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Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
The biochemical attachment of photolyase to ultraviolet (uv) absorbed DNA molecules provides a method for registering whether a source has emitted photons. Here using laws of chemical kinetics and related experimental methods we argue that…
Cell division is a process that involves many biochemical steps and complex biophysical mechanisms. To simplify the understanding of what triggers cell division, three basic models that subsume more microscopic cellular processes associated…
Probabilistic model checking for systems with large or unbounded state space is a challenging computational problem in formal modelling and its applications. Numerical algorithms require an explicit representation of the state space, while…
In this paper we present the experimental results that more clearly than any theory suggest an answer to the question: when in detection of large (probably) prime numbers to apply, a very resource demanding, Miller-Rabin algorithm. Or, to…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
Models of counts-of-counts data have been extensively used in the biological sciences, for example in cancer, population genetics, sampling theory and ecology. In this paper we explore properties of one model that is embedded into a…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Uncontrolled cell division in the brain is what gives rise to brain tumors. If the tumor size increases by more than half, there is little hope for the patient's recovery. This emphasizes the need of rapid and precise brain tumor diagnosis.…
In exponentially proliferating populations of microbes, the population typically doubles at a rate less than the average doubling time of a single-cell due to variability at the single-cell level. It is known that the distribution of…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
The problem of the detection statistics of a quantum walker has received increasing interest, connected as it is to the problem of quantum search. We investigate the effect of employing a moving detector, using a projective measurement…
With the routine collection of massive-dimensional predictors in many application areas, screening methods that rapidly identify a small subset of promising predictors have become commonplace. We propose a new MOdular Bayes Screening (MOBS)…
We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
Minimizers and convolutional neural networks (CNNs) are two quite distinct popular techniques that have both been employed to analyze categorical biological sequences. At face value, the methods seem entirely dissimilar. Minimizers use…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
If we follow an asexually reproducing population through time, then the amount of time that has passed since the most recent common ancestor (MRCA) of all current individuals lived will change as time progresses. The resulting "MRCA age"…
We reconsider the Moran model in continuous time with population size $N$, two allelic types, and selection. We introduce a new particle representation, which we call the labelled Moran model, and which has the same distribution of type…