Related papers: Peptipedia: a comprehensive database for peptide r…
This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…
We present ClinicalTrialsHub, an interactive search-focused platform that consolidates all data from ClinicalTrials.gov and augments it by automatically extracting and structuring trial-relevant information from PubMed research articles.…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
The exponential growth of neuroscientific data necessitates platforms that facilitate data management and multidisciplinary collaboration. In this paper, we introduce Pennsieve - an open-source, cloud-based scientific data management…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…
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…
In recent years, natural language processing (NLP) models have demonstrated remarkable capabilities in various domains beyond traditional text generation. In this work, we introduce PeptideGPT, a protein language model tailored to generate…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
PubMed's current search interface makes it tedious to systematically search for medical and research literature on drugs that could potentially be used to treat a given pathology, including patients with genetically altered tumors. This is…
Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…
Ensuring the reproducibility of scientific work is crucial as it allows the consistent verification of scientific claims and facilitates the advancement of knowledge by providing a reliable foundation for future research. However,…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
Even though several publicly accessible pharmacovigilance databases are available, extracting data from them is a technically challenging process. Existing tools typically focus on a single database. We present SurVigilance, an open-source…
In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…
With the rapid development of biomedical software and hardware, a large amount of relational data interlinking genes, proteins, chemical components, drugs, diseases, and symptoms has been collected for modern biomedical research. Many…
Converting peptide sequences into useful representations for downstream analysis is a common step in computational modeling and cheminformatics. Furthermore, peptide drugs (e.g., Semaglutide, Degarelix) often take advantage of the diverse…
Reliable parameter extraction from experimental data is central to quantitative analysis in spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. We present FitED, a Python-based desktop…
Data is a precious resource in today's society, and is generated at an unprecedented and constantly growing pace. The need to store, analyze, and make data promptly available to a multitude of users introduces formidable challenges in…
Curated databases have become important sources of information across scientific disciplines, and due to the manual work of experts, often become important reference works. Features such as provenance tracking, archiving, and data citation…