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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: van heesch s. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. bioRxiv. 2024. PMID: 39314370 Free PMC article. Preprint.
Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Hofman DA, et al. Among authors: van heesch s. bioRxiv [Preprint]. 2023 May 6:2023.05.04.539399. doi: 10.1101/2023.05.04.539399. bioRxiv. 2023. Update in: Mol Cell. 2024 Jan 18;84(2):261-276.e18. doi: 10.1016/j.molcel.2023.12.003 PMID: 37205492 Free PMC article. Updated. Preprint.
What can Ribo-seq and proteomics tell us about the non-canonical proteome?
Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Deutsch EW, van Heesch S. Prensner JR, et al. Among authors: van heesch s. bioRxiv [Preprint]. 2023 May 18:2023.05.16.541049. doi: 10.1101/2023.05.16.541049. bioRxiv. 2023. Update in: Mol Cell Proteomics. 2023 Sep;22(9):100631. doi: 10.1016/j.mcpro.2023.100631 PMID: 37292611 Free PMC article. Updated. 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: van heesch s. 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.
Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.
Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N. Sandmann CL, et al. Among authors: van heesch s. Mol Cell. 2023 Mar 16;83(6):994-1011.e18. doi: 10.1016/j.molcel.2023.01.023. Epub 2023 Feb 17. Mol Cell. 2023. PMID: 36806354 Free PMC article.
Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Hofman DA, et al. Among authors: van heesch s. Mol Cell. 2024 Jan 18;84(2):261-276.e18. doi: 10.1016/j.molcel.2023.12.003. Epub 2024 Jan 3. Mol Cell. 2024. PMID: 38176414 Free article.
Evolution and implications of de novo genes in humans.
Broeils LA, Ruiz-Orera J, Snel B, Hubner N, van Heesch S. Broeils LA, et al. Among authors: van heesch s. Nat Ecol Evol. 2023 Jun;7(6):804-815. doi: 10.1038/s41559-023-02014-y. Epub 2023 Mar 16. Nat Ecol Evol. 2023. PMID: 36928843 Review.
Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes.
Ansari SA, Dantoft W, Ruiz-Orera J, Syed AP, Blachut S, van Heesch S, Hübner N, Uhlenhaut NH. Ansari SA, et al. Among authors: van heesch s. Comput Struct Biotechnol J. 2022 Oct 3;20:5622-5638. doi: 10.1016/j.csbj.2022.09.042. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 36284713 Free PMC article.
45 results