Related papers: Data compression and genomes: a two dimensional li…
Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to…
This paper proposes and illustrates a general framework to integrate the areas of vision research and complex networks. Each image pixel is associated to a network node and the Euclidean distance between the visual properties (e.g.…
We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
We describe a universal information compression scheme that compresses any pure quantum i.i.d. source asymptotically to its von Neumann entropy, with no prior knowledge of the structure of the source. We introduce a diagonalisation…
Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
Researchers in the field of DNA-based chaotic cryptography have recently proposed a set of novel and efficient image encryption algorithms. In this paper, we present a comprehensive summary of those techniques, which are available in the…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…
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…
How information is encoded in bio-molecular sequences is difficult to quantify since such an analysis usually requires sampling an exponentially large genetic space. Here we show how information theory reveals both robust and compressed…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…
A new framework is introduced for examining and evaluating the fundamental limits of lossless data compression, that emphasizes genuinely non-asymptotic results. The {\em sample complexity} of compressing a given source is defined as the…