Related papers: Constructing Bio-molecular Databases on a DNA-base…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Sequencing large number of candidate disease genes which cause diseases in order to identify the relationship between them is an expensive and time-consuming task. To handle these challenges, different computational approaches have been…
In this work, we present a new method for predicting bioaccumulation factor of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
While several paths have emerged in microelectronics and computing as follow-ons to Turing architectures, and have been implemented using essentially silicon circuits, very little beyond Moore research has considered: (1) first biological…
Codd's Theorem, a fundamental result of database theory, asserts that relational algebra and relational calculus have the same expressive power on relational databases. We explore Codd's Theorem for databases over semirings and establish…
Computer-based information technologies have been extensively used to help many organizations, private companies, and academic and education institutions manage their processes and information systems hereby become their nervous centre. The…
Beyond identifying genetic variants, we introduce a set of Boolean relations that allows for a comprehensive classification of the relations for every pair of variants by taking all minimal alignments into account. We present an efficient…
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
This work describes preliminary steps towards nano-scale reservoir computing using quantum dots. Our research has focused on the development of an accumulator-based sensing system that reacts to changes in the environment, as well as the…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
Because of several technological limitations of traditional silicon based computing, for past few years a paradigm shift, from silicon to carbon, is occurring in computational world. DNA computing has been considered to be quite promising…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
Biological systems can be studied at multiple levels of information, including gene, protein, RNA and different interaction networks levels. The goal of this work is to explore how the fusion of systems' level information with temporal…
Conventionally, high-throughput computational materials searches start from an input set of bulk compounds extracted from material databases, and this set is screened for candidate materials for specific applications. In contrast, many…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…