propose a gate-based quantum algorithm for the prediction step of Bayesian state estimation based on the Fokker-Planck equation on a discretized position-velocity state space. The probability density is encoded in the amplitudes of a…
Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Causality testing, the act of determining cause and effect from measurements, is widely used in physics, climatology, neuroscience, econometrics and other disciplines. As a result, a large number of causality testing methods based on…
Soft biometrics analysis is seen as an important research topic, given its relevance to various applications. However, even though it is frequently seen as a solved task, it can still be very hard to perform in wild conditions, under…
This thesis responds to the challenges of using a large number, such as thousands, of features in regression and classification problems. There are two situations where such high dimensional features arise. One is when high dimensional…
An understanding of quantum theory in terms of new, underlying descriptions capable of explaining the existence of non-classical correlations, non-commutativity of measurements and other unique and counter-intuitive phenomena remains still…
The study of adaptive dynamics, involving many degrees of freedom on two separated timescales, one for fast changes of state variables and another for the slow adaptation of parameters controlling the former's dynamics is crucial for…
In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models…
In this paper, we present that genotype-phenotype mapping can be theoretically interpreted using the concept of quotient space in mathematics. Quotient space can be considered as mathematically-defined phenotype space in the evolutionary…