Related papers: Properties and constructions of constrained codes …
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
The efficient storage of digital data is becoming very challenging over the years due to the exponential increase in the generation of data which can't compete with the existing storage resources. Furthermore, the infrequently accessed data…
Some recent studies have suggested using GANs for numeric data generation such as to generate data for completing the imbalanced numeric data. Considering the significant difference between the dimensions of the numeric data and images, as…
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…
In various wireless systems, such as sensor RFID networks and body area networks with implantable devices, the transmitted signals are simultaneously used both for information transmission and for energy transfer. In order to satisfy the…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…
We develop upper bounds on code size for an independent and identically distributed deletion and insertion channels for a given code length and target frame error probability. The bounds are obtained as a variation of a general converse…
This work introduces a novel approach to constructing DNA codes from linear codes over a non-chain extension of $\mathbb{Z}_4$. We study $(\text{\textbaro},\mathfrak{d}, \gamma)$-constacyclic codes over the ring…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
Motivated by the duplication-correcting problem for data storage in live DNA, we study the construction of constant-weight codes in $\ell_1$-metric. By using packings and group divisible designs in combinatorial design theory, we give…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
Large-scale distributed storage systems typically use erasure codes to provide durability of data in the face of failures. A set of $k$ blocks to be stored is encoded using an $[n, k]$ code to generate $n$ blocks that are then stored on…
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,…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…