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Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning.
Cappelletti L, Rekerle L, Fontana T, Hansen P, Casiraghi E, Ravanmehr V, Mungall CJ, Yang JJ, Spranger L, Karlebach G, Caufield JH, Carmody L, Coleman B, Oprea TI, Reese J, Valentini G, Robinson PN. Cappelletti L, et al. Among authors: oprea ti. Bioinform Adv. 2024 Mar 4;4(1):vbae036. doi: 10.1093/bioadv/vbae036. eCollection 2024. Bioinform Adv. 2024. PMID: 38577542 Free PMC article.
Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer.
Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, Mungall C, Oprea TI, Robinson PN. Ravanmehr V, et al. Among authors: oprea ti. NAR Genom Bioinform. 2021 Dec 8;3(4):lqab113. doi: 10.1093/nargab/lqab113. eCollection 2021 Dec. NAR Genom Bioinform. 2021. PMID: 34888523 Free PMC article.
TIGA: target illumination GWAS analytics.
Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ, Oprea TI. Yang JJ, et al. Among authors: oprea ti. Bioinformatics. 2021 Nov 5;37(21):3865-3873. doi: 10.1093/bioinformatics/btab427. Bioinformatics. 2021. PMID: 34086846 Free PMC article.
Badapple: promiscuity patterns from noisy evidence.
Yang JJ, Ursu O, Lipinski CA, Sklar LA, Oprea TI, Bologa CG. Yang JJ, et al. Among authors: oprea ti. J Cheminform. 2016 May 28;8:29. doi: 10.1186/s13321-016-0137-3. eCollection 2016. J Cheminform. 2016. PMID: 27239230 Free PMC article.
TIN-X: target importance and novelty explorer.
Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG, Oprea TI. Cannon DC, et al. Among authors: oprea ti. Bioinformatics. 2017 Aug 15;33(16):2601-2603. doi: 10.1093/bioinformatics/btx200. Bioinformatics. 2017. PMID: 28398460 Free PMC article.
The CARLSBAD database: a confederated database of chemical bioactivities.
Mathias SL, Hines-Kay J, Yang JJ, Zahoransky-Kohalmi G, Bologa CG, Ursu O, Oprea TI. Mathias SL, et al. Among authors: oprea ti. Database (Oxford). 2013 Jun 21;2013:bat044. doi: 10.1093/database/bat044. Print 2013. Database (Oxford). 2013. PMID: 23794735 Free PMC article.
DrugCentral: online drug compendium.
Ursu O, Holmes J, Knockel J, Bologa CG, Yang JJ, Mathias SL, Nelson SJ, Oprea TI. Ursu O, et al. Among authors: oprea ti. Nucleic Acids Res. 2017 Jan 4;45(D1):D932-D939. doi: 10.1093/nar/gkw993. Epub 2016 Oct 26. Nucleic Acids Res. 2017. PMID: 27789690 Free PMC article.
How to Illuminate the Druggable Genome Using Pharos.
Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI. Sheils T, et al. Among authors: oprea ti. Curr Protoc Bioinformatics. 2020 Mar;69(1):e92. doi: 10.1002/cpbi.92. Curr Protoc Bioinformatics. 2020. PMID: 31898878 Free PMC article.
Toxicology knowledge graph for structural birth defects.
Evangelista JE, Clarke DJB, Xie Z, Marino GB, Utti V, Jenkins SL, Ahooyi TM, Bologa CG, Yang JJ, Binder JL, Kumar P, Lambert CG, Grethe JS, Wenger E, Taylor D, Oprea TI, de Bono B, Ma'ayan A. Evangelista JE, et al. Among authors: oprea ti. Commun Med (Lond). 2023 Jul 17;3(1):98. doi: 10.1038/s43856-023-00329-2. Commun Med (Lond). 2023. PMID: 37460679 Free PMC article.
208 results