Related papers: Inverted Repeats in Viral Genomes
The problem of detecting a sinusoidal signal with randomly varying frequency has a long history. It is one of the core problems in signal processing, arising in many applications including, for example, underwater acoustic frequency line…
Shape restricted regressions, including isotonic regression and concave regression as special cases, are studied using priors on Bernstein polynomials and Markov chain Monte Carlo methods. These priors have large supports, select only…
Recently, studies have shown the potential of integrating field-type iterative methods with deep learning (DL) techniques in solving inverse scattering problems (ISPs). In this article, we propose a novel Variational Born Iterative Network,…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
One of the pivotal security threats for the embedded computing systems is malicious software a.k.a malware. With efficiency and efficacy, Machine Learning (ML) has been widely adopted for malware detection in recent times. Despite being…
Genetic variants identified to date by genome-wide association studies only explain a small fraction of total heritability. Gene-by-gene interaction is one important potential source of unexplained heritability. In the first part of this…
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…
It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made…
In this paper, we consider the nonasymptotic sequential estimation of means of random variables bounded in between zero and one. We have rigorously demonstrated that, in order to guarantee prescribed relative precision and confidence level,…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful…
This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied: (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not…
We investigate the heterogeneity of outcomes of repeated instances of percolation experiments in complex networks using a message passing approach to evaluate heterogeneous, node dependent probabilities of belonging to the giant or…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…
A reflexive generalized inverse and the Moore-Penrose inverse are often confused in statistical literature but in fact they have completely different behaviour in case the population covariance matrix is not a multiple of identity. In this…