Related papers: DNA Storage in the Short Molecule Regime
Wyner's soft-covering lemma is the central analysis step for achievability proofs of information theoretic security, resolvability, and channel synthesis. It can also be used for simple achievability proofs in lossy source coding. This work…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
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…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
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…
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…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We study the problem of efficient compression of a stochastic source of probability distributions. It can be viewed as a generalization of Shannon's source coding problem. It has relation to the theory of common randomness, as well as to…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…
We consider the lossless compression bound of any individual data sequence. If we fit the data by a parametric model, the entropy quantity $nH({\hat \theta}_n)$ obtained by plugging in the maximum likelihood estimate is an underestimate of…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
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…
Fairly recently, a new encryption scheme for audio data encryption has been proposed by Naskar, P.K., et al. The cryptosystem is based on substitution-permutation encryption structure using DNA encoding at the substitution stage, in which…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
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…
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…