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DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
Statistical pattern recognition methods based on the Coherence Length Diagram (CLD) have been proposed for medical image analyses, such as quantitative characterisation of human skin textures, and for polarized light microscopy of liquid…
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…
Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Time series data extracted from individual…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
This commentary discusses a recently proposed measure of heterogeneity of DNA sequences and compares with the measures of complexity.
We establish some results for the rate of convergence in total variation of a Gibbs sampler to its equilibrium distribution. This sampler is motivated by a hierarchical Bayesian inference construction for a gamma random variable. Our…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
This paper studies the distribution of chain and maximal chain lengths in a causal set. We first provide a new derivation for these distributions for a causal set uniformly embedded in Minkowski space, for various dimensionalities, which…
This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
Modelling and understanding directional gene networks is a major challenge in biology as they play an important role in the architecture and function of genetic systems. Copula Directional Dependence (CDD) can measure the directed…
Like other pseudorandom sequences, decimal sequences may be used in designing a Code Division Multiple Access (CDMA) system. They appear to be ideally suited for this since the cross-correlation of d-sequences taken over the LCM of their…
A time series is a sequence of data items; typical examples are videos, stock ticker data, or streams of temperature measurements. Quite some research has been devoted to comparing and indexing simple time series, i.e., time series where…
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,…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…