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Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Winick-Ng W, et al. Among authors: thieme cj. Nature. 2021 Nov;599(7886):684-691. doi: 10.1038/s41586-021-04081-2. Epub 2021 Nov 17. Nature. 2021. PMID: 34789882 Free PMC article.
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie RA, Thieme CJ, Annunziatella C, Baugher C, Zhang Y, Schueler M, Kukalev A, Kempfer R, Chiariello AM, Bianco S, Li Y, Davis T, Scialdone A, Welch LR, Nicodemi M, Pombo A. Beagrie RA, et al. Among authors: thieme cj. Nat Methods. 2023 Jul;20(7):1037-1047. doi: 10.1038/s41592-023-01903-1. Epub 2023 Jun 19. Nat Methods. 2023. PMID: 37336949 Free PMC article.
tRNA-Related Sequences Trigger Systemic mRNA Transport in Plants.
Zhang W, Thieme CJ, Kollwig G, Apelt F, Yang L, Winter N, Andresen N, Walther D, Kragler F. Zhang W, et al. Among authors: thieme cj. Plant Cell. 2016 Jun;28(6):1237-49. doi: 10.1105/tpc.15.01056. Epub 2016 Jun 7. Plant Cell. 2016. PMID: 27268430 Free PMC article.
Extensive folding variability between homologous chromosomes in mammalian cells.
Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Irastorza-Azcarate I, et al. Among authors: thieme cj. bioRxiv [Preprint]. 2024 May 10:2024.05.08.591087. doi: 10.1101/2024.05.08.591087. bioRxiv. 2024. PMID: 38766012 Free PMC article. Preprint.
Endogenous Arabidopsis messenger RNAs transported to distant tissues.
Thieme CJ, Rojas-Triana M, Stecyk E, Schudoma C, Zhang W, Yang L, Miñambres M, Walther D, Schulze WX, Paz-Ares J, Scheible WR, Kragler F. Thieme CJ, et al. Nat Plants. 2015 Mar 23;1(4):15025. doi: 10.1038/nplants.2015.25. Nat Plants. 2015. PMID: 27247031
SplamiR--prediction of spliced miRNAs in plants.
Thieme CJ, Gramzow L, Lobbes D, Theissen G. Thieme CJ, et al. Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17. Bioinformatics. 2011. PMID: 21421552