| PyKEEN 1.0: A python library for training and evaluating knowledge graph emebddings M Ali, M Berrendorf, CT Hoyt, L Vermue, S Sharifzadeh, V Tresp, ... arXiv preprint arXiv:2007.14175, 2020 | 218 | 2020 |
| Bringing light into the dark: A large-scale evaluation of knowledge graph embedding models under a unified framework M Ali, M Berrendorf, CT Hoyt, L Vermue, M Galkin, S Sharifzadeh, ... IEEE Transactions on Pattern Analysis and Machine Intelligence 44 (12), 8825 …, 2021 | 157 | 2021 |
| The impact of pathway database choice on statistical enrichment analysis and predictive modeling S Mubeen, CT Hoyt, A Gemünd, M Hofmann-Apitius, H Fröhlich, ... Frontiers in genetics 10, 1203, 2019 | 112 | 2019 |
| A review of biomedical datasets relating to drug discovery: a knowledge graph perspective S Bonner, IP Barrett, C Ye, R Swiers, O Engkvist, A Bender, CT Hoyt, ... Briefings in Bioinformatics 23 (6), bbac404, 2022 | 98 | 2022 |
| The role of metadata in reproducible computational research J Leipzig, D Nüst, CT Hoyt, K Ram, J Greenberg Patterns 2 (9), 2021 | 94 | 2021 |
| Mondo: Unifying diseases for the world, by the world NA Vasilevsky, NA Matentzoglu, S Toro, JE Flack IV, H Hegde, DR Unni, ... MedRxiv, 2022.04. 13.22273750, 2022 | 72 | 2022 |
| The Human Phenotype Ontology in 2024: phenotypes around the world MA Gargano, N Matentzoglu, B Coleman, EB Addo-Lartey, ... Nucleic Acids Research, gkad1005, 2023 | 69* | 2023 |
| A simple standard for sharing ontological mappings (SSSOM) N Matentzoglu, JP Balhoff, SM Bello, C Bizon, M Brush, TJ Callahan, ... Database 2022, baac035, 2022 | 66 | 2022 |
| ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases D Domingo-Fernández, CT Hoyt, C Bobis-Álvarez, J Marín-Llaó, ... NPJ systems biology and applications 4 (1), 43, 2018 | 61* | 2018 |
| Understanding the performance of knowledge graph embeddings in drug discovery S Bonner, IP Barrett, C Ye, R Swiers, O Engkvist, CT Hoyt, WL Hamilton Artificial Intelligence in the Life Sciences 2, 100036, 2022 | 60 | 2022 |
| PyBEL: a computational framework for Biological Expression Language CT Hoyt, A Konotopez, C Ebeling Bioinformatics 34 (4), 703-704, 2018 | 44 | 2018 |
| Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies N Matentzoglu, D Goutte-Gattat, SZK Tan, JP Balhoff, S Carbon, ... Database 2022, baac087, 2022 | 43 | 2022 |
| PathMe: merging and exploring mechanistic pathway knowledge D Domingo-Fernández, S Mubeen, J Marín-Llaó, CT Hoyt, ... BMC bioinformatics 20, 1-12, 2019 | 43 | 2019 |
| Democratizing knowledge representation with BioCypher S Lobentanzer, P Aloy, J Baumbach, B Bohar, VJ Carey, P Charoentong, ... Nature Biotechnology 41 (8), 1056-1059, 2023 | 39 | 2023 |
| BioKEEN: a library for learning and evaluating biological knowledge graph embeddings M Ali, CT Hoyt, D Domingo-Fernández, J Lehmann, H Jabeen Bioinformatics 35 (18), 3538-3540, 2019 | 35 | 2019 |
| Repurposing human PDE4 inhibitors for neglected tropical diseases: Design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 … E Amata, ND Bland, CT Hoyt, L Settimo, RK Campbell, MP Pollastri Bioorganic & medicinal chemistry letters 24 (17), 4084-4089, 2014 | 34 | 2014 |
| Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes LM Doherty, CE Mills, SA Boswell, X Liu, CT Hoyt, B Gyori, SJ Buhrlage, ... Elife 11, e72879, 2022 | 33 | 2022 |
| Identifying the parametric occurrence of multiple steady states for some biological networks R Bradford, JH Davenport, M England, H Errami, V Gerdt, D Grigoriev, ... Journal of Symbolic Computation 98, 84-119, 2020 | 31 | 2020 |
| Re-curation and rational enrichment of knowledge graphs in Biological Expression Language CT Hoyt, D Domingo-Fernández, R Aldisi, L Xu, K Kolpeja, S Spalek, ... Database 2019, baz068, 2019 | 31 | 2019 |
| A case study on the parametric occurrence of multiple steady states R Bradford, JH Davenport, M England, H Errami, V Gerdt, D Grigoriev, ... Proceedings of the 2017 ACM on International Symposium on Symbolic and …, 2017 | 29 | 2017 |
Daniel Domingo-FernándezEnveda BiosciencesVerified email at envedabio.com
