Related papers: The Updated Genome Warehouse: Enhancing Data Value…
Over the last several decades, there has been rapid growth in the number and scope of agricultural genetics, genomics and breeding (GGB) databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44…
This paper presents Bancroft, a computational genomics acceleration platform that provides the illusion of practically infinite on-device memory capacity by compressing genomic data movement over PCIe. Bancroft introduces novel…
The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…
Data Warehouse provides storage for huge amounts of historical data from heterogeneous operational sources in the form of multidimensional views, thus supplying sensitive and useful information which help decision-makers to improve the…
Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of…
Providing provenance in scientific workflows is essential for reproducibility and auditability purposes. Workflow systems model and record provenance describing the steps performed to obtain the final results of a computation. In this work,…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…
This paper presents the evaluation of the architecture of healthcare data warehouse specific to cancer diseases. This data warehouse containing relevant cancer medical information and patient data. The data warehouse provides the source for…
Rapid advancements in technology have led to an increased use of artificial intelligence (AI) technologies in medicine and bioinformatics research. In anticipation of this, the National Institutes of Health (NIH) assembled the Bridge to…
Since late 2022, generative AI has taken the world by storm, with widespread use of tools including ChatGPT, Gemini, and Claude. Generative AI and large language model (LLM) applications are transforming how individuals find and access data…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
Public repositories for genome and proteome annotations, such as the Gene Ontology (GO), rarely stores negative annotations, i.e. proteins not possessing a given function. This leaves undefined or ill defined the set of negative examples,…
In order to achieve high data rate and ubiquitous connectivity in future wireless networks, a key task is to efficiently manage the radio resource by judicious beamforming and power allocation. Unfortunately, the iterative nature of the…
Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing…
Efficient inventory management is crucial for both small and large enterprises to optimize operational workflows and reduce overhead costs. This paper explores the development and implementation of a Progressive Web Application (PWA)…
This paper presents our Linked Open Data (LOD) infrastructures for genomic and experimental data related to microRNA biomolecules. Legacy data from two well-known microRNA databases with experimental data and observations, as well as change…
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters…