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ALL-tRNAseq enables robust tRNA profiling in tissue samples.
Scheepbouwer C, Aparicio-Puerta E, Gomez-Martin C, Verschueren H, van Eijndhoven M, Wedekind LE, Giannoukakos S, Hijmering N, Gasparotto L, van der Galien HT, van Rijn RS, Aronica E, Kibbelaar R, Heine VM, Wesseling P, Noske DP, Vandertop WP, de Jong D, Pegtel DM, Hackenberg M, Wurdinger T, Gerber A, Koppers-Lalic D. Scheepbouwer C, et al. Among authors: aparicio puerta e. Genes Dev. 2023 Mar 1;37(5-6):243-257. doi: 10.1101/gad.350233.122. Epub 2023 Feb 21. Genes Dev. 2023. PMID: 36810209 Free PMC article.
Validation of human microRNA target pathways enables evaluation of target prediction tools.
Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, Fehlmann T, Kahraman M, Rheinheimer S, Aparicio-Puerta E, Wagner S, Ludwig N, Backes C, Lenhof HP, von Briesen H, Hart M, Keller A, Meese E. Kern F, et al. Nucleic Acids Res. 2021 Jan 11;49(1):127-144. doi: 10.1093/nar/gkaa1161. Nucleic Acids Res. 2021. PMID: 33305319 Free PMC article.
isomiRdb: microRNA expression at isoform resolution.
Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. Aparicio-Puerta E, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D179-D185. doi: 10.1093/nar/gkac884. Nucleic Acids Res. 2023. PMID: 36243964 Free PMC article.
Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing.
Gómez-Martín C, Aparicio-Puerta E, van Eijndhoven MAJ, Medina JM, Hackenberg M, Pegtel DM. Gómez-Martín C, et al. Among authors: aparicio puerta e. Cell Rep Methods. 2023 May 16;3(5):100480. doi: 10.1016/j.crmeth.2023.100480. eCollection 2023 May 22. Cell Rep Methods. 2023. PMID: 37323569 Free PMC article.
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.
Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Desvignes T, et al. Bioinformatics. 2020 Feb 1;36(3):698-703. doi: 10.1093/bioinformatics/btz675. Bioinformatics. 2020. PMID: 31504201 Free PMC article.
MirGeneDB 2.0: the metazoan microRNA complement.
Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. Fromm B, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D132-D141. doi: 10.1093/nar/gkz885. Nucleic Acids Res. 2020. PMID: 31598695 Free PMC article.
28 results