Viral deubiquitinating proteases and the promising strategies of their inhibition (pdf)
van Vliet VJE, De Silva A, Mark BL, Kikkert M. Virus Res. 2024
Deubiquitinating activity of SARS-CoV-2 papain-like protease does not influence virus replication or innate immune responses in vivo (pdf)
van Huizen M, Bloeme-Ter Horst JR, de Gruyter HLM, Geurink PP, van der Heden van Noort GJ, Knaap RCM, Nelemans T, Ogando NS, Leijs AA, Urakova N, Mark BL, Snijder EJ, Myeni SK, Kikkert M. PLoS Pathog. 2024
The Main Protease of Middle East Respiratory Syndrome Coronavirus Induces Cleavage of Mitochondrial Antiviral Signaling Protein to Antagonize the Innate Immune Response (pdf)
van Huizen M, Vendrell XM, de Gruyter HLM, Boomaars-van der Zanden AL, van der Meer Y, Snijder EJ, Kikkert M, Myeni SK. Viruses. 2024
Influenza A virus propagation requires the activation of the unfolded protein response and the accumulation of insoluble protein aggregates (pdf)
Marques M, Ramos B, Albuquerque H, Pereira M, Ribeiro DR, Nunes A, Sarabando J, Brás D, Ferreira AR, Vitorino R, Amorim MJ, Silva AMS, Soares AR, Ribeiro D. iScience. 2024
Emerging roles of the Protein Phosphatase 1 (PP1) in the context of viral infections. (pdf)
Corda P, Bollen M, Ribeiro D, Fardilha M. Cell Commun Signal. 2024
Temporal resolution of NAIL-MS of tRNA, rRNA and Poly-A RNA is overcome by actinomycin D. (pdf)
Hagelskamp F, Borland K, Ammann G, Kaiser SM. RSC Chem Biol. 2023
Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry.
Ammann G, Berg M, Dalwigk JF, Kaiser SM. Acc Chem Res. 2023.
Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis.
Bailey-Elkin BA, Knaap RCM, De Silva A, Boekhoud IM, Mous S, van Vught N, Khajehpour M, van den Born E, Kikkert M, Mark BL. PLoS Pathog. 2023
Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis (pdf)
Pereira M, Ribeiro DR, Berg M, Tsai AP, Dong C, Nho K, Kaiser S, Moutinho M, Soares AR. Biochim Biophys Acta Mol Basis Dis. 2023
The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections (pdf)
Ribeiro DR, Nunes A, Ribeiro D, Soares AR. Front Genet. 2023
Novel approaches for the rapid development of rationally designed arbovirus vaccines. (pdf) van Bree JWM, Visser I, Duyvestyn JM, Aguilar-Bretones M, Marshall EM, van Hemert MJ, Pijlman GP, van Nierop GP, Kikkert M, Rockx BHG, Miesen P, Fros JJ. One Health. 2023
Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. (pdf) Yared MJ, Yoluç Y, Catala M, Tisné C, Kaiser S, Barraud P. Nucleic Acids Res. 2023.
Determining the Importance of Peroxisomal Proteins for Viral Infections in Cultured Mammalian Cells (pdf)
Marques M, Ferreira AR, Ribeiro D. Methods Mol Biol. 2023
Tools to Investigate the Peroxisome-Dependent Antiviral Response (pdf)
Ramos B., Ferreira A.R., Ribeiro D. Methods Mol Biol. 2023
Peroxisomes and Viruses: Overview on Current Knowledge and Experimental Approaches (pdf)
Ferreira V., Ferreira A. R., Ribeiro D. Methods Mol Biol. 2023
The physiological functions of human peroxisomes (pdf)
Wanders R. J. A, Baes M., Ribeiro D., Ferdinandusse S. and Waterham H. Physiological Reviews 2023
Engineering potent live attenuated coronavirus vaccines by targeted inactivation of the immune evasive viral deubiquitinase (pdf)
Myeni S.K., Bredenbeek P.J., Knaap R.C.M., Dalebout T.J., Morales S.T., Sidorov I.A., Linger M.E., Oreshkova N., van Zanen-Gerhardt S., Zander S.A.L., Enjuanes L., Sola I., Snijder E.J., Kikkert M. Nat Commun. 2023
Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site (pdf)
van Vliet V.J.E., Huynh N., Palà J., Patel A., Singer A., Slater C., Chung J., van Huizen M., Teyra J., Miersch S., Luu G.K., Ye W., Sharma N., Ganaie S. Russell R., Chen C., Maynard M., Amarasinghe G.K., Mark B.L., Kikkert M., Sidhu S.S. PLoS Pathog. 2022
Editorial: Viruses and Epitranscriptomes: Regulation of Infection and Antiviral Response (pdf)
Soares A. R., Kikkert M., Kaiser-Kellner S., Ribeiro D., Front. Cell Dev. Biol., 2022
Upregulation of tRNA-Ser-AGA-2-1 Promotes Malignant Behavior in Normal Bronchial Cells (pdf)
Santos M., Fidalgo A., Varanda A. S., Soares A. R., Almeida G. M., Martins D., Mendes N., Oliveira C., Santos M. A. S., Front. Mol. Biosci., 2022
Human Cytomegalovirus vMIA Inhibits MAVS Oligomerization at Peroxisomes in an MFF-Dependent Manner (pdf)
Ferreira A. R., Gouveia A., Magalhães A. C., Valença I., Marques M., Kagan J. C., Ribeiro D. Front. Cell Dev. Biol., 2022, 10:871977.
Emerging roles of peroxisomes in viral infections (pdf)
Ferreira A.R., Marques M., Ramos B., Kagan J.C., Ribeiro D., Trends in Cell Biolgy, 2022, 32(2):124-139.
m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs (pdf)
Pereira M., Ribeiro D. R., Pinheiro M. M., Ferreira M., Kellner S., Soares A. R. Int. J. Mol. Sci. 2021, 22(6), 2941.
Emerging Roles of tRNAs in RNA Virus Infections (pdf)
Nunes A., Ribeiro D. R., Marques M., Santos M. A. S., Ribeiro D., Soares A. R. Trends in Biochemical Sciences 2020, 45(9):794-805.