Related papers: Mutually Uncorrelated Primers for DNA-Based Data S…
We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based storage systems and synchronization protocols. WMU sequences are characterized by the property that no sufficiently long suffix…
Mutually Uncorrelated (MU) codes are a class of codes in which no proper prefix of one codeword is a suffix of another codeword. These codes were originally studied for synchronization purposes and recently, Yazdi et al. showed their…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
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…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
Massive multi-user (MU) multiple-input multiple- output (MIMO) is widely believed to be a core technology for the upcoming fifth-generation (5G) wireless communication standards. The use of low-precision digital-to-analog converters (DACs)…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
Unitary matrices are the basis of a large number of signal processing applications. In many of these applications, finding ways to efficiently store, and even transmit these matrices, can significantly reduce memory and throughput…
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…
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…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
In this paper, we propose {\em distributed network compression via memory}. We consider two spatially separated sources with correlated unknown source parameters. We wish to study the universal compression of a sequence of length $n$ from…
Certain applications require the use of signals that combine both the capability to operate with low signal-to-noise ratios and the ability to support multiple users without interference. In the case where many users have very different…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Speculative techniques in microarchitectures relax various dependencies in programs, which contributes to the complexity of (weak) memory models. We show using WMM, a new weak memory model, that the model becomes simpler if it includes…