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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.
Genome Biol. 2019.
PMID: 31744546
Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A…
See abstract for full author list ➔
Jiang Y, et al. Among authors: kaewphan s.
Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.
Genome Biol. 2016.
PMID: 27604469
Free PMC article.
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Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling.
Kaewphan S, Hakala K, Miekka N, Salakoski T, Ginter F.
Kaewphan S, et al.
Database (Oxford). 2018 Jan 1;2018:1-10. doi: 10.1093/database/bay096.
Database (Oxford). 2018.
PMID: 30239666
Free PMC article.
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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. Among authors: kaewphan s.
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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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: kaewphan s.
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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Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining.
Kreula SM, Kaewphan S, Ginter F, Jones PR.
Kreula SM, et al. Among authors: kaewphan s.
PeerJ. 2018 May 23;6:e4806. doi: 10.7717/peerj.4806. eCollection 2018.
PeerJ. 2018.
PMID: 29844966
Free PMC article.
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Cell line name recognition in support of the identification of synthetic lethality in cancer from text.
Kaewphan S, Van Landeghem S, Ohta T, Van de Peer Y, Ginter F, Pyysalo S.
Kaewphan S, et al.
Bioinformatics. 2016 Jan 15;32(2):276-82. doi: 10.1093/bioinformatics/btv570. Epub 2015 Oct 1.
Bioinformatics. 2016.
PMID: 26428294
Free PMC article.
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Lysophosphatidic acid and sphingosine-1-phosphate promote morphogenesis and block invasion of prostate cancer cells in three-dimensional organotypic models.
Härmä V, Knuuttila M, Virtanen J, Mirtti T, Kohonen P, Kovanen P, Happonen A, Kaewphan S, Ahonen I, Kallioniemi O, Grafström R, Lötjönen J, Nees M.
Härmä V, et al. Among authors: kaewphan s.
Oncogene. 2012 Apr 19;31(16):2075-89. doi: 10.1038/onc.2011.396. Epub 2011 Sep 26.
Oncogene. 2012.
PMID: 21996742
Free PMC article.
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