Related papers: Codes for Limited-Magnitude Probability Error in D…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
Maximum-likelihood (ML) decoding can be used to obtain the optimal performance of error correction codes. However, the size of the search space and consequently the decoding complexity grows exponentially, making it impractical to be…
Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…
This paper presents a novel coding scheme for distributed storage systems containing nodes with adversarial errors. The key challenge in such systems is the propagation of erroneous data from a single corrupted node to the rest of the…
This paper studies the problem of reconstructing a word given several of its noisy copies. This setup is motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is…
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…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
Codes for correcting sticky insertions/deletions and limited-magnitude errors have attracted significant attention due to their applications of flash memories, racetrack memories, and DNA data storage systems. In this paper, we first…
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…
DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
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…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
The code that combines channel estimation and error protection has received general attention recently, and has been considered a promising methodology to compensate multi-path fading effect. It has been shown by simulations that such code…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
This paper tackles two problems that fall under the study of coding for insertions and deletions. These problems are motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm,…