Related papers: Information encoded in gene-frequency trajectories
This paper presents novel method for distribution-free robust trajectory optimization and control of discrete-time, nonlinear, and non-Gaussian stochastic systems, with closed-loop guarantees on chance constraint satisfaction. Our framework…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
We extend a recently developed exact schema based, or coarse grained, formulation of genetic dynamics \cite{stewael,stewael1,stewael2} and its associated exact Schema theorem to an arbitrary selection scheme and a general crossover…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
The key findings of classical population genetics are derived using a framework based on information theory using the entropies of the allele frequency distribution as a basis. The common results for drift, mutation, selection, and gene…
Encoding a sequence of observations is an essential task with many applications. The encoding can become highly efficient when the observations are generated by a dynamical system. A dynamical system imposes regularities on the observations…
Convergence of discrete-time Markov chains with two timescales is a powerful tool to study stochastic evolutionary games in subdivided populations. Focusing on linear games within demes, convergence to a diffusion process for the strategy…
Approximate Bayesian Computation is widely used in systems biology for inferring parameters in stochastic gene regulatory network models. Its performance hinges critically on the ability to summarize high-dimensional system responses such…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
This paper describes the software implementation of genetic algorithm for identifying and selecting most relevant results received during sequentially executed subject search operations. Simulated evolutionary process generates sustainable…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Stochastic evolution equations describing the dynamics of systems under the influence of both deterministic and stochastic forces are prevalent in all fields of science. Yet, identifying these systems from sparse-in-time observations…
Diffusion theory is a central tool of modern population genetics, yielding simple expressions for fixation probabilities and other quantities that are not easily derived from the underlying Wright-Fisher model. Unfortunately, the textbook…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
We investigate the evolutionary dynamics in directed and/or weighted networks. We study the fixation probability of a mutant in finite populations in stochastic voter-type dynamics for several update rules. The fixation probability is…
A succesful method to describe the asymptotic behavior of a discrete time stochastic process governed by some recursive formula is to relate it to the limit sets of a well chosen mean differential equation. Under an attainability condition,…
Stochastic quantum trajectories, such as pure state evolutions under unitary dynamics and random measurements, offer a crucial ensemble description of many-body open system dynamics. Recent studies have highlighted that individual quantum…