Related papers: Properties and constructions of constrained codes …
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…
This thesis makes several significant contributions to the theory of both Regenerating (RG) and Locally Recoverable (LR) codes. The two principal contributions are characterizing the optimal rate of an LR code designed to recover from $t$…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
In this paper, we describe a new type of DNA codes over two noncommutative rings $E$ and $F$ of order four with characteristic 2. Our DNA codes are based on quasi self-dual codes over $E$ and $F$. Using quasi self-duality, we can describe…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation,…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
Resource constrained job scheduling is a hard combinatorial optimisation problem that originates in the mining industry. Off-the-shelf solvers cannot solve this problem satisfactorily in reasonable timeframes, while other solution methods…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
As transistor dimensions continue to shrink, binary devices are rapidly approaching their fundamental limits in power density. In response, multi-valued systems have attracted significant attention due to their enhanced information density.…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…