Related papers: DNA data storage, sequencing data-carrying DNA

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…

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 $M$…

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…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics as well as biological research. The charge migration rate is controlled by the…

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…

We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…

DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…

The DNA cryptography is a new and very promising direction in cryptography research. DNA can be used in cryptography for storing and transmitting the information, as well as for computation. Although in its primitive stage, DNA cryptography…

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 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…

The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…

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…

Accurate genome sequencing can improve our understanding of biology and the genetic basis of disease. The standard approach for generating DNA sequences from PacBio instruments relies on HMM-based models. Here, we introduce Distilled…

First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…

The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…

DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…

The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…

Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…