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CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.
Li S, van der Velde KJ, de Ridder D, van Dijk ADJ, Soudis D, Zwerwer LR, Deelen P, Hendriksen D, Charbon B, van Gijn ME, Abbott K, Sikkema-Raddatz B, van Diemen CC, Kerstjens-Frederikse WS, Sinke RJ, Swertz MA. Li S, et al. Among authors: van der velde kj, van dijk adj, van gijn me, van diemen cc. Genome Med. 2020 Aug 24;12(1):75. doi: 10.1186/s13073-020-00775-w. Genome Med. 2020. PMID: 32831124 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, Rehma… See abstract for full author list ➔ Jiang Y, et al. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Sequence-based analysis of protein degradation rates.
Correa Marrero M, van Dijk ADJ, de Ridder D. Correa Marrero M, et al. Among authors: van dijk adj. Proteins. 2017 Sep;85(9):1593-1601. doi: 10.1002/prot.25323. Epub 2017 Jun 10. Proteins. 2017. PMID: 28547871
An analysis of characterized plant sesquiterpene synthases.
Durairaj J, Di Girolamo A, Bouwmeester HJ, de Ridder D, Beekwilder J, van Dijk AD. Durairaj J, et al. Phytochemistry. 2019 Feb;158:157-165. doi: 10.1016/j.phytochem.2018.10.020. Epub 2018 Nov 13. Phytochemistry. 2019. PMID: 30446165
Designing Eukaryotic Gene Expression Regulation Using Machine Learning.
de Jongh RPH, van Dijk ADJ, Julsing MK, Schaap PJ, de Ridder D. de Jongh RPH, et al. Among authors: van dijk adj. Trends Biotechnol. 2020 Feb;38(2):191-201. doi: 10.1016/j.tibtech.2019.07.007. Epub 2019 Aug 17. Trends Biotechnol. 2020. PMID: 31431299 Review.
88 results