相关论文: Simplifying the mosaic description of DNA sequence…
Accurate variant descriptions are of paramount importance in the field of genomics. The domain is confronted with increasingly complex variants, e.g., combinations of multiple indels, making it challenging to generate proper variant…
Black box deep learning models trained on genomic sequences excel at predicting the outcomes of different gene regulatory mechanisms. Therefore, interpreting these models may provide novel insights into the underlying biology, supporting…
DNA detection is of great significance in the point-of-care diagnostics. The stiffness of DNA, varying with its sequence and mechanochemical environment, could be a potential marker for DNA identification. The steric configurations of DNA…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Generalization capabilities of learning-based medical image segmentation across domains are currently limited by the performance degradation caused by the domain shift, particularly for ultrasound (US) imaging. The quality of US images…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…