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Page 1
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. Deutsch EW, et al. Among authors: menschaert g. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. bioRxiv. 2024. PMID: 39314370 Free PMC article. Preprint.
Standardized annotation of translated open reading frames.
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Mudge JM, et al. Among authors: menschaert g. Nat Biotechnol. 2022 Jul;40(7):994-999. doi: 10.1038/s41587-022-01369-0. Nat Biotechnol. 2022. PMID: 35831657 Free PMC article. No abstract available.
TIS Transformer: remapping the human proteome using deep learning.
Clauwaert J, McVey Z, Gupta R, Menschaert G. Clauwaert J, et al. Among authors: menschaert g. NAR Genom Bioinform. 2023 Mar 3;5(1):lqad021. doi: 10.1093/nargab/lqad021. eCollection 2023 Mar. NAR Genom Bioinform. 2023. PMID: 36879896 Free PMC article.
Explainability in transformer models for functional genomics.
Clauwaert J, Menschaert G, Waegeman W. Clauwaert J, et al. Among authors: menschaert g. Brief Bioinform. 2021 Sep 2;22(5):bbab060. doi: 10.1093/bib/bbab060. Brief Bioinform. 2021. PMID: 33834200 Free PMC article.
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Deutsch EW, et al. Among authors: menschaert g. J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15. J Proteome Res. 2017. PMID: 28849660 Free PMC article.
CpG Transformer for imputation of single-cell methylomes.
De Waele G, Clauwaert J, Menschaert G, Waegeman W. De Waele G, et al. Among authors: menschaert g. Bioinformatics. 2022 Jan 12;38(3):597-603. doi: 10.1093/bioinformatics/btab746. Bioinformatics. 2022. PMID: 34718418 Free PMC article.
67 results