Related papers: Constrained Consensus Sequence Algorithm for DNA A…

Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…

Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…

Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…

Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with spurious homologous matches and variant calling artifacts. While algorithms for identifying LC sequences exist, they…

A novel framework for consensus clustering is presented which has the ability to determine both the number of clusters and a final solution using multiple algorithms. A consensus similarity matrix is formed from an ensemble using multiple…

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…

We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…

The US Decennial Census provides valuable data for both research and policy purposes. Census data are subject to a variety of disclosure avoidance techniques prior to release in order to preserve respondent confidentiality. While many are…

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…

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…

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…

Dataset Condensation aims to condense a large dataset into a smaller one while maintaining its ability to train a well-performing model, thus reducing the storage cost and training effort in deep learning applications. However, conventional…

Dataset Condensation is a newly emerging technique aiming at learning a tiny dataset that captures the rich information encoded in the original dataset. As the size of datasets contemporary machine learning models rely on becomes…

Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…

We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…

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 trade-offs of DNA-based storage systems by introducing a new channel model, which we…

Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…