Related papers: DNA storage approaching the information-theoretic …
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…
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…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
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…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
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,…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Regenerating codes enable trading off repair bandwidth for storage in distributed storage systems (DSS). Due to their distributed nature, these systems are intrinsically susceptible to attacks, and they may also be subject to multiple…
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far,…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage…