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The Units Ontology: a tool for integrating units of measurement in science.
Gkoutos GV, Schofield PN, Hoehndorf R. Gkoutos GV, et al. Among authors: hoehndorf r. Database (Oxford). 2012 Oct 10;2012:bas033. doi: 10.1093/database/bas033. Print 2012. Database (Oxford). 2012. PMID: 23060432 Free PMC article.
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. Vos RA, et al. Among authors: hoehndorf r. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. eCollection 2020. F1000Res. 2020. PMID: 32308977 Free PMC article.
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs).
Othoum G, Prigent S, Derouiche A, Shi L, Bokhari A, Alamoudi S, Bougouffa S, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H, Lafi FF, Nielsen J, Bajic VB, Mijakovic I, Essack M. Othoum G, et al. Among authors: hoehndorf r. Sci Rep. 2019 Dec 17;9(1):19254. doi: 10.1038/s41598-019-55726-2. Sci Rep. 2019. PMID: 31848398 Free PMC article.
DeepGOPlus: improved protein function prediction from sequence.
Kulmanov M, Hoehndorf R. Kulmanov M, et al. Among authors: hoehndorf r. Bioinformatics. 2020 Jan 15;36(2):422-429. doi: 10.1093/bioinformatics/btz595. Bioinformatics. 2020. PMID: 31350877
Integrating systems biology models and biomedical ontologies.
Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Hoehndorf R, et al. BMC Syst Biol. 2011 Aug 11;5:124. doi: 10.1186/1752-0509-5-124. BMC Syst Biol. 2011. PMID: 21835028 Free PMC article.
PIDO: the primary immunodeficiency disease ontology.
Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C. Adams N, et al. Among authors: hoehndorf r. Bioinformatics. 2011 Nov 15;27(22):3193-9. doi: 10.1093/bioinformatics/btr531. Epub 2011 Sep 22. Bioinformatics. 2011. PMID: 21949270
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.
Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B. Wimalaratne SM, et al. Among authors: hoehndorf r. Bioinformatics. 2012 Feb 1;28(3):448-50. doi: 10.1093/bioinformatics/btr662. Epub 2011 Nov 29. Bioinformatics. 2012. PMID: 22130590
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Hoehndorf R, et al. Bioinformatics. 2012 Jul 1;28(13):1783-9. doi: 10.1093/bioinformatics/bts250. Epub 2012 Apr 26. Bioinformatics. 2012. PMID: 22539675 Free PMC article.
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.
Hoehndorf R, Dumontier M, Gkoutos GV. Hoehndorf R, et al. Bioinformatics. 2012 Aug 15;28(16):2169-75. doi: 10.1093/bioinformatics/bts350. Epub 2012 Jun 17. Bioinformatics. 2012. PMID: 22711793 Free PMC article.
Computational tools for comparative phenomics: the role and promise of ontologies.
Gkoutos GV, Schofield PN, Hoehndorf R. Gkoutos GV, et al. Among authors: hoehndorf r. Mamm Genome. 2012 Oct;23(9-10):669-79. doi: 10.1007/s00335-012-9404-4. Epub 2012 Jul 20. Mamm Genome. 2012. PMID: 22814867 Free PMC article. Review.
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