Related papers: Deletion Correcting Codes for Efficient DNA Synthe…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
We study codes that can detect the exact number of deletions and insertions in concatenated binary strings. We construct optimal codes for the case of detecting up to $\del$ deletions. We prove the optimality of these codes by deriving a…
Software-defined networking (SDN) is revolutionizing the networking industry, but current SDN programming platforms do not provide automated mechanisms for updating global configurations on the fly. Implementing updates by hand is…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
The problem of reconstructing a source sequence with the presence of decoder side-information that is mis-synchronized to the source due to deletions is studied in a distributed source coding framework. Motivated by practical applications,…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
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 work constructs codes that are efficiently decodable from a constant fraction of \emph{worst-case} insertion and deletion errors in three parameter settings: (i) Binary codes with rate approaching 1; (ii) Codes with constant rate for…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
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…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
In this paper, we study error exponents for a concatataned coding based class of DNA storage codes in which the number of reads performed can be variable. That is, the decoder can sequentially perform reads and choose whether to output the…