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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…
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…
Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
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 $M$…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
Distributed storage systems provide reliable access to data through redundancy spread over individually unreliable nodes. Application scenarios include data centers, peer-to-peer storage systems, and storage in wireless networks. Storing…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
Noisy shuffling channels capture the main characteristics of DNA storage systems where distinct segments of data are received out of order, after being corrupted by substitution errors. For realistic schemes with short-length segments,…