Related papers: Inverted Repeats in Viral Genomes
We consider the problem of automatically prescribing oblique planes (short axis, 4 chamber and 2 chamber views) in Cardiac Magnetic Resonance Imaging (MRI). A concern with technologist-driven acquisitions of these planes is the quality and…
For numerous parameter and state estimation problems, assimilating new data as they become available can help produce accurate and fast inference of unknown quantities. While most existing algorithms for solving those kind of ill-posed…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
Several recent works have empirically observed that Convolutional Neural Nets (CNNs) are (approximately) invertible. To understand this approximate invertibility phenomenon and how to leverage it more effectively, we focus on a theoretical…
In dynamic malware analysis, programs are classified as malware or benign based on their execution logs. We propose a concept of applying monotonic classification models to the analysis process, to make the trained model's predictions…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the…
The random reversal graph offers new perspectives, allowing to study the connectivity of genomes as well as their most likely distance as a function of the reversal rate. Our main result shows that the structure of the random reversal graph…
Recurrent neural networks (RNNs) have been used extensively and with increasing success to model various types of sequential data. Much of this progress has been achieved through devising recurrent units and architectures with the…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
We conduct a systematic study of backdoor vulnerabilities in normally trained Deep Learning models. They are as dangerous as backdoors injected by data poisoning because both can be equally exploited. We leverage 20 different types of…
A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the…
BRCA genes, comprising BRCA1 and BRCA2 play indispensable roles in preserving genomic stability and facilitating DNA repair mechanisms. The presence of germline mutations in these genes has been associated with increased susceptibility to…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
All one-condition generalized inverses of the Markovian kernel I - P, where P is the transition matrix of a finite irreducible Markov chain, can be uniquely specified in terms of the stationary probabilities and the mean first passage times…
Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible…