Related papers: Constrained Consensus Sequence Algorithm for DNA A…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
The dominant approach to sequence generation is to produce a sequence in some predefined order, e.g. left to right. In contrast, we propose a more general model that can generate the output sequence by inserting tokens in any arbitrary…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Average consensus algorithms can be implemented over wireless sensor networks (WSN), where global statistics can be computed using communications among sensor nodes locally. Simple execution, robustness to global topology changes due to…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
A primary goal of online deliberation platforms is to identify ideas that are broadly agreeable to a community of users through their expressed preferences. Yet, consensus elicitation should ideally extend beyond the specific statements…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
Agreement among a set of processes and in the presence of partial failures is one of the fundamental problems of distributed systems. In the most general case, many decisions must be agreed upon over the lifetime of a system with…
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 sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
We consider a classifier whose test set is exposed to various perturbations that are not present in the training set. These test samples still contain enough features to map them to the same class as their unperturbed counterpart. Current…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…