Related papers: Managing Reliability Skew in DNA Storage
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
The exponential growth of data necessitates distributed storage models, such as peer-to-peer systems and data federations. While distributed storage can reduce costs and increase reliability, the heterogeneity in storage capacity, I/O…
Small to medium-scale data science experiments often rely on research software developed ad-hoc by individual scientists or small teams. Often there is no time to make the research software fast, reusable, and open access. The consequence…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
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…
Increasingly, artificial intelligence (AI) and machine learning (ML) are used in eScience applications [9]. While these approaches have great potential, the literature has shown that ML-based approaches frequently suffer from results that…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
We examine the problem of allocating a given total storage budget in a distributed storage system for maximum reliability. A source has a single data object that is to be coded and stored over a set of storage nodes; it is allowed to store…
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 problem of storing a data object in a set of data nodes that fail independently with given probabilities. Our problem is a natural generalization of a homogenous storage allocation problem where all the nodes had the same…
The field of deep learning has witnessed significant breakthroughs, spanning various applications, and fundamentally transforming current software capabilities. However, alongside these advancements, there have been increasing concerns…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Future extreme-scale computer systems may expose silent data corruption (SDC) to applications, in order to save energy or increase performance. However, resilience research struggles to come up with useful abstract programming models for…
Neural networks (NNs) can achieved high performance in various fields such as computer vision, and natural language processing. However, deploying NNs in resource-constrained safety-critical systems has challenges due to uncertainty in the…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…