Many of these publications are available Open Access. If not, let us know and we will send a pdf.

Preprints

The COVID Moonshot Consortium, Achdout H, Aimon A, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bobby ML, Brun J, Sarma BVNBS, Calmiano M, Carbery A, Cattermole E, Chodera JD, Clyde A, Coffland JE, Cohen G, Cole J, Contini A, Cox L, Cvitkovic M, Dias A, Douangamath A, Duberstein S, Dudgeon T, Dunnett L, Eastman PK, Erez N, Fairhead M, Fearon D, Fedorov O, Ferla M, Foster H, Foster R, Gabizon R, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen R, Glinert I, Gorichko M, Gorrie-Stone T, Griffen EJ, Heer J, Hill M, Horrell S, Hurley MFD, Israely T, Jajack A, Jnoff E, John T, Kantsadi AL, Kenny PW, Kiappes JL, Koekemoer L, Kovar B, Krojer T, Lee AA, Lefker BA, Levy H, London N, Lukacik P, Macdonald HB, MacLean B, Malla TR, Matviiuk T, McCorkindale W, Melamed S, Michurin O, Mikolajek H, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Neto JB, Oleinikovas V, Overheul GJ, Owen D, Pai R, Pan J, Paran N, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Psenak V, Puni R, Rangel VL, Reddi RN, St Patrick Reid, Resnick E, Robinson MC, Robinson RP, Rufa D, Schofield C, Shaikh A, Shi J, Shurrush K, Sittner A, Skyner R, Smalley A, Smilova MD, Spencer J, Strain-Damerell C, Swamy V, Tamir H, Tennant R, Thompson A, Thompson W, Tomasio S, Tumber A, Vakonakis I, van Rij RP, Varghese FS, Vaschetto M, Vitner EB, Voelz V, von Delft A, von Delft F, Walsh M, Ward W, Weatherall C, Weiss S, Wild CF, Wittmann M, Wright N, Yahalom-Ronen Y, Zaidmann D, Zidane H, Zitzmann N. (2020) COVID Moonshot: Open Science discovery of SARS-CoV-2 main protease inhibitors by combining crowdsourcing, high-throughput experiments, computational simulations, and machine learning. bioRxiv 10.1101/2020.10.29.339317

Betting V*, Joosten J*, Halbach R*, Thaler M, Miesen P, Van Rij RP. (2020) A regulatory network of a piRNA and lncRNA initiates responder and trailer piRNA formation during embryonic development of Aedes mosquitoes. bioRxiv DOI:10.1101/2020.03.23003038
*equal contribution

Crava C, Varghese FS, Pischedda E, Halbach R, Palatini U, Marconcini M, Mattia A, Redmond S, Afrane Y, Ayala D, Paupy C, Carballar-Lejarazu R, Miesen P, Van Rij RP*, Bonizzoni M* (2020) Endogenous viral elements in Aedes aegypti. Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective. bioRxiv DOI:10.1101/2020.04.02.022509.
*Corresponding authors

Joosten J, Van Rij RP, Miesen P. (2020) Slicing of viral RNA guided by endogenous piRNAs triggers the production of responder and trailer piRNAs in Aedes mosquitoes. bioRxiv 10.1101/2020.07.08.193029.

Peer-reviewed publications

Halbach R, Miesen P, Joosten J, Taşköprü E, Pennings B, Vogels C, Merkling SH, Koenraadt CJ, Lambrechts L, Van Rij RP, (2020) A satellite repeat-derived piRNA controls embryonic development of Aedes. Nature 580:274–277. DOI:10.1038/s41586-020-2159-2

Hermanns K, Marklewitz M, Zirkel F, Overheul GJ, Page RA, Drosten C, Van Rij RP, Junglen S (2020) Agua Salud alphavirus defines a novel lineage of insect-specific alphaviruses discovered in the New World. J Gen Virol. 101:96-104. DOI:10.1099/jgv.0.001344.

Palatini U, Masri RA, Cosme L, Koren S, Thibaud F, Biedler J, Krstivevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux A, Pischedda E, Michele M, Ghurye J, Rhie A, Caccone A, Sharma A, Karagodin DA, Jenrette J, Gamez S, Miesen P, Sharakova M, Zhijian Tu, Papathanos P, Van Rij RP, Akbari O, Powell J, Phillippy AM, Bonizzoni M. (2020) Improved reference genome of the arbovirus vector Aedes albopictus. Genome Biology 21:215. DOI:10.1186/s13059-020-02141-w.

Suzuki Y, Baidaliuk A, Miesen P, Frangeul L, Crist AB, Merkling SH, Fontaine A, Lequime S, Moltini-Conclois I, Blanc H, Van Rij RP, Lambrechts L, Saleh MC. (2020) Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries. Current Biology 30: 3495-3506.

Genzel L, Adan R, Berns A, van den Beucken JJJP, Blokland A, Boddeke EHWGM, Bogers WM, Bontrop R, Bulthuis R, Bousema T, Clevers H, Coenen TCJJ, van Dam AM, Deen PMT, van Dijk KW, Eggen BJL, Elgersma Y, Erdogan I, Englitz B, Fentener van Vlissingen JM, la Fleur S, Fouchier R, Fitzsimons CP, Frieling W, Haagmans B, Heesters BA, Henckens MJAG, Herfst S, Hol E, van den Hove D, de Jonge MI, Jonkers J, Joosten LAB, Kalsbeek A, Kamermans M, Kampinga HH, Kas MJ, Keijer JA, Kersten S, Kiliaan AJ, Kooij TWA, Kooijman S, Koopman WJH, Korosi A, Krugers HJ, Kuiken T, Kushner SA, Langermans JAM, Lesscher HMB, Lucassen PJ, Lutgens E, Netea MG, Noldus LPJJ, van der Meer JWM, Meye FJ, Mul JD, van Oers K, Olivier JDA, Pasterkamp RJ, Philippens IHCHM, Prickaerts J, Pollux BJA, Rensen PCN, van Rheenen J, van Rij RP, Ritsma L, Rockx BHG, Roozendaal B, van Schothorst EM, Stittelaar K, Stockhofe N, Swaab DF, de Swart RL, Vanderschuren LJMJ, de Vries TJ, de Vrij F, van Wezel R, Wierenga CJ, Wiesmann M, Willuhn I, de Zeeuw CI, Homberg JR. (2020), How the COVID-19 pandemic highlights the necessity of research. Current Biology 30: R1014-R1018 DOI:10.1016/j.cub.2020.08.030.

Betting V & Van Rij RP (2020) Countering counter-defense to antiviral RNAi. Trends in Microbiology 28:600-602. DOI:10.1016/j.tim.2020.05.018.

Leonetti P, Miesen P, Van Rij RP*, Pantaleo V* (2020) Viral And Sub-Viral Derived Small RNAs as Pathogenic Determinants in plants and insects. Adv Virus Res. 107:1-36. DOI:10.1016/bs.aivir.2020.04.001.
*corresponding authors.

Bronkhorst AW*, Vogels R*, Overheul GJ*, Pennings B, Gausson-Dorey V, Miesen P, Van Rij RP (2019) A DNA virus-encoded immune antagonist fully masks the potent antiviral activity of RNAi in Drosophila. Proc Natl Acad Sci U S A. 116:24296-24302. DOI:10.1073/pnas.1909183116.

Schuster S, Overheul GJ, Lisa Bauer, Van Kuppeveld FJ, van Rij RP. (2019) No evidence for viral siRNA production and antiviral function of Argonaute 2 in human cells. Scientific Reports. 9:13752. DOI: 10.1038/s41598-019-50287-w.

Schuster S, Miesen P, van Rij RP. (2019) Antiviral RNAi in insects and mammals: parallels and differences. Viruses. 11(5). E448. DOI: 10.3390/v11050448.

Göertz GP, Miesen P, Overheul GJ, van Rij RP, van Oers MM, Pijlman GP. (2019) Mosquito small RNA responses against West Nile and insect-specific virus infections in Aedes and Culex mosquito cells. Viruses 11:E271. DOI:10.3390/v11030271.

Riahi H, Brekelmans C, Foriel S, Merkling SH, Lyons TA, Itskov PM, Kleefstra T, Ribiero C, van Rij RP, Kramer JM, Schenck A. (2019) The histone methyltransferase G9a regulates tolerance to oxidative stress-induced energy consumption. PLoS Biology, 17: e2006146 DOI:10.1371/journal.pbio.2006146.

Merkling SH, Riahi H, Overheul GJ, Schenck A, Van Rij RP. (2019) The peroxisome-associated Sgroppino is associated with altered fat metabolism and reduced survival after RNA virus infection in Drosophila. Scientific Reports, 9:2065. DOI:10.1038/s41598-019-38559-x.

Miesen P & van Rij RP. (2019) Crossing the mucosal barrier: A bacterial symbiont gives dengue virus a leg-up in the mosquito midgut. Cell Host & Microbe 25:1-2. DOI: 10.1016/j.chom.2018.12.009.

Riswari SF, Tunjungputri RN, Kullaya V, Garishah FM, Utari GSR, Farhanah N, Overheul GJ, Alisjahbana B, Gasem MH, Urbanus RT, de Groot PG, Lefeber DJ, van Rij RP, van der Ven A, de Mast Q. (2019) Desialylation of platelets induced by VWF is a novel mechanism of platelet clearance in dengue. PLoS Pathogens 15(3): e1007500, DOI:10.1371/journal.ppat.1007500.

Joosten J, Miesen P, Tasköprü E, Pennings B, Jansen PW, Huynen MA, Vermeulen M, Van Rij RP. (2019). The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes. Nucleic Acids Res. 47: 2546–2559, DOI:10.1093/nar/gky1266.

Palmer WH, Joosten J, Overheul GJ, Jansen PW, Vermeulen M, Obbard DJ, Van Rij RP. (2018). Induction and Suppression of NF-κB Signalling by a DNA Virus of Drosophila. J Virol. 93(3):e01443-18. DOI:10.1128/JVI.01443-18.

Meutiawati F, Bezemer B, Strating JRPM, Overheul GJ, Žusinaite E, van Kuppeveld FJM, van Cleef KWR, van Rij RP (2018). Posaconazole inhibits dengue virus replication by targeting oxysterol-binding protein. Antiviral Res.157:68-79. DOI:10.1016/j.antiviral.2018.06.017.

Palmer WH, Varghese FS, van Rij RP (2018). Natural variation in resistance to virus infection in dipteran insects. Viruses. 10(3):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. 46:3187-3197. DOI:10.1093/nar/gkx1316.
* corresponding authors

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. 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. 2(4): 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. 22:16-27. DOI:10.1016/j.cois.2017.05.004.

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. 18:512. DOI:10.1186/s12864-017-3903-3.
* Equal contribution

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. 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. 45(8):4881-4892. DOI:10.1093/nar/gkw1368.
*equal contribution.

Miesen P, Joosten J, van Rij RP (2016). PIWIs Go Viral: Arbovirus-Derived piRNAs in Vector Mosquitoes. PLoS Path. 12, e1006017. DOI:10.1371/journal.ppat.1006017.

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. 22:13-21. DOI:10.1016/j.coviro.2016.11.005.

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 SH, Overheul GJ, van Mierlo JT, Arends D, Gilissen C, van Rij RP (2015) The heat shock response restricts virus infection in Drosophila. Scientific Reports, 5, 12758. DOI:10.1038/srep12758.

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 SH & van Rij RP (2015) Analysis of resistance and tolerance to virus infection in Drosophila. Nature Protocols, 10(7), 1084–1097. DOI:10.1038/nprot.2015.071.

Miesen P, Girardi E, van Rij RP (2015) Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Research, 43:6545-56. DOI:10.1093/nar/gkv590.

Merkling SH, Bronkhorst AW, Kramer JM, Overheul GJ, Schenck A, van Rij RP. (2015) The Epigenetic Regulator G9a Mediates Tolerance to RNA Virus Infection in Drosophila.  PLoS Pathogens 11(4):e1004692. DOI:10.1371/journal.ppat.1004692.

Bronkhorst AW, Van Cleef KWR, Venselaar H, Van Rij RP. (2014) A dsRNA-binding protein from a complex DNA virus suppresses the Drosophila RNAi response. Nucleic Acids Res, 42:12237-48. DOI:10.1093/nar/gku910.

Schuster S, Zirkel F, Kurth A, van Cleef KW, Drosten C, van Rij RP*, Junglen S*. 2014. A unique Nodavirus with novel features: Mosinovirus expresses two subgenomic RNAs, a capsid gene of unknown origin, and a suppressor of the antiviral RNAi pathway. J Virol, 88:13447-13459.
*Corresponding authors

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.

Van Cleef KW, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S, 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.

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.

Bronkhorst AW, Miesen P, Van Rij RP (2013) Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects. Fly, 7(4), 216–223. 

Van Cleef KWR, Overheul GJ, Thomassen MC, Kaptein SJF, Davidson AD, Jacobs M, Neyts J, Van Kuppeveld FJ, Van Rij RP (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

Libri V*, Miesen P*, Van Rij RP**, Buck AH (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.
*equal contribution; **corresponding authors. 

Bronkhorst AW, van Cleef KWR, Vodovar N, Ince IA, Blanc H, Vlak JM, Saleh MC, Van Rij RP (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 109:E3604-13. DOI:10.1073/pnas.1207213109

Feng Q, Hato SV, Langereis MA, Zoll J, Virgen-Slane R, Peisley A, Hur S, Semler BL, Van Rij RP, Van Kuppeveld FJ (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

Grimm D, Dalmay T, van Rij RP (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

van Mierlo JT, Bronkhorst AW, Overheul GJ, Sadanandan SA, Ekström J-O, Heestermans M, Hultmark D, Antoniewski C, Van Rij RP (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

Merkling SH & van Rij RP (2012) Beyond RNAi: Antiviral defense strategies in Drosophila and mosquito. Journal of insect physiology 59:159-70. DOI:10.1016/j.jinsphys.2012.07.004

Vodovar N, Bronkhorst AW, van Cleef KWR, Miesen P, Blanc H, van Rij RP*, Saleh MC* (2012). Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells. PloS ONE, 7, e30861. DOI:10.1371/journal.pone.0030861 *Corresponding authors.

van Mierlo JT, van Cleef KW, van Rij RP (2011) Defense and counter-defense in the Drosophila RNAi-based antiviral immune system. Methods Mol Biol, 721: 3-22.

van Cleef KW, van Mierlo JT, van den Beek M, van Rij RP (2011) Identification of viral suppressors of RNAi using reporter assays in Drosophila S2 cell culture. Methods Mol Biol, 721: 201-213.

van Mierlo JT, van Cleef KWR, van Rij RP (2010) Small Silencing RNAs: Piecing Together a Viral Genome. Cell host & microbe, 7(2), 87–9. DOI:10.1016/j.chom.2010.02.001

van Rij RP & 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

Saleh MR, Tassetto M*, van Rij RP*, 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.

van Rij RP (2008) Virus meets RNAi. Symposium on antiviral applications of RNA interference. EMBO reports, 9, 725–9. DOI:10.1038/embor.2008.133

van Rij RP, Saleh MC, 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

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

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

van Rij RP & 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 MC*, Van Rij RP*, and Andino R (2004) RNA silencing in viral infections: insights from poliovirus. Virus Res 102:11-17.
*equal contribution.

Complete list of publications in PubMed or Google Scholar.