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Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over 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…
Phase change memory (PCM) has recently emerged as a promising technology to meet the fast growing demand for large capacity memory in computer systems, replacing DRAM that is impeded by physical limitations. Multi-level cell (MLC) PCM…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…
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…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Generalized bicycle (GB) codes have emerged as a promising class of quantum error-correcting codes with practical decoding capabilities. While numerous asymptotically good quantum codes and quantum low-density parity-check code…
Guessing Codeword Decoding (GCD) is a recently proposed soft-input forward error correction decoder for arbitrary binary linear codes. Inspired by recent proposals that leverage binary linear codebook structure to reduce the number of…
We examine an error-correcting coding framework in which each coded symbol is constrained to be a function of a fixed subset of the message symbols. With an eye toward distributed storage applications, we seek to design systematic codes…
In this paper, we focus on the design of binary constant weight codes that admit low-complexity encoding and decoding algorithms, and that have a size $M=2^k$. For every integer $\ell \geq 3$, we construct a $(n=2^\ell, M=2^{k_{\ell}},…
DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…