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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.
Genome Biol. 2016.
PMID: 27604469
Free PMC article.
Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.
Mehryary F, Kaewphan S, Hakala K, Ginter F.
Mehryary F, et al.
J Biomed Semantics. 2016 May 11;7:27. doi: 10.1186/s13326-016-0070-4. eCollection 2016.
J Biomed Semantics. 2016.
PMID: 27175227
Free PMC article.
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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.
Sarker A, Belousov M, Friedrichs J, Hakala K, Kiritchenko S, Mehryary F, Han S, Tran T, Rios A, Kavuluru R, de Bruijn B, Ginter F, Mahata D, Mohammad SM, Nenadic G, Gonzalez-Hernandez G.
Sarker A, et al. Among authors: mehryary f.
J Am Med Inform Assoc. 2018 Oct 1;25(10):1274-1283. doi: 10.1093/jamia/ocy114.
J Am Med Inform Assoc. 2018.
PMID: 30272184
Free PMC article.
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Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction.
Mehryary F, Björne J, Salakoski T, Ginter F.
Mehryary F, et al.
Database (Oxford). 2018 Jan 1;2018:bay120. doi: 10.1093/database/bay120.
Database (Oxford). 2018.
PMID: 30576487
Free PMC article.
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Lar…
See abstract for full author list ➔
Zhou N, et al. Among authors: mehryary f.
Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.
Genome Biol. 2019.
PMID: 31744546
Free PMC article.
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Neural Network and Random Forest Models in Protein Function Prediction.
Hakala K, Kaewphan S, Bjorne J, Mehryary F, Moen H, Tolvanen M, Salakoski T, Ginter F.
Hakala K, et al. Among authors: mehryary f.
IEEE/ACM Trans Comput Biol Bioinform. 2022 May-Jun;19(3):1772-1781. doi: 10.1109/TCBB.2020.3044230. Epub 2022 Jun 3.
IEEE/ACM Trans Comput Biol Bioinform. 2022.
PMID: 33306472
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Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations.
Miranda-Escalada A, Mehryary F, Luoma J, Estrada-Zavala D, Gasco L, Pyysalo S, Valencia A, Krallinger M.
Miranda-Escalada A, et al. Among authors: mehryary f.
Database (Oxford). 2023 Nov 28;2023:baad080. doi: 10.1093/database/baad080.
Database (Oxford). 2023.
PMID: 38015956
Free PMC article.
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The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C.
Szklarczyk D, et al. Among authors: mehryary f.
Nucleic Acids Res. 2023 Jan 6;51(D1):D638-D646. doi: 10.1093/nar/gkac1000.
Nucleic Acids Res. 2023.
PMID: 36370105
Free PMC article.
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