Related papers: The Updated Genome Warehouse: Enhancing Data Value…
This paper presents Global Benchmark Database (GBD), a comprehensive suite of tools for provisioning and sustainably maintaining benchmark instances and their metadata. The availability of benchmark metadata is essential for many tasks in…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
The multiplication of platforms offering open data has facilitated access to information that can be used for research, innovation, and decision-making. Providing transparency and availability, open data is regularly updated, allowing us to…
We describe the status of the HepData database system, following a major re-development in time for the advent of LHC data. The new HepData system benefits from use of modern database and programming language technologies, as well as a…
Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The DOME recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data…
Motivation: Over the past decade, network-based approaches have proven useful in identifying disease modules within the human interactome, often providing insights into key mechanisms and guiding the quest for therapeutic targets. This is…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
One of the purposes of Big Data systems is to support analysis of data gathered from heterogeneous data sources. Since data warehouses have been used for several decades to achieve the same goal, they could be leveraged also to provide…
Attribute extrapolation in sample generation is challenging for deep neural networks operating beyond the training distribution. We formulate a new task for extrapolation in sequence generation, focusing on natural language and proteins,…
With the growing use of new technologies, healthcare is nowadays undergoing significant changes. Information-based medicine has to exploit medical decision-support systems and requires the analysis of various, heterogeneous data, such as…
Up-to-date meta-databases are vital for the analysis of biological data. However,the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an…
Sharing diverse genomic and other biomedical datasets is critical to advance scientific discoveries and their equitable translation to improve human health. However, data sharing remains challenging in the context of legacy datasets,…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
Summary: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data…
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…
Due to its hereditary nature, genomic data is not only linked to its owner but to that of close relatives as well. As a result, its sensitivity does not really degrade over time; in fact, the relevance of a genomic sequence is likely to be…
We developed a high-performance one-stop system for large-scale genome data analysis with secure secondary use of the data by the data owner and multiple users with different levels of data access control.
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
The problem addressed here is that of simultaneous treatment of several gene expression datasets, possibly collected under different experimental conditions and/or platforms. Using robust statistics, a large scale statistical analysis has…