Related papers: Inverted Repeats in Viral Genomes
We introduce a new approach to a linear-circular regression problem that relates multiple linear predictors to a circular response. We follow a modeling approach of a wrapped normal distribution that describes angular variables and angular…
Metamorphic viruses engage different mutation techniques to escape from string signature based scanning. They try to change their code in new offspring so that the variants appear non-similar and have no common sequences of string as…
Given a mathematical model quantifying the viral infection of pandemic influenza H1N1pdm09-H275 wild type (WT) and H1N1pdm09-H275Y mutant (MUT) strains, we describe a simple method of estimating the model's constant parameters using Monte…
We study the random times between successive cases in a transmission chain of infectious diseases with asymptomatic carriers. We derive the probability distribution of this generation time (in days) from a discrete-time epidemic model with…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
Early diagnosis of treatable diseases is essential for improving healthcare, and many diseases' onsets are predictable from annual lab tests and their temporal trends. We introduce a multi-resolution convolutional neural network for early…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
Viruses constantly undergo mutations with genomic changes. The propagation of variants of viruses is an interesting problem. We perform numerical simulations of the microscopic epidemic model based on network theory for the spread of…
Because of its relevance to everyday life, the spreading of viral infections has been of central interest in a variety of scientific communities involved in fighting, preventing and theoretically interpreting epidemic processes. Recent…
Immune repertoires rely on diversity of T-cell and B-cell receptors to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out…
This study independently reproduces the malware detection methodology presented by Felli cious et al. [7], which employs order-invariant API call frequency analysis using Random Forest classification. We utilized the original public dataset…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
Major unresolved questions in evolutionary genetics include determining the contributions of different mutational sources to the total pool of genetic variation in a species, and understanding how these different forms of genetic variation…
This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The…
In this paper we propose an open anomalous semi-Markovian random neural networks model with negative and positive signals with arbitrary random waiting times. We investigate the signal flow process in the anomalous random neural networks…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…
Neural network systems describe complex mappings that can be very difficult to understand. In this paper, we study the inverse problem of determining the input images that get mapped to specific neural network classes. Ultimately, we expect…
We consider the problem of multivariate density deconvolution where the distribution of a random vector needs to be estimated from replicates contaminated with conditionally heteroscedastic measurement errors. We propose a conceptually…
The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…
The emergence of a predominant phenotype within a cell population is often triggered by a rare accumulation of DNA mutations in a single cell. For example, tumors may be initiated by a single cell in which multiple mutations cooperate to…