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A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
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…
We study the inherent space requirements of shared storage algorithms in asynchronous fault-prone systems. Previous works use codes to achieve a better storage cost than the well-known replication approach. However, a closer look reveals…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Slow running or straggler tasks can significantly reduce computation speed in distributed computation. Recently, coding-theory-inspired approaches have been applied to mitigate the effect of straggling, through embedding redundancy in…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
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…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
The pivotal storage density win achieved by solid-state devices over magnetic devices in 2015 is a result of multiple innovations in physics, architecture, and signal processing. One of the most important innovations in that regard is…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much…
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…
In this paper we study the problem of storing reliably an archive of versioned data. Specifically, we focus on systems where the differences (deltas) between subsequent versions rather than the whole objects are stored - a typical model for…
Proposals for quantum computing devices are many and varied. They each have unique noise processes that make none of them fully reliable at this time. There are several error correction/avoidance techniques which are valuable for reducing…
Entanglement distribution is a core mechanism for the future quantum Internet. The quantum world is, however, a faulty environment. Hence, successful entanglement swapping is error-prone. The occurrence of quantum state errors can be…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Distributed storage systems support failures of individual devices by the use of replication or erasure correcting codes. While erasure correcting codes offer a better storage efficiency than replication for similar fault tolerance, they…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…