Carbonell, A.*, López, C. and Daròs, J.A. (2018). Fast-forward identification of highly effective artificial small RNAs against different Tomato spotted wilt virus isolates. Molecular Plant-Microbe Interactions (in press). doi: 10.1094/MPMI-05-18-0117-TA (https://doi.org/10.1094/MPMI-05-18-0117-TA).

Carbonell, A. (ed) (2017). Plant Argonaute Proteins: Methods and Protocols. Methods in Molecular Biology, vol. 1640. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-4939-7164-0. doi: 10.1007/978-1-4939-7165-7 (http://dx.doi.org/10.1007/978-1-4939-7165-7).

Carbonell, A.* (2017). Plant ARGONAUTEs: features, functions and unknowns. In: Plant Argonaute Proteins: Methods and Protocols (Ed. Alberto Carbonell). Methods in Molecular Biology 1640: 1-21. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-4939-7164-0. doi: 10.1007/978-1-4939-7165-7_1 (http://dx.doi.org/10.1007/978-1-4939-7165-7_1).

Carbonell, A.* (2017). Immunoprecipitation and high-throughput sequencing of ARGONAUTE-bound RNAs from plants. In: Plant Argonaute Proteins: Methods and Protocols (Ed. Alberto Carbonell). Methods in Molecular Biology 1640: 93-112. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-4939-7164-0. doi: 10.1007/978-1-4939-7165-7_6 (http://dx.doi.org/10.1007/978-1-4939-7165-7_6).

Kénesi, E., Carbonell, A., Lózsa, R., Vértessy, B.* and Lakatos, L.* (2017). A viral suppressor of RNA silencing inhibits ARGONAUTE 1 function by precluding target RNA binding to pre-assembled RISC. Nucleic Acids Research 45 (13): 7736-7750. doi: 10.1093/nar/gkx379 (http://dx.doi.org/10.1093/nar/gkx379).

Carbonell, A.* (2017). Artificial small RNA-based strategies for effective and specific gene silencing in plants. In: Plant Gene Silencing: Mechanisms and Applications (Ed. Tamas Dalmay), ch. 6, pp 110-127. CABI Biotechnology Series, CABI Publishing, Wallingford, UK. ISBN: 9781780647678. (http://www.cabi.org/bookshop/book/9781780647678).

Carbonell, A.* and Daròs, J.A. (2017). Artificial microRNAs and synthetic trans-acting small interfering RNAs interfere with viroid infection. Molecular Plant Pathology 18 (5): 746-753. doi: 10.1111/mpp.12529 (http://dx.doi.org/10.1111/mpp.12529).

Cordero, T., Cerdán, L., Carbonell, A., Katsarou, K., Kalantidis, K. and and Daròs*, J.A. (2017). Dicer-like 4 is involved in restricting the systemic movement of Zucchini yellow mosaic virus in Nicotiana benthamiana. Molecular Plant-Microbe Interactions 30 (1): 63-71. doi: 10.1094/MPMI-11-16-0239-R (https://doi.org/10.1094/MPMI-11-16-0239-R).

Carbonell, A.* (2016). El análisis de mutantes del hongo fitopatógeno Colletotrichum higginsianum deficientes en componentes clave de la maquinaria de silenciamiento génico revela la presencia inesperada de un nuevo micovirus. Virología 19 (2): 83-84 (http://sevirologia.es/media/uploads/10-comentarios 19-2.pdf).

Carbonell, A.*, García, J.A., Simón-Mateo, C. and Hernández, C. (2016). Plant virus RNA replication. In: eLS. John Wiley & Sons Ltd, Chichester, UK. ISBN: 9780470015902. doi: 10.1002/9780470015902.a0022338 (http://dx.doi.org/10.1002/9780470015902.a0022338).

Carbonell, A.*, Carrington, J.C.C. and Daròs, J.A. (2016). Fast-forward generation of effective artificial small RNAs for enhanced antiviral defense in plants. RNA and Disease 3: e 1130. doi: 10.14800/rd.1130 (http://dx.doi.org/10.14800/rd.1130).

Fahlgren, N.*, Hill, S.T., Carrington, J.C. and Carbonell, A.* (2016). P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design. Bioinformatics 32 (1): 157-158. doi: 10.1093/bioinformatics/btv534 (http://dx.doi.org/10.1093/bioinformatics/btv534).

Carbonell, A.* (2015). Trading defense for vigour. Nature Plants 1 (11), 15174. doi: 10.1038/nplants.2015.174 (http://dx.doi.org/10.1038/nplants.2015.174).

Carbonell, A.* and Carrington, J.C. (2015). Antiviral roles of plant ARGONAUTES. Current Opinion in Plant Biology 27: 111-117. doi: 10.1016/j.pbi.2015.06.013 (http://dx.doi.org/10.1016/j.pbi.2015.06.013).

Carbonell A*., Fahlgren, N., Mitchell, S., Cox Jr., K.L., Reilly, K.C., Mockler, T.C. and Carrington, J.C.* (2015). Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors. The Plant Journal 82 (6): 1061-1075. doi: 10.1111/tpj.12835 (http://dx.doi.org/10.1111/tpj.12835).

Garcia-Ruiz, H.G., Carbonell, A., Hoyer, J.S., Fahlgren, N., Gilbert, K.B., Takeda, A., Giampetruzzi, A., Garcia-Ruiz, M.T., Lottes, M.M., Lowery, N., Martinez-Albaladejo, M.T. and Carrington, J.C.* (2015). Roles and programming of ARGONAUTE proteins during Turnip Mosaic Virus infection in Arabidopsis. PLOS Pathogens 11 (3): e1004755. doi: 10.1371/journal.ppat.1004755 (http://dx.doi.org/10.1371/journal.ppat.1004755).

Flores, R.*, Minoia, S., Carbonell, A., Gisel, A., Delgado, S., López-Carrasco, A., Navarro, B. and Di Serio, F. (2015). Viroids, the simplest RNA replicons: how they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Research 209: 136-145. doi: 10.1016/j.virusres.2015.02.027 (http://dx.doi.org/10.1016/j.virusres.2015.02.027).

Shan, H.**, Pasin, F.**,*, Valli, A., Castillo Di Giacinto, C., Rajulu, C., Carbonell, A., Simón-Mateo, C., García*, J.A. and Rodamilans, B.* (2015). The Potyviridae P1a leader protease contributes to host range specificity. Virology 476, 264-270. doi: 10.1016/j.virol.2014.12.013 (http://dx.doi.org/10.1016/j.virol.2014.12.013).

Zhang, X., Niu, D., Carbonell, A., Wang. A., Lee, A., Tun, V., Wang, Z.,
Carrington, J.C., Chang, C.A. and Jin, H.* (2014). Argonaute PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nature Communications 5, 5468. doi: 10.1038/ncomms6468 (http://dx.doi.org/10.138/ncomms6468).

Gilbert, K.B., Fahlgren, N., Kasschau, K.D., Chapman, E. J., Carrington, J.C. and Carbonell, A.* (2014). Preparation of multiplexed small RNA libraries from plants. Bio-protocol 4 (21): e1275. http://www.bio-protocol.org/e1275. ISSN: 2331-8325.

Minoia, S., Carbonell, A., Di Serio, F., Gisel, A., Carrington, J.C., Navarro, B.* and Flores, R.* (2014). Specific ARGONAUTES bind selectively small RNAs derived from Potato spindle tuber viroid and attenuate viroid accumulation in vivo. Journal of Virology 88 (20), 11933-11945. doi: 10.1128/JVI.01404-14 (http://dx.doi.org/10.1128/JVI.01404-14).

Carbonell, A., Takeda, A., Fahlgren, N., Johnson, S.C., Cuperus, J.T. and Carrington, J.C.* (2014). New generation of artificial microRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis. Plant Physiology 165 (1), 15-29. doi: 10.1104/pp.113.234989 (http://dx.doi.org/10.1104/pp.113.234989).

Carbonell, A.**, Maliogka, V.I.*, de Jesús Pérez, J., Salvador, B., San León, D., García, J.A.* and Simón-Mateo, C.* (2013). Diverse amino acid changes at specific positions in the N-terminal region of the coat protein allow Plum pox virus to adapt to new hosts. Molecular Plant-Microbe Interactions 26 (10), 1211-1224. doi: 10.1094/MPMI-04-13-0093-R (http://dx.doi.org/10.1094/MPMI-04-13-0093-R).

Carbonell, A., Fahlgren, N, García-Ruíz, H., Gilbert, K.B., Montgomery T.A., Nguyen, T., Cuperus, J.T. and Carrington, J.C.* (2012). Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. The Plant Cell 24 (9), 3613-3629. doi: 10.1105/tpc.112.099945 (http://dx.doi.org/10.1105/tpc.112.099945).

Maliogka, V.I.**, Salvador, B.**, Carbonell, A., Sáenz, P., San León, D., Oliveros, J.C., Delgadillo, M.O., García, J.A.* and Simón-Mateo, C.* (2012). Virus variants with differences in the P1 protein coexist in a Plum pox virus population and display particular host-dependent pathogenicity features. Molecular Plant Pathology 13 (8), 877-886. doi: 10.1111/j.1364-3703.2012.00796.x (http://dx.doi.org/10.1111/j.1364-3703.2012.00796.x).

Maliogka, V.I., Calvo, M., Carbonell, A., García, J.A.* and Valli, A.* (2012). Heterologous RNA silencing suppressors from both plant- and animal-infecting viruses support Plum pox virus infection. Journal of General Virology 93 (7), 1601-1611. doi: 10.1099/vir.0.042168-0 (http://dx.doi.org/10.1099/vir.0.042168-0).

Carbonell, A., Flores, R.* and Gago, S.* (2012). Hammerhead ribozymes against virus and viroid RNAs. In: From Nucleic Acids Sequences to Molecular Medicine (Eds. Volker A. Erdmann and Jan Barciszewski), pp 411-427. RNA Technologies Series, Springer-Verlag Berlin Heidelberg. ISBN: 978-3-642-27425-1. doi: 10.1007/978-3-642-27426-8_16 (http://dx.doi.org/10.1007/978-3-642-27426-8_16).

Carbonell, A., Dujovny, G., García, J.A.* and Valli, A.* (2012). The Cucumber vein yellowing virus silencing suppressor P1b can functionally replace HCPro in Plum pox virus infection in a host-specific manner. Molecular Plant-Microbe Interactions 25 (2), 151-164. doi: 10.1094/MPMI-08-11-0216 (http://dx.doi.org/10.1094/MPMI-08-11-0216).


Carbonell, A., Flores, R. and Gago, S.* (2011). Trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA. Nucleic Acids Research 39 (6), 2432-2444. doi: 10.1093/nar/gkq1051 (http://dx.doi.org/10.1093/nar/gkq1051).

Cuperus, J.T.**, Carbonell, A.**, Fahlgren, N., Garcia-Ruiz, H., Burke, R.T., Takeda, A., Sullivan, C.M., Gilbert, S.D., Montgomery, T.A. and Carrington, J.C.* (2010). Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature Structural Molecular Biology 17 (8), 997-1003. doi: 10.1038/nsmb.1866 (http://dx.doi.org/10.1038/nsmb.1866).

Flores, R.*, Gas, M.E., Molina-Serrano, D., Nohales, M.A., Carbonell, A., Gago, S., De la Peña, M. and Daròs, J.A. (2009). Viroid replication: rolling-circles, enzymes and ribozymes. Viruses 1 (2), 317-334. doi: 10.3390/v1020317 (http://dx.doi.org/10.3390/v1020317).

Carbonell, A., Martínez de Alba, A.E., Flores, R.* and Gago, S. (2008). Double-stranded RNA interferes in a sequence-specific manner with infection of representative members of the two viroid families. Virology 371 (1), 44-53. doi 10.1016/j.virol.2007.09.031 (http://dx.doi.org/10.1016/j.virol.2007.09.031).

Flores, R.*, Carbonell, A., Gago, S., Martínez de Alba, A.E., Delgado, S, Rodio, M.E. and Di Serio, F. (2008). Viroid-host interactions: a molecular dialogue between two uneven partners. In: Biology of Plant Microbe Interactions (Eds. M. Lorito, S.L. Woo and F. Scala), vol. 6, ch. 58, pp. 1-9. International Society for Molecular Plant-Microbe Interactions, St. Paul, MN (USA). ISBN: 978-0-9654625-5-6. doi: 10.13140/2.1.4049.1847 (http://dx.doi.org/10.13140/2.1.4049.1847).

Carbonell, A. Resistencia a viroides inducida por ribozimas de cabeza de martillo y RNAs interferentes (2008). PhD Dissertation. doi: 10.13140/2.1.4966.6880 (http://dx.doi.org/10.13140/2.1.4966.6880).

Flores, R.*, Carbonell, A., De la Peña, M., and Gago, S. (2008). RNAs autocatalíticos: ribozimas de cabeza de martillo. In: Herramientas Biotecnológicas en Fitopatología (Eds. V. Pallas, P. Rodríguez-Palenzuela, C. Escobar and J.F. Marcos), ch. 22, pp. 407-420. Mundi-Prensa-SEF, Madrid, Spain. ISBN: 84-8476-319-6. doi: 10.13140/2.1.3787.0408 (http://dx.doi.org/10.13140/2.1.3787.0408).

Carbonell, A., De la Peña, M., Flores, R.* and Gago, S. (2006). Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of AUC in most natural hammerheads. Nucleic Acids Research 34 (19), 5613-5622. doi: 10.1093/nar/gkl717 (http://dx.doi.org/10.1093/nar/gkl717).

Flores, R.*, Delgado, S., Gas, M.E., Carbonell, A., Molina, D., Gago, S. and De la Peña M. (2004). Viroids: the minimal non-coding RNAs with autonomous replication. FEBS Letters. 567 (1), 42-48. doi: 10.1016/j.febslet.2004.03.118 (http://dx.doi.org/10.1016/j.febslet.2004.03.118).

Carbonell, A. Degradación in vitro de un RNA nucleolar por un ribozima incluido en un pequeño RNA nucleolar (2001). Graduation Project. doi: 10.13140/2.1.1034.5284 (http://dx.doi.org/10.13140/2.1.1034.5284).