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Gigascience|January 21, 2026
nf-core/proteinfamilies: A scalable pipeline for the generation of protein familiesEvangelos Karatzas, Martin Beracochea, Fotis A Baltoumas, et al.
Bioinformatics (Oxford, England)|August 4, 2023
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sourcesEvangelos Karatzas, Fotis A Baltoumas, Eleni Aplakidou, et al.
Frontiers in Bioinformatics|March 24, 2023
Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clustersFotis A Baltoumas, Evangelos Karatzas, David Paez-Espino, et al.
Computational and Structural Biotechnology Journal|May 20, 2024
Visualizing metagenomic and metatranscriptomic data: A comprehensive reviewEleni Aplakidou, Nikolaos Vergoulidis, Maria Chasapi, et al.
Nucleic Acids Research|September 1, 2025
metagRoot: a comprehensive database of protein families associated with plant root microbiomesMaria N Chasapi, Iro N Chasapi, Eleni Aplakidou, et al.
Computational and Structural Biotechnology Journal|May 7, 2024
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each speciesIoannis Mouratidis, Fotis A Baltoumas, Nikol Chantzi, et al.
Computational and Structural Biotechnology Journal|July 2, 2025
Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associationsFotis A Baltoumas, Evangelos Karatzas, Nefeli K Venetsianou, et al.
Genome Research|August 26, 2025
Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of lifeNikol Chantzi, Akshatha Nayak, Fotis A Baltoumas, et al.
Briefings in Bioinformatics|May 19, 2026
Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approachesMaria N Chasapi, Nicholas Kontis, Robert Lehmann, et al.
Nucleic Acids Research|November 28, 2025
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomesMateus B Fiamenghi, Antonio Pedro Camargo, Iro N Chasapi, et al.
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