Palmer WH, Varghese FS, van Rij RP (2018). Natural variation in resistance to virus infection in dipteran insects. Viruses. Mar 9;10(3). pii: E118. doi: 10.3390/v10030118.

Varghese FS, van Rij RP (2018). Insect virus discovery by metagenomic and cell culture-based approaches. Methods Mol Biol. 1746:197-213. doi: 10.1007/978-1-4939-7683-6_16.

Fareh M, van Lopik J, Katechis I, Bronkhorst AW, Haagsma AC, van Rij RP, Joo C (2018). Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA. Nucleic Acids Res. Jan 9. doi: 10.1093/nar/gkx1316.

Melia CE, van der Schaar HM, Lyoo H, Limpens RWAL, Feng Q, Wahedi M, Overheul GJ, van Rij RP, Snijder EJ, Koster AJ, Bárcena M, van Kuppeveld FJM (2017). Escaping host factor PI4KB inhibition: enterovirus genomic RNA replication in the absence of replication organelles. Cell Rep. Oct 17;21(3):587-599. doi: 10.1016/j.celrep.2017.09.068.

Schuster S, Tholen LE, Overheul GJ, van Kuppeveld FJM, van Rij RP (2017). Deletion of cytoplasmic double-stranded RNA sensors does not uncover viral small interfering RNA production in human cells. mSphere. Aug 16;2(4). pii: e00333-17. doi: 10.1128/mSphere.00333-17.

Halbach R, Junglen S, van Rij RP (2017). Mosquito-specific and mosquito-borne viruses: evolution, infection, and host defense. Curr Opin Insect Sci. Aug;22:16-27. doi: 10.1016/j.cois.2017.05.004. Epub 2017 May 6.

Palatini U, Miesen P, Carballar-Lejarazu R, Ometto L, Rizzo E, Tu Z, van Rij RP, Bonizzoni M (2017). Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics. Jul 5;18(1):512. doi: 10.1186/s12864-017-3903-3.

Doublet V, Poeschl Y, Gogol-Döring A, Alaux C, Annoscia D, Aurori C, Barribeau SM, Bedoya-Reina OC, Brown MJ, Bull JC, Flenniken ML, Galbraith DA, Genersch E, Gisder S, Grosse I, Holt HL, Hultmark D, Lattorff HM, Le Conte Y, Manfredini F, McMahon DP, Moritz RF, Nazzi F, Niño EL, Nowick K, van Rij RP, Paxton RJ, Grozinger CM (2017). Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens. BMC Genomics. Mar 2;18(1):207. doi: 10.1186/s12864-017-3597-6

Girardi E, Miesen P, Pennings B, Frangeul L, Saleh MC, van Rij RP (2017). Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 in Aedes aegypti. Nucleic Acids Res. May 5;45(8):4881-4892. doi: 10.1093/nar/gkw1368.

Miesen P, Joosten J, van Rij RP (2016). PIWIs Go Viral: Arbovirus-Derived piRNAs in Vector Mosquitoes. PLoS Path. 12, e1006017.

Martina BE, Barzon L, Pijlman GP, de la Fuente J, Rizzoli A, Wammes LJ, Takken W, van Rij RP, Papa A (2016). Human to human transmission of arthropod-borne pathogens. Curr Opin Virol. doi:10.1016/j.coviro.2016.11.005. [Epub ahead of print]

Göertz GP, Fros JJ, Miesen P, Vogels CB, van der Bent ML, Geertsema C, Koenraadt CJ, van Rij RP, van Oers MM, Pijlman GP (2016). Non-coding subgenomic flavivirus RNA is processed by the mosquito RNAi machinery and determines West Nile virus transmission by Culex pipiens mosquitoes. J Virol, 90, 10145-59.

Miesen P, Ivens A, Buck AH, van Rij RP (2016). Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs. PLoS Negl Trop Dis, 10, e0004452. doi: 10.1371/journal.pntd.0004452.

van Cleef KW, Overheul GJ, Thomassen MC, Marjakangas JM, van Rij RP (2016). Escape Mutations in NS4B Render Dengue Virus Insensitive to the Antiviral Activity of the Paracetamol Metabolite AM404. Antimicrob Agents Chemother., 60, 2554-7. doi: 10.1128/AAC.02462-15.

Merkling, S. H., Overheul, G. J., van Mierlo, J. T., Arends, D., Gilissen, C., & van Rij, R. P. (2015). The heat shock response restricts virus infection in Drosophila. Scientific Reports, 5, 12758. doi:10.1038/srep12758. PDF

Fros JJ, Miesen O, Vogels CB, Gaibani P, Sambri V, Martina BE, Koenraadt CJ, Van Rij RP, Vlak JM, Takken W, Pijlman GP (2015). Comparative Usutu and West Nile virus transmission potential by local Culex pipiens mosquitoes in north-western Europe. One Health, 1, 31-36. doi:10.1016/j.onehlt.2015.08.002.

Merkling, S. H., & van Rij, R. P. (2015). Analysis of resistance and tolerance to virus infection in Drosophila. Nature Protocols, 10(7), 1084–1097. doi:10.1038/nprot.2015.071. PDF

Miesen, P., Girardi, E., & van Rij, R. P. (2015). Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Research, 1–12. doi:10.1093/nar/gkv590. PDF

Merkling, S. H., Bronkhorst, A. W., Kramer, J. M., Overheul, G. J., Schenck A., van Rij RP. (2015). The Epigenetic Regulator G9a Mediates Tolerance to RNA Virus Infection in Drosophila.  PLoS Pathogens. doi:10.1371/journal.ppat.1004692. PDF

Van Mierlo JT, Overheul GJ, Obadia B, van Cleef KW, Webster CL, Saleh MC, Obbard DJ, van Rij RP. (2014). Novel Drosophila viruses encode host-specific suppressors of RNAi. PLoS Pathogens, 10: e1004256. doi:10.1371/journal.ppat.1004256. PDF

Van Cleef KW, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S, and van Rij RP. (2014). Mosquito and Drosophila entomobirnaviruses suppress dsRNA and siRNA-induced RNAi. Nucleic Acids Res, 42(13):8732-44. doi:10.1093/nar/gku528. PDF

Bronkhorst AW & van Rij RP. (2014). The long and short of antiviral defense: small RNA-based immunity in insects. Current Opinion in Virology, 7C, 19–28. doi:10.1016/j.coviro.2014.03.010. PDF

Bronkhorst, A. W., Miesen, P., Van Rij, R. P.. (2013). Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects. Fly7(4), 216–223. PDF

Van Cleef, K. W. R., Overheul, G. J., Thomassen, M. C., Kaptein, S. J. F., Davidson, A. D., Jacobs, M., Neyts, J., Van Kuppeveld, F. J. Van Rij, R. P. (2013). Identification of a new dengue virus inhibitor that targets the viral NS4B protein and restricts genomic RNA replication. Antiviral research, 99(2), 165–171. doi:10.1016/j.antiviral.2013.05.011 PDF

Libri, V., Miesen, P., Van Rij, R. P., & Buck, A. H. (2013). Regulation of microRNA biogenesis and turnover by animals and their viruses. Cellular and molecular life sciences, 70, 3525–3544. doi:10.1007/s00018-012-1257-1 PDF

Bronkhorst, A. W., van Cleef, K. W. R., Vodovar, N., Ince, I. A., Blanc, H., Vlak, J. M., Saleh, M.-C., & Van Rij, R. P. (2012). The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery. Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1207213109 PDF

Feng, Q., Hato, S. V, Langereis, M. A, Zoll, J., Virgen-Slane, R., Peisley, A., Hur, S., Semler, B.L., Van Rij, R.P., & Van Kuppeveld, F.J. (2012). MDA5 Detects the Double-Stranded RNA Replicative Form in Picornavirus-Infected Cells. Cell reports, 2(5), 1187–1196. doi:10.1016/j.celrep.2012.10.005 PDF

Grimm, D., Dalmay, T., & van Rij, R. P. (2012). Everybody wins! Poland hosts thrilling competitions of viruses, RNAi and football teams. EMBO reports, 13(10), 874–6. doi:10.1038/embor.2012.136 PDF

van Mierlo, J. T., Bronkhorst, A. W., Overheul, G. J., Sadanandan, S. A, Ekström, J.-O., Heestermans, M., Hultmark, D., Antoniewski, C. & Van Rij, R.P. (2012). Convergent evolution of argonaute-2 slicer antagonism in two distinct insect RNA viruses. PLoS pathogens, 8(8), e1002872. doi:10.1371/journal.ppat.1002872 PDF

Merkling, S. H., & van Rij, R. P. (2012). Beyond RNAi: Antiviral defense strategies in Drosophila and mosquito. Journal of insect physiology. doi:10.1016/j.jinsphys.2012.07.004 PDF

Vodovar, N., Bronkhorst, A. W., van Cleef, K. W. R., Miesen, P., Blanc, H., van Rij, R. P.*, & Saleh, M.-C.* (2012). Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells. PloS ONE, 7(1), e30861. doi:10.1371/journal.pone.0030861 *Corresponding authors. PDF

J.T. van Mierlo, K.W. van Cleef, & R.P. van Rij, 2011. Defense and counter-defense in the Drosophila RNAi-based antiviral immune system. Methods Mol Biol, 721: 3-22. PDF

K.W. van Cleef, J.T. van Mierlo, M. van den Beek, & R.P. van Rij, 2011. Identification of viral suppressors of RNAi using reporter assays in Drosophila S2 cell culture. Methods Mol Biol, 721: 201-213.PDF

van Mierlo, J. T., van Cleef, K. W. R., & van Rij, R. P. (2010). Small Silencing RNAs: Piecing Together a Viral Genome. Cell host & microbe, 7(2), 87–9. doi:10.1016/j.chom.2010.02.001 PDF

van Rij, R. P., & Berezikov, E. (2009).Small RNAs and the control of transposons and viruses in Drosophila. Trends in microbiology, 17(4), 163–71. doi:10.1016/j.tim.2009.01.003 PDF

Saleh, M.-C., Tassetto, M.*, van Rij, R. P.*, Goic, B., Gausson, V., Berry, B., Jacquier, C., Antoniewski, C. & Andino, R. (2009). Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature, 458(7236), 346–50. doi:10.1038/nature07712 (* equal contribution). PDF

van Rij, R. P. (2008). Virus meets RNAi. Symposium on antiviral applications of RNA interference. EMBO reports, 9(8), 725–9. doi:10.1038/embor.2008.133 PDF

van Rij, R. P., Saleh, M.-C., Berry, B., Foo, C., Houk, A., Antoniewski, C., & Andino, R. (2006). The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes & development, 20(21), 2985–95. doi:10.1101/gad.1482006 PDF

Saleh MC*, Van Rij RP*., Hekele, A., Gillis, A., Foley, E., O’Farrell, P. H., & Andino, R. (2006). The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing. Nature cell biology, 8(8), 793–802. doi:10.1038/ncb1439 (*equal contribution). PDF

van Rij, R.P. & Andino, R. 2008. Complex interactions of viruses and the RNAi machinery: a driving force in viral evolution. In Origin and Evolution of Viruses. E. Domingo, C. Parrish, J.J. Holland, editors., 2nd edition, Elsevier.

van Rij, R.P. & Andino, R. 2006. The silent treatment: RNAi as a defense against virus infection in mammals. Trends Biotechnol 24:186-193. PDF

van Rij, R.P. & Andino, R. 2005. RNAi as an antiviral mechanism and therapeutic approach. In Molecular pathogenesis of viral infections, Society for General Microbiology Symposia No. 64. P. Digard, A.A. Nash, and R.E. Randall, editors. Cambridge University Press.

Saleh, M.C.*, Van Rij, R.P.*, and Andino, R. 2004. RNA silencing in viral infections: insights from poliovirus. Virus Res 102:11-17. (*equal contribution). PDF

Complete list of publications in PubMed