Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

Abstract The Genomes Online Database (GOLD)(https://gold. jgi. doe. gov) is a manually
curated data management system that catalogs sequencing projects with associated …

Technological advances in high-throughput techniques have resulted in tremendous growth
of complex biological datasets providing evidence regarding various biomolecular …

Simple Summary Manipulation of multiple gene lists when going through a functional
enrichment analysis is often a hefty task. In this article, we present FLAME, a web application …

Manually annotated data is key to develo** text-mining and information-extraction
algorithms. However, human annotation requires considerable time, effort and expertise …

Finding, exploring and filtering frequent sentence-based associations between a disease
and a biomedical entity, co-mentioned in disease-related PubMed literature, is a challenge …

Named-entity recognition aims at identifying the fragments of text that mention entities of
interest, that afterwards could be linked to a knowledge base where those entities are …

Functional enrichment is the process of identifying implicated functional terms from a given
input list of genes or proteins. In this article, we present Flame (v2. 0), a web tool which offers …

To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in
which environments (where) and which microorganisms carry them out (who). Here, we …

Extracting and processing information from documents is of great importance as lots of
experimental results and findings are stored in local files. Therefore, extracting and …