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OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff AM, Train CM, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova HS, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. Altenhoff AM, et al. Among authors: mendes de farias t. Nucleic Acids Res. 2021 Jan 8;49(D1):D373-D379. doi: 10.1093/nar/gkaa1007. Nucleic Acids Res. 2021. PMID: 33174605 Free PMC article.
Enabling semantic queries across federated bioinformatics databases.
Sima AC, Mendes de Farias T, Zbinden E, Anisimova M, Gil M, Stockinger H, Stockinger K, Robinson-Rechavi M, Dessimoz C. Sima AC, et al. Among authors: mendes de farias t. Database (Oxford). 2019 Jan 1;2019:baz106. doi: 10.1093/database/baz106. Database (Oxford). 2019. PMID: 31697362 Free PMC article.
The SIB Swiss Institute of Bioinformatics Semantic Web of data.
SIB Swiss Institute of Bioinformatics RDF Group Members. SIB Swiss Institute of Bioinformatics RDF Group Members. Nucleic Acids Res. 2024 Jan 5;52(D1):D44-D51. doi: 10.1093/nar/gkad902. Nucleic Acids Res. 2024. PMID: 37878411 Free PMC article.
Accessing scientific data through knowledge graphs with Ontop.
Calvanese D, Lanti D, Mendes De Farias T, Mosca A, Xiao G. Calvanese D, et al. Among authors: mendes de farias t. Patterns (N Y). 2021 Oct 8;2(10):100346. doi: 10.1016/j.patter.2021.100346. eCollection 2021 Oct 8. Patterns (N Y). 2021. PMID: 34693372 Free PMC article. Review.
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.
Bastian FB, Cammarata AB, Carsanaro S, Detering H, Huang WT, Joye S, Niknejad A, Nyamari M, Mendes de Farias T, Moretti S, Tzivanopoulou M, Wollbrett J, Robinson-Rechavi M. Bastian FB, et al. Among authors: mendes de farias t. Nucleic Acids Res. 2025 Jan 6;53(D1):D878-D885. doi: 10.1093/nar/gkae1118. Nucleic Acids Res. 2025. PMID: 39656924 Free PMC article.