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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…
Quantum information processing is the emerging field that defines and realizes computing devices that make use of quantum mechanical principles, like the superposition principle, entanglement, and interference. In this review we study the…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
The lack of uniqueness arising by oversampling of Fourier coefficients is shown to provide a way of transmitting hidden information. A basic encoding/decoding system, developed on the basis of such a possibility, is discussed. The system is…
Molecular communication is a novel approach for data transmission between miniaturized devices, especially in contexts where electrical signals are to be avoided. The communication is based on sending molecules (or other particles) at nano…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Advanced quantum networking systems rely on efficient quantum error correction codes for their optimal realization. The rate at which the encoded information is transmitted is a fundamental limit that affects the performance of such…
This paper presents a new quantum protocol designed to simultaneously transmit information from one source to many recipients. The proposed protocol, which is based on the phenomenon of entanglement, is completely distributed and is…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Quantum algorithms reformulate computational problems as quantum evolutions in a large Hilbert space. Most quantum algorithms assume that the time-evolution is perfectly unitary and that the full Hilbert space is available. However, in…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
It is desirable that a distributed quantum computer can operate despite the replacement or failure of its constituent components, allowing the reliability of the distributed system to exceed that of its subcomponents. We first show that…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Codes are widely used in many engineering applications to offer robustness against noise. In large-scale systems there are several types of noise that can affect the performance of distributed machine learning algorithms -- straggler nodes,…
Quantum repeaters are enabling technologies for long-distance quantum communications. Despite the significant progress in the field, we still not only face implementation challenges but also need theoretical solutions that better meet all…
Data-driven modeling can suffer from a constant demand for data, leading to reduced accuracy and impractical for engineering applications due to the high cost and scarcity of information. To address this challenge, we propose a progressive…
Building large-scale quantum communication networks has its unique challenges. Here, we demonstrate that a network-wide synergistic usage of quantum memories distributed in a quantum communication network offers a fundamental advantage. We…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…