# first author; *corresponding author


Ferreira-Cerca S. (Editor). Archaea : Methods and Protocols. New York: Humana Press; 2022. https://doi.org/10.1007/978-1-0716-2445-6.


Pre_2: Baes R, Grünberger F, Pyr dit Ruys S, Couturier M, De Keulenaer S, Skevin S, Van Nieuwerburgh F, Vertommen D, Grohmann D, Ferreira-Cerca S and Peeters E *. Transcriptional and translational dynamics underlying heat shock response in the thermophilic Crenarchaeon Sulfolobus acidocaldarius. BioRxiv 2022. https://doi.org/10.1101/2022.12.17.520879.

Pre_1: Grünberger F, Knüppel R, Jüttner M, Fenk M, Borst A, Reichelt R, Hausner W, Soppa J, Ferreira-Cerca S * and Dina Grohmann *. Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications. BioRxiv 2020. https://doi.org/10.1101/2019.12.18.880849. Highlighted in Nanopore White paper on Microbiology


30: Grünberger F, Jüttner M, Knüppel R, Ferreira-Cerca S * and Dina Grohmann *. Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing. BioRxiv 2022. https://doi.org/10.1101/2021.06.14.448286. Accepted, in the press.


29: Ferreira-Cerca S *. The dark side of the ribosome life cycle. RNA Biology 2022; 19:1, 1045–1049. https://doi.org/10.1080/15476286.2022.2121421. PMID36082947.

28: Jüttner M & Ferreira-Cerca S *. Ribosomenbiogenese in Archaeen. BIOspektrum 2022; 28, 478–480. https://doi.org/10.1007/s12268-022-1815-5.

27: Kern M & Ferreira-Cerca S *. Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea. Methods Mol Biol. 2022; 2533:229-246. https://doi.org/10.1007/978-1-0716-2501-9_14. PMID: 35796992.

26: Braun C #, Knüppel R #, Perez-Fernandez J *, Ferreira-Cerca S *. Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil. Methods Mol Biol. 2022; 2533:199-213. https://doi.org/10.1007/978-1-0716-2501-9_12. PMID: 35796990.

25: Jüttner M & Ferreira-Cerca S *. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. Methods Mol Biol. 2022; 2533:3-22. https://doi.org/10.1007/978-1-0716-2501-9_1. PMID: 35796979

24: Jüttner M & Ferreira-Cerca S *. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Molecular Biology and Evolution 2022. https://doi.org/10.1093/molbev/msac054


23: Grünberger F, Ferreira-Cerca S and Dina Grohmann. Nanopore sequencing of RNA and cDNA molecules in Escherichia coli. RNA 2021. https://doi.org/10.1261/rna.078937.121. PMID: 34906997 

22: Ferreira-Cerca S *, A La Teana * and Londei P *. Ribosome Editorial: Archaeal Ribosomes: Biogenesis, Structure and Function. Front. Microbiol. 2021; 12:800052. https://doi.org/10.3389/fmicb.2021.800052.

21: Londei P * and Ferreira-Cerca S *. Ribosome Biogenesis in Archaea. Front. Microbiol. 2021; 12:686977. https://doi.org/10.3389/fmicb.2021.686977. PMID: 34367089.

20: Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax T.E.F, Albers S.-V., Oeffinger M and Ferreira-Cerca S *. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res. 2021. https://doi.org/10.1093/nar/gkaa1268. PMID: 33434266.


19: Schwarz TS, Berkemer SJ, Bernhart SH, Weiß M, Ferreira-Cerca S, Stadler PF and Marchfelder A. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in ArchaeaFront. Microbiol. 2020; 11:594838. https://doi.org/10.3389/fmicb.2020.594838. PMID: 33329479; PMCID: PMC7714728.

18: Schulze S, Adams Z, Cerletti M, De Castro R, Ferreira-Cerca S, Fufezan C, Giménez MI, Hippler M, Jevtic Z, Knüppel R, Legerme G, Lenz C, Marchfelder A, Maupin-Furlow J, Paggi RA, Pfeiffer F, Poetsch A, Urlaub H, Pohlschroder M. The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun. 2020 Jun 19;11(1):3145. https://doi.org/10.1038/s41467-020-16784-7. PMID: 32561711; PMCID: PMC7305310.

17: Knüppel R #, Fenk M #, Jüttner M, Ferreira-Cerca S *. In Vivo RNA Chemical Footprinting Analysis in Archaea. Methods Mol Biol. 2020;2106:193-208. https://doi.org/10.1007/978-1-0716-0231-7_12. PMID: 31889259.

16: Jüttner M, Weiß M, Ostheimer N, Reglin C, Kern M, Knüppel R, Ferreira-Cerca S*. A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea. Nucleic Acids Res. 2020 Feb 28;48(4):2073-2090. http://doi.org/10.1093/nar/gkz1156. PMID: 31828323; PMCID: PMC7038931.


15: Mitterer V, Shayan R, Ferreira-Cerca S *, Murat G, Enne T, Rinaldi D, Weigl S, Omanic H, Gleizes PE, Kressler D *, Plisson-Chastang C *, Pertschy B *. Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism. Nat Commun. 2019 Jun 21;10(1):2754. https://doi.org/10.1038/s41467-019-10678-z. PMID: 31227701; PMCID: PMC6588571.

14: Linnemann J, Pöll G, Jakob S, Ferreira-Cerca S, Griesenbeck J, Tschochner H, Milkereit P. Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One. 2019 Jan 17;14(1):e0203415. https://doi.org/10.1371/journal.pone.0203415. PMID: 30653518; PMCID: PMC6336269.

13: Berto G, Ferreira-Cerca S, De Wulf P. The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr Genet. 2019 Apr;65(2):457-466. https://doi.org/10.1007/s00294-018-0912-y. Epub 2018 Dec 4. PMID: 30515528.


12: Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient activated network in Saccharomyces cerevisiae. Nucleic Acids Res. 2018 Sep 6;46(15):7586-7611. https://doi.org/10.1093/nar/gky618. PMID: 30011030; PMCID: PMC6125641.

11: Knüppel R, Christensen RH, Gray FC, Esser D, Strauß D, Medenbach J, Siebers B, MacNeill SA, LaRonde N, Ferreira-Cerca S *. Insights into the evolutionary conserved regulation of Rio ATPase activity. Nucleic Acids Res. 2018 Feb 16;46(3):1441-1456. https://doi.org/10.1093/nar/gkx1236. PMID: 29237037; PMCID: PMC5815136.


10: Ferreira-Cerca S *. (2017) Life and Death of Ribosomes in Archaea. In: Clouet-d’Orval B. (eds) RNA Metabolism and Gene Expression in Archaea. Nucleic Acids and Molecular Biology, vol 32. Springer, Cham. https://doi.org/10.1007/978-3-319-65795-0_6

9: Knüppel R #, Kuttenberger C #, Ferreira-Cerca S*. Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil. Front Microbiol. 2017 Feb 24;8:286. https://doi.org/10.3389/fmicb.2017.00286. PMID: 28286499; PMCID: PMC5323407.


8: Iacovella MG, Golfieri C, Massari LF, Busnelli S, Pagliuca C, Dal Maschio M, Infantino V, Visintin R, Mechtler K, Ferreira-Cerca S, De Wulf P. Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation. Nat Commun. 2015 Apr 8;6:6643. https://doi.org/10.1038/ncomms7643. PMID: 25851096.


7: Ferreira-Cerca S #*, Kiburu I #, Thomson E, LaRonde N *, Hurt E *. Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes. Nucleic Acids Res. 2014 Jul;42(13):8635-47. https://doi.org/10.1093/nar/gku542. Epub 2014 Jun 19. PMID: 24948609; PMCID: PMC4117770.


6: Thomson E #*, Ferreira-Cerca S #*, Hurt E. Eukaryotic ribosome biogenesis at a glance. J Cell Sci. 2013 Nov 1;126(Pt 21):4815-21. https://doi.org/10.1242/jcs.111948. PMID: 24172536.

2004 – 2012

5: Ferreira-Cerca S #, Sagar V #, Schäfer T, Diop M, Wesseling AM, Lu H, Chai E, Hurt E, LaRonde-LeBlanc N. ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit. Nat Struct Mol Biol. 2012 Dec;19(12):1316-23. https://doi.org/10.1038/nsmb.2403. Epub 2012 Oct 28. PMID: 23104056; PMCID: PMC3515705.

4: Ferreira-Cerca S, Hurt E. Cell biology: Arrest by ribosome. Nature. 2009 May 7;459(7243):46-7. https://doi.org/10.1038/459046a. PMID: 19424147.

3: Ferreira-Cerca S, Pöll G, Kühn H, Neueder A, Jakob S, Tschochner H, Milkereit P. Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins. Mol Cell. 2007 Nov 9;28(3):446-57. doi: 10.1016/j.molcel.2007.09.029. PMID: 17996708.

2: Ferreira-Cerca S, Pöll G, Gleizes PE, Tschochner H, Milkereit P. Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function. Mol Cell. 2005 Oct 28;20(2):263-75. https://doi.org/10.1016/j.molcel.2005.09.005. PMID: 16246728.

1: Léger-Silvestre I, Milkereit P, Ferreira-Cerca S, Saveanu C, Rousselle JC, Choesmel V, Guinefoleau C, Gas N, Gleizes PE. The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast. EMBO J. 2004 Jun 16;23(12):2336-47. https://doi.org/10.1038/sj.emboj.7600252. Epub 2004 May 27. PMID: 15167894; PMCID: PMC423291.