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We resolve the question of optimality for a well-studied packetized implementation of random linear network coding, called PNC. In PNC, in contrast to the classical memoryless setting, nodes store received information in memory to later…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
In a distributed storage system based on erasure coding, an important problem is the \emph{repair problem}: If a node storing a coded piece fails, in order to maintain the same level of reliability, we need to create a new encoded piece and…
We consider a setting in which a sender wishes to broadcast a block of K data packets to a set of wireless receivers, where each of the receivers has a subset of the data packets already available to it (e.g., from prior transmissions) and…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
Let $\mathcal{D}$ be a collection of $D$ documents, which are strings over an alphabet of size $\sigma$, of total length $n$. We describe a data structure that uses linear space and and reports $k$ most relevant documents that contain a…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
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 yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Erasure codes have become an integral part of distributed storage systems as a tool for providing data reliability and durability under the constant threat of device failures. In such systems, an $[n, k]$ code over a finite field…
We study the top-$k$ selection problem under the differential privacy model: $m$ items are rated according to votes of a set of clients. We consider a setting in which algorithms can retrieve data via a sequence of accesses, each either a…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
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…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…