Adriana E. Cisneros, Tamara Martín-García, Anamarija Primc, Wojtek Kuziuta, Javier Sánchez-Vicente Verónica Aragonés, José-Antonio Daròs, Alberto Carbonell* (2023). Transgene-free, virus-based gene silencing in plant by artificial microRNAs derived from minimal precursors. Nucleic Acids Research 51 (19): 10719–10736. PDF.

Adriana E. Cisneros, Purificación Lisón, Laura Campos, Joan Manel López-Tubau, Teresa Altabella, Albert Ferrer, José-Antonio Daròs, Alberto Carbonell (2023). Down-regulation of Tomato STEROL GLYCOSYLTRANSFERASE 1 Perturbs Plant Development and Facilitates Viroid Infection. Journal of Experimental Botany 74 (5): 1564-1578. PDF.
Francesco Di Serio, Robert A. Owens, Beatriz Navarro, Pedro Serra, Ángel Emilio Martínez de Alba, Sonia Delgado, Alberto Carbonell, Selma Gago-Zachert (2023). Role of RNA silencing in plant-viroid interaction and in viroid pathogenesis. Virus Research 323, 198964. PDF.


María-Carmen Marqués, Javier Sánchez-Vicente, Raúl Ruiz, Roser Montagud-Martínez, Rosa Márquez-Costa, Gustavo Gómez, Alberto Carbonell, José-Antonio Daròs, Guillermo Rodrigo (2022). Diagnostics of plant viral infections with CRISPR-Cas12a and CRISPR-Cas13d. ACS Synthetic Biology 11 (7): 2384-2393. PDF.

Adriana E. Cisneros, Ainhoa de la Torre-Montaña, Alberto Carbonell (2022). Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAsThe Plant Journal 110 (4): 1166-1181. PDF.

Lucio López-Dolz, Maria Spada, José-Antonio Daròs and Alberto Carbonell (2022). Fine-tune control of plant gene expression by synthetic trans-acting small interfering RNAs. In: Plant Gene Silencing: Methods and Protocols (Eds. Kirankumar Mysore and Muthappa Senthil-Kumar). Methods in Molecular Biology 2408: 227-242. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-0716-1875-2. PDF.

Alberto Carbonell (2022). RNAi tools for controlling viroid diseasesVirus Research 313, 198729. PDF.

Vicente Pallás, Carmen Hernández, Jose Francisco Marcos, José-Antonio Daròs, Beatriz Navarro, José Antonio Navarro, Marcos de la Peña, Selma Gago-Zachert, María Eugenia Gas, Alberto Carbonell, Carmelo López, Ángel Emilio Martínez de Alba, Francesco Di Serio, Pedro Moreno (2022). In memoriam of Ricardo Flores: the career, achievements, and legacy of an inspirational plant virologistVirus Research 312, 198718. PDF.


Vicente Pallás Benet, Alberto Carbonell, Miguel Aranda, Blanca Landa del Castillo, Carlos López Herrera, Enrique Moriones Alonso, Juan A. Navas Cortés, Félix Ortego Alonso, Rafael Zas Arregui (2021). Plant health. Resistance to pests and diseases. In: Sustainable primary production (Eds. Enrique Olmos Aranda, Mónica Venegas Calerón), vol. 6: 85-105. CSIC Scientific Challenges: Towards 2030. Editorial CSIC. ISBN: 978-84-00-10748-2. PDF.

Adriana E. Cisneros, Ainhoa De la Torre-Montaña, Tamara Martín-García, Alberto Carbonell (2021). Artificial small RNAs for functional genomics in plants. In: RNA-Based Technologies for Functional Genomics in Plants (Eds. Guiliang Tang, Sachin Teotia, Xiaoqing Tang, Deepali Singh). Concepts and Strategies in Plant Sciences 16076: 1-29. Springer Nature. eBook ISBN: 978-3-030-64994-4. PDF.


Minglei Yang, Hugh Woolfenden, Yueying Zhang, Xiaofeng Fang, Qi Liu, Maria Louisa Vigh, Jitender Cheema, Xiaofei Yang, Matthew Norris, Sha Yu, Hang Zhang, Alberto Carbonell, Peter Brodersen, Jiawei Wang, Caroline Dean, Yiliang Ding (2020). RNA structure-dependent activation of endonuclease RISC promotes miRNA cleavage in vivoNucleic Acids Research 48 (15): 8767-8781. PDF.

Adriana E. Cisneros and Alberto Carbonell (2020). Art-sRNAi for enhanced antiviral resistanceEncyclopedia (ISSN 2309-3366). PDF.

Lucio López-Dolz, Maria Spada, José-Antonio Daròs, Alberto Carbonell (2020). Fine-tune control of targeted RNAi efficacy by plant artificial small RNAsNucleic Acids Research 48 (11): 6234-6250. PDF.

Adriana E. Cisneros and Alberto Carbonell (2020). Artificial small RNA-based silencing tools for antiviral resistance in plantsPlants 9 (6): 669. PDF.

Pedro Serra, Alberto Carbonell, Beatriz Navarro, Selma Gago-Zachert, Shifang Li, Francesco Di Serio, Ricardo Flores (2020). Symptomatic plant viroid infections in phytopathogenic fungi: a request for a critical reassessmentProceedings of the National Academy of Science 117 (19): 10126-10128. PDF.


Carbonell, A.Purificación Lisón and Daròs, J.A. (2019). Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistanceThe Plant Journal 100: 720-737. PDF.

Cervera-Seco, L., Marqués, M.C., Sanz-Carbonell, A., Márquez-Molins, J., Carbonell, A.,  Daròs, J.A. and Gómez, G. (2019) Identification and characterization of a stress-responsive TAS3-derived tasiRNA in melonPlant and Cell Physiology 60 (11): 2382-2393. PDF.

Carbonell, A. and Daròs, J.A. (2019). Design, Synthesis, and Functional Analysis of Highly Specific Artificial Small RNAs With Antiviral Activity in Plants. In: Antiviral Resistance in Plants: Methods and Protocols (Eds. Kappei Kobayashi and Masamichi Nishiguchi). Methods in Molecular Biology 2028: 231-246. PDF.

Carbonell, A. (2019). Secondary small interfering RNA-based silencing tools in plants: an updateFrontiers in Plant Science 10: 687. PDF.

Carbonell, A. (2019). Design and high-throughput generation of artificial small RNA constructs for plants. In: Plant MicroRNAs: Methods and Protocols (Ed. Stephan de Folter). Methods in Molecular Biology 1932: 247-260. PDF.

Carbonell, A., López, C. and Daròs, J.A. (2019). Fast-forward identification of highly effective artificial small RNAs against different Tomato spotted wilt virus isolatesMolecular Plant-Microbe Interactions 32 (2): 142-156. PDF.


Carbonell, A. (ed) (2017). Plant Argonaute Proteins: Methods and ProtocolsMethods in Molecular Biology, vol. 1640. Springer Protocols series, Humana Press, NY, USA. ISBN: 978-1-4939-7164-0. PDF.

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. PDF.

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. PDF.

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 RISCNucleic Acids Research 45 (13): 7736-7750. PDF.

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. PDF.

Carbonell, A. and Daròs, J.A. (2017). Artificial microRNAs and synthetic trans-acting small interfering RNAs interfere with viroid infectionMolecular Plant Pathology 18 (5): 746-753. PDF.

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. PDF.


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 micovirusVirología 19 (2): 83-84. PDF.

Carbonell, A., García, J.A., Simón-Mateo, C. and Hernández, C. (2016). Plant virus RNA replication. In: eLS. John Wiley & Sons Ltd. PDF.

Carbonell, A., Carrington, J.C.C. and Daròs, J.A. (2016). Fast-forward generation of effective artificial small RNAs for enhanced antiviral defense in plantsRNA and Disease 3: e 1130. PDF.

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 designBioinformatics 32 (1): 157-158. PDF.


Carbonell, A. (2015). Trading defense for vigour. Nature Plants 1 (11), 15174. PDF.

Carbonell, A. and Carrington, J.C. (2015). Antiviral roles of plant ARGONAUTESCurrent Opinion in Plant Biology 27: 111-117. PDF.

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 precursorsThe Plant Journal 82 (6): 1061-1075. PDF.

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 ArabidopsisPLOS Pathogens 11 (3): e1004755. PDF.

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 infectionVirus Research 209: 136-145. PDF.

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 specificityVirology 476, 264-270. PDF.


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 ArabidopsisNature Communications 5, 5468. PDF.

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 plantsBio-protocol 4 (21): e1275. PDF.

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 vivoJournal of Virology 88 (20), 11933-11945. PDF.

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 ArabidopsisPlant Physiology 165 (1), 15-29. PDF.


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 hostsMolecular Plant-Microbe Interactions 26 (10), 1211-1224. PDF.


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 mutantsThe Plant Cell 24 (9), 3613-3629. PDF.

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 viruspopulation and display particular host-dependent pathogenicity featuresMolecular Plant Pathology 13 (8), 877-886. PDF.

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 infectionJournal of General Virology 93 (7), 1601-1611. PDF.

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. PDF.

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 mannerMolecular Plant-Microbe Interactions 25 (2), 151-164. PDF.


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 RNANucleic Acids Research 39 (6), 2432-2444. PDF.


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 ArabidopsisNature Structural Molecular Biology 17 (8), 997-1003. PDF.


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 ribozymesViruses 1 (2), 317-334. PDF.


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 familiesVirology 371 (1), 44-53. PDF.

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. PDF.

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. PDF.


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 hammerheadsNucleic Acids Research 34 (19), 5613-5622. PDF.


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 replicationFEBS Letters. 567 (1), 42-48. PDF.