Related papers: Constructing Bio-molecular Databases on a DNA-base…
Recent developments in Omics-technologies revolutionized the investigation of biology by producing molecular data in multiple dimensions and scale. This breakthrough in biology raises the crucial issue of their interpretation based on…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
Although database systems perform well in data access and manipulation, their relational model hinders data scientists from formulating machine learning algorithms in SQL. Nevertheless, we argue that modern database systems perform well for…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
To store information at extremely high-density and data-rate, we propose to adapt, integrate, and extend the techniques developed by chemists and molecular biologists for the purpose of manipulating biological and other macromolecules. In…
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…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Table (database) / Relational database Classification for big/smart/fast data machine learning is one of the most important tasks of predictive analytics and extracting valuable information from data. It is core applied technique for what…
The sophisticated tools and techniques employed by Nature for purposeful storage of information stand in stark contrast to the primitive and relatively inefficient means used by man. We describe some impressive features of biological data…
Amorphous materials exhibit unique properties that make them suitable for various applications in science and technology, ranging from optical and electronic devices and solid-state batteries to protective coatings. However, data-driven…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that…
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
We introduce the Computational 2D Materials Database (C2DB), which organises a variety of structural, thermodynamic, elastic, electronic, magnetic, and optical properties of around 1500 two-dimensional materials distributed over more than…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…