Related papers: Rank modulation codes for DNA storage
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
It is generally difficult to predict the positions of mutations in genomic DNA at the nucleotide level. Retroviral DNA insertion is one mode of mutation, resulting in host infections that are difficult to treat. This mutation process…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
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…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…