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QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
Genomics Proteomics Bioinformatics. 2021 Dec;19(6):998-1011. doi: 10.1016/j.gpb.2021.02.001. Epub 2021 Feb 23.
Genomics Proteomics Bioinformatics. 2021.
PMID: 33631427
Free PMC article.
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.
Smaili FZ, Gao X, Hoehndorf R.
Smaili FZ, et al.
Bioinformatics. 2018 Jul 1;34(13):i52-i60. doi: 10.1093/bioinformatics/bty259.
Bioinformatics. 2018.
PMID: 29949999
Free PMC article.
Item in Clipboard
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.
Smaili FZ, Gao X, Hoehndorf R.
Smaili FZ, et al.
Bioinformatics. 2019 Jun 1;35(12):2133-2140. doi: 10.1093/bioinformatics/bty933.
Bioinformatics. 2019.
PMID: 30407490
Item in Clipboard
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Smaili FZ, Gao X, Hoehndorf R.
Smaili FZ, et al.
Bioinformatics. 2020 Apr 1;36(7):2229-2236. doi: 10.1093/bioinformatics/btz920.
Bioinformatics. 2020.
PMID: 31821406
Free PMC article.
Item in Clipboard
Semantic similarity and machine learning with ontologies.
Kulmanov M, Smaili FZ, Gao X, Hoehndorf R.
Kulmanov M, et al. Among authors: smaili fz.
Brief Bioinform. 2021 Jul 20;22(4):bbaa199. doi: 10.1093/bib/bbaa199.
Brief Bioinform. 2021.
PMID: 33049044
Free PMC article.
Review.
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A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
He Y, Yu H, Huffman A, Lin AY, Natale DA, Beverley J, Zheng L, Perl Y, Wang Z, Liu Y, Ong E, Wang Y, Huang P, Tran L, Du J, Shah Z, Shah E, Desai R, Huang HH, Tian Y, Merrell E, Duncan WD, Arabandi S, Schriml LM, Zheng J, Masci AM, Wang L, Liu H, Smaili FZ, Hoehndorf R, Pendlington ZM, Roncaglia P, Ye X, Xie J, Tang YW, Yang X, Peng S, Zhang L, Chen L, Hur J, Omenn GS, Athey B, Smith B.
He Y, et al. Among authors: smaili fz.
J Biomed Semantics. 2022 Oct 21;13(1):25. doi: 10.1186/s13326-022-00279-z.
J Biomed Semantics. 2022.
PMID: 36271389
Free PMC article.
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