Related papers: An Introduction to RNA Databases
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…
This paper is an introduction to natural language interfaces to databases (NLIDBs). A brief overview of the history of NLIDBs is first given. Some advantages and disadvantages of NLIDBs are then discussed, comparing NLIDBs to formal query…
Databases, collections of related data, are as old as the written word. A database can be anything from a homemaker's metal recipe file to a sophisticated data warehouse. Yet today, when we think of a database we invariably think of…
Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology…
In this document, I present the main notions of NoSQL databases and compare four selected products (Riak, MongoDB, Cassandra, Neo4J) according to their capabilities with respect to consistency, availability, and partition tolerance, as well…
In the last decade, the discovery of noncoding RNA(ncRNA) has exploded. Classifying these ncRNA is critical todetermining their function. This thesis proposes a new methodemploying deep convolutional neural networks (CNNs) to classifyncRNA…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type…
Biological databases can be analysed as a complex network which may reveal some its underlying biological mechanisms. Frequently, such databases are identified as scale-free networks or as hierarchical networks depending on connectivity…
Big Data concern large-volume, growing data sets that are complex and have multiple autonomous sources. Earlier technologies were not able to handle storage and processing of huge data thus Big Data concept comes into existence. This is a…
Variability inherently exists in databases in various contexts which creates database variants. For example, variants of a database could have different schemas/content (database evolution problem), variants of a database could root from…
Data security is one of the most crucial and a major challenge in the digital world. Security, privacy and integrity of data are demanded in every operation performed on internet. Whenever security of data is discussed, it is mostly in the…
The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…
Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
This paper provides an introduction to the Patstat patent database. It offers guided examples of ten popular queries that are relevant for research purposes and that cover the most important data tables. It is targeted at academic…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…