Related papers: Neural Replicator Analysis of the genus Flavivirus
We have presented some arguments to substantiate the usefulness of neural replicator analysis (NRA) for constructing variants of the natural binomial classification of virus genomes based only on knowledge of their complete genomic…
In 2022, a group of basic and clinical virologists, bioinformaticians, and evolutionary and structural biologists met in Oxford, UK, to develop a consensus on methodologies used to classify viruses. They concluded that virus taxonomy, which…
Mosquitos are the main transmissive agents of arboviral diseases. Manual classification of their neuronal spike patterns is very labor-intensive and expensive. Most available deep learning solutions require fully labeled spike datasets and…
The brain is likely the most complex organ, given the variety of functions it controls, the number of cells it comprises, and their corresponding diversity. Studying and identifying neurons, the brain's primary building blocks, is a crucial…
We consider a general mathematical model of a within-host viral infection with $n$ virus strains and explicit age-since-infection structure for infected cells. In the model, multiple virus strains compete for a population of target cells.…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
The hominid-specific non-LTR retrotransposon termed SINE VNTR Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about thirteen millions years ago ago, and…
In nature, the process of cellular growth and differentiation has lead to an amazing diversity of organisms -- algae, starfish, giant sequoia, tardigrades, and orcas are all created by the same generative process. Inspired by the incredible…
Zebrafish are a common model organism used to identify new disease therapeutics. High-throughput drug screens can be performed on larval zebrafish in multi-well plates by observing changes in behaviour following a treatment. Analysis of…
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
Neurodegenerative diseases are characterized as the progressive loss of neural cells, e.g. neurons, glial cells. Ageing, monogenic variations, viral infections, and many other factors are determined and speculated as causes for them. While…
A Triangle Generative Adversarial Network ($\Delta$-GAN) is developed for semi-supervised cross-domain joint distribution matching, where the training data consists of samples from each domain, and supervision of domain correspondence is…
Due to the world's demand for security systems, biometrics can be seen as an important topic of research in computer vision. One of the biometric forms that has been gaining attention is the recognition based on sclera. The initial and…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
Implicit neural representations (INRs) offer continuous coordinate-based encodings for atlas registration, cross-modality resampling, sparse-view completion, and compact sharing of neuroanatomical data. Yet reproducible evaluation is…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Over 30 papers have proposed to use convolutional neural network (CNN) for AD classification from anatomical MRI. However, the classification performance is difficult to compare across studies due to variations in components such as…
Viruses can amplify their genomes following different replication modes (RMs) ranging from the stamping machine replication (SMR) model to the geometric replication (GR) model. Different RMs are expected to produce different evolutionary…