Related papers: SparkGOR: A unified framework for genomic data ana…
The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
Genetic Algorithms (GAs) are powerful metaheuristic techniques mostly used in many real-world applications. The sequential execution of GAs requires considerable computational power both in time and resources. Nevertheless, GAs are…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
Distributed computation is always a tricky topic to deal with, especially in context of various requirements in various scenarios. A popular solution is to use Apache Spark with a setup of multiple systems forming a cluster. However, the…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
Many interesting data sets available on the Internet are of a medium size---too big to fit into a personal computer's memory, but not so large that they won't fit comfortably on its hard disk. In the coming years, data sets of this…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Distributed data processing ecosystems are widespread and their components are highly specialized, such that efficient interoperability is urgent. Recently, Apache Arrow was chosen by the community to serve as a format mediator, providing…
Data analysis in fundamental sciences nowadays is an essential process that pushes frontiers of our knowledge and leads to new discoveries. At the same time we can see that complexity of those analyses increases fast due to a)~enormous…
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…
Despite improved digital access to scholarly literature in the last decades, the fundamental principles of scholarly communication remain unchanged and continue to be largely document-based. Scholarly knowledge remains locked in…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Text-to-SQL systems enable users to query databases using natural language, democratizing access to data analytics. However, they face challenges in understanding ambiguous phrasing, domain-specific vocabulary, and complex schema…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
A new family of Intensional RDBs (IRDBs), introduced in [1], extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all preexisting user's…
Graph data management (also called NoSQL) has revealed beneficial characteristics in terms of flexibility and scalability by differently balancing between query expressivity and schema flexibility. This peculiar advantage has resulted into…
RDF data in the linked open data (LOD) cloud is very valuable for many different applications. In order to unlock the full value of this data, users should be able to issue complex queries on the RDF datasets in the LOD cloud. SPARQL can…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…