| The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ... Nucleic acids research 51 (D1), D638-D646, 2023 | 1109 | 2023 |
| An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ... Genome biology 17, 1-19, 2016 | 412 | 2016 |
| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019 | 351 | 2019 |
| Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task A Sarker, M Belousov, J Friedrichs, K Hakala, S Kiritchenko, F Mehryary, ... Journal of the American Medical Informatics Association 25 (10), 1274-1283, 2018 | 88 | 2018 |
| Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations A Miranda, F Mehryary, J Luoma, S Pyysalo, A Valencia, M Krallinger Proceedings of the seventh BioCreative challenge evaluation workshop, 11-21, 2021 | 69 | 2021 |
| Deep learning with minimal training data: TurkuNLP entry in the BioNLP shared task 2016 F Mehryary, J Björne, S Pyysalo, T Salakoski, F Ginter Proceedings of the 4th BioNLP shared task workshop, 73-81, 2016 | 42 | 2016 |
| The STRING database in 2023: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest., 2023, 51, pp D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ... D638-D646. DOI: https://doi. org/10.1093/nar/gkac1000, 0 | 27 | |
| Neural network and random forest models in protein function prediction K Hakala, S Kaewphan, J Björne, F Mehryary, H Moen, M Tolvanen, ... IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (3 …, 2020 | 26 | 2020 |
| Combining support vector machines and LSTM networks for chemical–protein relation extraction F Mehryary, J Björne, T Salakoski, F Ginter Proceedings of the BioCreative VI Workshop 1, 176-80, 2017 | 15 | 2017 |
| Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction F Mehryary, J Björne, T Salakoski, F Ginter Database 2018, bay120, 2018 | 14 | 2018 |
| End-to-end system for bacteria habitat extraction F Mehryary, K Hakala, S Kaewphan, J Björne, T Salakoski, F Ginter BioNLP 2017, 80-90, 2017 | 14 | 2017 |
| TurkuNLP entry for interactive Bio-ID assignment S Kaewphan, F Mehryary, K Hakala, T Salakoski, F Ginter Proceedings of the BioCreative VI Workshop, 32-35, 2017 | 6 | 2017 |
| Entity-Pair Embeddings for Improving Relation Extraction in the Biomedical Domain. F Mehryary, H Moen, T Salakoski, F Ginter ESANN, 613-618, 2020 | 3 | 2020 |
| Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations A Miranda-Escalada, F Mehryary, J Luoma, D Estrada-Zavala, L Gasco, ... Database 2023, baad080, 2023 | 2 | 2023 |
| DrugProt shared task (BioCreative VII track 1-2021) text mining drug-protein/gene interactions (DrugProt) shared task M Krallinger, A Miranda, F Mehryary, J Luoma, S Pyysalo, A Valencia | 2 | 2020 |
| Detecting mentions of pain and acute confusion in Finnish clinical text H Moen, K Hakala, F Mehryary, LM Peltonen, T Salakoski, F Ginter, ... BioNLP 2017, 365-372, 2017 | 2 | 2017 |
| Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification F Mehryary, S Kaewphan, K Hakala, F Ginter Journal of Biomedical Semantics 7, 1-13, 2016 | 2 | 2016 |
| Hypothesis generation in large-scale event networks K Hakala, F Mehryary, S Kaewphan, F Ginter, F Rinaldi, K Jin-Dong Proceedings of the 5th International Symposium on Languages in Biology and …, 2013 | 2 | 2013 |
| STRING-ing together protein complexes: extracting physical protein interactions from the literature F Mehryary, K Nastou, T Ohta, LJ Jensen, S Pyysalo bioRxiv, 2023.12. 10.570999, 2023 | 1 | 2023 |
| Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter. K Hakala, F Mehryary, H Moen, S Kaewphan, T Salakoski, F Ginter SMM4H@ AMIA, 59-63, 2017 | 1 | 2017 |
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