Related papers: Mining DNA Sequences Based on Spatially Coded Tech…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
The conjugation of multiple spatial light modulators (SLMs) enables the construction of optical diffractive neural networks (DNNs). To accelerate training, which is limited by the low refresh rate of SLMs, spatial multiplexing of the input…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages…
3D engineering of matter has opened up new avenues for designing systems that can perform various computational tasks through light-matter interaction. Here, we demonstrate the design of optical networks in the form of multiple diffractive…
Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…