Related papers: A time series model of CDS sequences in complete g…
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
We examine the use of time series data, derived from Electric Cell-substrate Impedance Sensing (ECIS), to differentiate between standard mammalian cell cultures and those infected with a mycoplasma organism. With the goal of interpretable…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
Counts in cells are used to analyse the higher order properties of the statistics of the EDSGC survey. The probability distribution is obtained from an equal area projection source catalog with infinite oversampling over the range…
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of…
We introduce a model for the spreading of epidemics by long-range infections and investigate the critical behaviour at the spreading transition. The model generalizes directed bond percolation and is characterized by a probability…
This paper proposes a novel similarity measure for clustering sequential data. We first construct a common state-space by training a single probabilistic model with all the sequences in order to get a unified representation for the dataset.…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
Progress on modern scientific questions regularly depends on using large-scale datasets to understand complex dynamical systems. An especially challenging case that has grown to prominence with advances in single-cell sequencing…
We set up a mathematical model for a DC current in a human tissue that shows an attenuation effect in an extended circuit. We give a positive lower bound on the time duration over which this is guaranteed to happen in terms of the…
In recent years, complementary sequence sets have found many important applications in multi-carrier code-division multiple-access (MC-CDMA) systems for their good correlation properties. In this paper, we propose a construction, which can…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
In this report, we will be interested at Dynamic Bayesian Network (DBNs) as a model that tries to incorporate temporal dimension with uncertainty. We start with basics of DBN where we especially focus in Inference and Learning concepts and…
The development of the algorithm of a neural network building by the corresponding parts of a DNA code is discussed.
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
Maintaining causal consistency in distributed shared memory systems using vector timestamps has received a lot of attention from both theoretical and practical prospective. However, most of the previous literature focuses on full…
The fields of time series and graphical models emerged and advanced separately. Previous work on the structure learning of continuous and real-valued time series utilizes the time domain, with a focus on either structural autoregressive…