Items where Author is "Moxon, Simon"

Article

Parasyraki, Eleftheria, Mallick, Medhavi, Hatch, Victoria, Vastolo, Viviana, Musheev, Michael U., Karaulanov, Emil, Gopanenko, Alexandr, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Méndez-Lago, Maria, Han, Dandan, Schomacher, Lars, Mukherjee, Debasish and Niehrs, Christof (2024) 5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming. Cell, 187 (21). 6088-6103.e18. ISSN 0092-8674

Peluso, Silvia, Aguilera-Gómez, Margarita, Bortolaia, Valeria, Catania, Francesco, Cocconcelli, Pier Sandro, Herman, Lieve, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Vernis, Laurence, Iacono, Giovanni, Lunardi, Simone, Pettenati, Elisa, Gallo, Arianna and Aguilera, Jaime and European Food Safety Authority (EFSA) (2024) Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives. EFSA Journal, 21 (7). ISSN 1831-4732

Kretov, Dmitry A., Folkes, Leighton, Mora-Martin, Alexandra, Walawalkar, Isha A., Syedah, Imrat Noreen, Vanuytsel, Kim, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Murphy, George J. and Cifuentes, Daniel (2024) The miR-144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. Nature Communications, 15. ISSN 2041-1723

César-Razquin, Adrián, Casacuberta, Josep, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Federici, Silvia, Jacchia, Sara, Kagkli, Dafni Maria, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Papadopoulou, Nikoletta and European Food Safety Authority (EFSA) (2024) Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants. EFSA Journal, 22 (4). ISSN 1831-4732

Bennett-Keki, Suzanne, Fowler, Emily K., Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Chapman, Tracey (2023) Sex-biased gene expression in nutrient-sensing pathways. Proceedings of the Royal Society B: Biological Sciences, 290 (1994). ISSN 0962-8452

Mills, Lauren A., Moreno-Cabezuelo, José Ángel, Włodarczyk, Artur, Victoria, Angelo J., Mejias, Rebeca, Nenninger, Anja, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Bombelli, Paolo, Selao, Tiago T., McCormick, Alistair J. and Lea-Smith, David ORCID: https://orcid.org/0000-0003-2463-406X (2022) Development of a biotechnology platform for the fast-growing cyanobacterium Synechococcus sp. PCC 11901. Biomolecules, 12 (7). ISSN 2218-273X

Billmeier, Martina, Green, Darrell ORCID: https://orcid.org/0000-0002-0217-3322, Hall, Adam, Turnbull, Carly, Singh, Archana, Xu, Ping, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2022) Mechanistic insights into non-coding Y RNA processing. RNA Biology, 19 (1). pp. 468-480. ISSN 1547-6286

Hotzy, Cosima, Fowler, Emily, Kiehl, Berrit, Francis, Roy, Mason, Janet, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Rostant, Wayne ORCID: https://orcid.org/0000-0002-3798-6251, Chapman, Tracey and Immler, Simone (2022) Evolutionary history of sexual selection affects microRNA profiles in Drosophila sperm. Evolution, 76 (2). pp. 310-319. ISSN 0014-3820

Kanakis, Ioannis, Alameddine, Moussira, Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Myrtziou, Ioanna, Ozanne, Susan, Peffers, Mandy, Goljanek-Whysall, Katarzyna and Vasilaki, Aphrodite (2021) Small-RNA sequencing reveals altered skeletal muscle microRNAs and snoRNAs signatures in weanling male offspring from mouse dams fed a low protein diet during lactation. Cells, 10 (5). ISSN 2073-4409

Mok, Gi Fay ORCID: https://orcid.org/0000-0002-5202-9062, Folkes, Leighton, Weldon, Shannon A., Maniou, Eirini, Martinez-Heredia, Victor, Godden, Alice M. ORCID: https://orcid.org/0000-0001-5760-011X, Williams, Ruth M., Sauka-Spengler, Tatjana, Wheeler, Grant N. ORCID: https://orcid.org/0000-0002-4335-8577, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Münsterberg, Andrea E. ORCID: https://orcid.org/0000-0002-4577-4240 (2021) Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension. Nature Communications, 12 (1). ISSN 2041-1723

Augusto Bovolenta, Luiz, Pinhal, Danillo, Luis Acencio, Marcio, Casulli de Oliveira, Arthur, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Martins, Cesar and Nemke, Ley (2020) miRTil: An extensive repository for Nile Tilapia microRNA next generation sequencing data. Cells, 9 (8). ISSN 2073-4409

Kretov, Dmitry, Isha, Walawalkar, Mora-Martin, Alexandra, Shafik, Andrew, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Cifuentes, Daniel (2020) Ago2-dependent processing allows miR-451 to evade the global microRNA turnover elicited during erythropoiesis. Molecular Cell, 78 (2). 317-328.e6. ISSN 1097-2765

Bradley, Thomas and Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 (2020) FilTar: Using RNA-Seq data to improve microRNA target prediction accuracy in animals. Bioinformatics, 36 (8). 2410–2416. ISSN 1367-4803

Fowler, Emily, Chapman, Tracey, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Bradley, Thomas (2019) Divergence in transcriptional and regulatory responses to mating in male and female fruitflies. Scientific Reports, 9. ISSN 2045-2322

Penso-Dolfin, Luca, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Haerty, Wilfried and Di Palma, Federica (2018) The evolutionary dynamics of microRNAs in domestic mammals. Scientific Reports, 8. ISSN 2045-2322

Stocks, Matthew B., Mohorianu, Irina, Beckers, Matthew, Paicu, Claudia, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Thody, Joshua, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs. Bioinformatics, 34 (19). 3382–3384. ISSN 1367-4803

Casacuberta, Josep, Nogué, Fabien, Naegeli, Hanspeter, Birch, Andrew Nicholas, De Schrijver, Adinda, Gralak, Mikołaj Antoni, Guerche, Philippe, Manachini, Barbara, Messéan, Antoine, Nielsen, Elsa Ebbesen, Robaglia, Christophe, Rostoks, Nils, Sweet, Jeremy, Tebbe, Christoph, Visioli, Francesco, Wal, Jean‐Michel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Schneeberger, Korbinian, Federici, Silvia, Ramon, Matthew, Papadopoulou, Nikoletta and Jones, Huw (2018) Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants. EFSA Journal, 16 (7). ISSN 1831-4732

Mok, Gi Fay ORCID: https://orcid.org/0000-0002-5202-9062, Lozano-Velasco, Estefania, Maniou, Eirini, Viaut, Camille, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Wheeler, Grant ORCID: https://orcid.org/0000-0002-4335-8577 and Münsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240 (2018) miR-133-mediated regulation of the Hedgehog pathway orchestrates embryo myogenesis. Development, 145 (12). ISSN 0950-1991

Pinhal, Danillo, Bovolenta, Luiz A., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Oliveira, Arthur C., Nachtigall, Pedro G., Acencio, Marcio L., Patton, James G., Hilsdorf, Alexandre W. S., Lemke, Ney and Martins, Cesar (2018) Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased arm switching and increasing complexity of expression throughout development. Scientific Reports, 8. ISSN 2045-2322

Curson, Andrew R. J., Williams, Beth T. ORCID: https://orcid.org/0000-0002-8594-1269, Pinchbeck, Benjamin J., Sims, Leanne P., Bermejo Martínez, Ana, Rivera, Peter Paolo L., Kumaresan, Deepak, Mercadé, Elena, Spurgin, Lewis G., Carrión, Ornella, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Cattolico, Rose Ann, Kuzhiumparambil, Unnikrishnan, Guagliardo, Paul, Clode, Peta L., Raina, Jean-Baptiste and Todd, Jonathan D. (2018) DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nature Microbiology, 3. 430–439.

Ward, Nicole, Green, Darrell ORCID: https://orcid.org/0000-0002-0217-3322, Higgins, Janet, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Munsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Wheeler, Grant ORCID: https://orcid.org/0000-0002-4335-8577 (2018) microRNAs associated with early neural crest development in Xenopus laevis. BMC Genomics, 19. ISSN 1471-2164

Paicu, Claudia, Mohorianu, Irina-Ioana, Stocks, Matthew, Xu, Ping, Coince, Aurore, Billmeier, Martina, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 (2017) miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics, 33 (16). 2446–2454. ISSN 1367-4803

Fishwick, Carl, Higgins, Janet, Percival-Alwyn, Lawrence, Hustler, Arianna, Pearson, Joanna, Bastkowski, Sarah, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Swarbreck, David, Greenman, Chris D. and Southgate, Jennifer (2017) Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium. Cell Death and Differentiation, 24. pp. 809-818. ISSN 1350-9047

Mathers, Thomas C., Chen, Yazhou, Kaithakottil, Gemy, Legeai, Fabrice, Mugford, Sam T., Baa-Puyoulet, Patrice, Bretaudeau, Anthony, Clavijo, Bernardo, Colella, Stefano, Collin, Olivier, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Derrien, Thomas, Feng, Honglin, Gabaldón, Toni, Jordan, Anna, Julca, Irene, Kettles, Graeme J., Kowitwanich, Krissana, Lavenier, Dominique, Lenzi, Paolo, Lopez-Gomollon, Sara, Loska, Damian, Mapleson, Daniel, Maumus, Florian, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Price, Daniel R. G., Sugio, Akiko, van Munster, Manuella, Uzest, Marilyne, Waite, Darren, Jander, Georg, Tagu, Denis, Wilson, Alex C. C., van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X, Swarbreck, David and Hogenhout, Saskia A. (2017) Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, 18. ISSN 1474-760X

Houston, Ross, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Nogué, Fabien, Papadopoulou, Nikoletta, Ramon, Matthew and Waigmann, Elisabeth and European Food Safety Authority (EFSA) (2017) Assessment of the potential integration of the DNA plasmid vaccine CLYNAV into the salmon genome. EFSA Journal, 15 (1). ISSN 1831-4732

Kontra, Levente, Csorba, Tibor, Tavazza, Mario, Lucioli, Alessandra, Tavazza, Raffaela, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Tisza, Viktória, Medzhiradsky, Anna, Turina, Massimo and Burgyan, Jozsef (2016) Distinct effects of p19 RNA silencing suppressor on small RNA mediated pathways in plants. PLoS Pathogens, 12 (10). ISSN 1553-7374

Hatch, Victoria, Marin Barba, Marta, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Ford, Christopher, Ward, Nicole, Tomlinson, Matthew, Desanlis, Ines, Hendry, Adam, Hontelez, Saartje, van Krujsbergen, Ila, Veenstra, Gert Jan, Munsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240 and Wheeler, Grant ORCID: https://orcid.org/0000-0002-4335-8577 (2016) The positive transcriptional elongation factor (P-TEFb) is required for neural crest specification. Developmental Biology, 416 (2). 361–372. ISSN 0012-1606

Giusti, Juliana, Pinhal, Danillo, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Lovaglio Campos, Camilla, Munsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240 and Martins, Cesar (2016) MicroRNA-10 modulates Hox genes expression during Nile tilapia embryonic development. Mechanisms of Development, 140. pp. 12-18. ISSN 0925-4773

Penso-Dolfin, Luca, Swofford, Ross, Johnson, Jeremy, Alföldi, Jessica, Lindblad-Toh, Kerstin, Swarbreck, David, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Di Palma, Federica (2016) An improved microRNA annotation of the canine genome. PLoS One, 11 (4). ISSN 1932-6203

Vij, Shubha, Kuhl, Heiner, Kuznetsova, Inna S., Komissarov, Aleksey, Yurchenko, Andrey A., Van Heusden, Peter, Singh, Siddharth, Thevasagayam, Natascha M., Prakki, Sai Rama Sridatta, Purushothaman, Kathiresan, Saju, Jolly M., Jiang, Junhui, Kimbung Mbandi, Stanley, Jonas, Mario, Tong, Amy Hin Yan, Mwangi, Sarah, Lau, Doreen, Ngoh, Si Yan, Liew, Woei Chang, Shen, Xueyan, Hon, Lawrence S., Drake, James P., Boitano, Matthew, Hall, Richard, Chin, Chen-Shan, Lachumanan, Ramkumar, Korlach, Jonas, Trifonov, Vladimir, Kabilov, Marsel, Tupikin, Alexey, Green, Darrell ORCID: https://orcid.org/0000-0002-0217-3322, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Garvin, Tyler, Sedlazeck, Fritz J., Vurture, Gregory W., Gopalapillai, Gopikrishna, Katneni, Vinaya Kumar, Noble, Tansyn H., Scaria, Vinod, Sivasubbu, Sridhar, Jerry, Dean R., O'Brien, Stephen J., Schatz, Michael C., Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Turner, Stephen W., Lok, Si, Christoffels, Alan and Orbán, László (2016) Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12 (4). ISSN 1553-7390

Hall, A E, Lu, W-T, Godfrey, J D, Antonov, A V, Paicu, C, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429, Wilczynska, A, Muller, P A J and Bushell, M (2016) The cytoskeleton adaptor protein ankyrin-1 is upregulated by p53 following DNA damage and alters cell migration. Cell Death & Disease, 7. ISSN 2041-4889

Ahmed, Ayisha, Ward, Nicole J., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Lopez-Gomollon, Sara, Viaut, Camille, Tomlinson, Matthew L., Patrushev, Ilya, Gilchrist, Michael J., Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Dotlic, Dario, Munsterberg, Andrea E. ORCID: https://orcid.org/0000-0002-4577-4240 and Wheeler, Grant N. ORCID: https://orcid.org/0000-0002-4335-8577 (2015) A database of microRNA expression patterns in Xenopus laevis. PLoS One, 10 (10). ISSN 1932-6203

Trieu, Trung Anh, Calo, Silvia, Nicolás, Francisco E., Vila, Ana, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Torres-Martínez, Santiago, Garre, Victoriano and Ruiz-Vázquez, Rosa M. (2015) A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi. PLoS Genetics, 11 (4). ISSN 1553-7390

Nicolás, Francisco E, Vila, Ana, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Cascales, María D, Torres-Martínez, Santiago, Ruiz-Vázquez, Rosa M and Garre, Victoriano (2015) The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides. BMC Genomics, 16. ISSN 1471-2164

Toseland, Andrew, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2014) Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics, 15. ISSN 1471-2164

Lopez-Gomollon, Sara, Beckers, Matthew, Rathjen, Tina, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Maumus, Florian, Mohorianu, Irina, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 (2014) Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 15 (1). ISSN 1471-2164

Cervantes, María, Vila, Ana, Nicolás, Francisco E., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, de Haro, Juan P., Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Torres-Martínez, Santiago and Ruiz-Vázquez, Rosa M. (2013) A single argonaute gene participates in exogenous and endogenous RNAi and controls cellular functions in the basal fungus Mucor circinelloides. PLoS One, 8 (7). ISSN 1932-6203

Mapleson, Daniel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2013) MirPlex:a tool for identifying miRNAs in high-throughput sRNA datasets without a genome. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 320 (1). pp. 47-56. ISSN 1552-5015

Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40 (13). ISSN 0305-1048

Stocks, Matthew B., Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Mapleson, Daniel, Woolfenden, Hugh C., Mohorianu, Irina, Folkes, Leighton, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics, 28 (15). pp. 2059-2061. ISSN 1367-4803

Bateman, Alex, Agrawal, Shipra, Birney, Ewan, Bruford, Elspeth A, Bujnicki, Janusz M, Cochrane, Guy, Cole, James R, Dinger, Marcel E, Enright, Anton J, Gardner, Paul P, Gautheret, Daniel, Griffiths-Jones, Sam, Harrow, Jen, Herrero, Javier, Holmes, Ian H, Huang, Hsien-Da, Kelly, Krystyna A, Kersey, Paul, Kozomara, Ana, Lowe, Todd M, Marz, Manja, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pruitt, Kim D, Samuelsson, Tore, Stadler, Peter F, Vilella, Albert J, Vogel, Jan-Hinnerk, Williams, Kelly P, Wright, Mathew W and Zwieb, Christian (2011) RNAcentral: A vision for an international database of RNA sequences. RNA, 17. pp. 1941-1946. ISSN 1355-8382

Mohorianu, I-I, Schwach, F, Jing, R, Lopez-Gomollon, S, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Szittya, G, Sorefan, K, Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429 (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. The Plant Journal, 67 (2). pp. 232-246. ISSN 1365-313X

Surridge, Alison K., Lopez-Gomollon, Sara, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Maroja, Luana S., Rathjen, Tina, Nadeau, Nicola J., Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Jiggins, Chris D. (2011) Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics, 12. ISSN 1471-2164

Szittya, Gyorgy, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pantaleo, Vitantonio, Toth, Gabor, Rusholme Pilcher, Rachel L., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Burgyan, Jozsef and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Structural and functional analysis of viral siRNAs. PLoS Pathogens, 6 (4). ISSN 1553-7374

Nicolas, Francisco Esteban, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, de Haro, Juan P., Calo, Silvia, Grigoriev, Igor V., Torres-Martinez, Santiago, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Ruiz-Vazquez, Rosa M. and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Research, 38 (16). pp. 5535-5541. ISSN 0305-1048

Pantaleo, Vitantonio, Saldarelli, Pasquale, Miozzi, Laura, Giampetruzzi, Annalisa, Gisel, Andreas, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Bisztray, György and Burgyan, Jozsef (2010) Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology, 408 (1). pp. 49-56. ISSN 1096-0341

Pantaleo, Vitantonio, Szittya, György, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Miozzi, Laura, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Burgyan, Jozsef (2010) Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis. The Plant Journal, 62 (6). pp. 960-976. ISSN 1365-313X

Navarro, Beatriz, Pantaleo, Vitantonio, Gisel, Andreas, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, Bisztray, György, Di Serio, Francesco and Burgyán, József (2009) Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One, 4 (11). ISSN 1932-6203

Schwach, Frank, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2009) Deciphering the diversity of small RNAs in plants: the long and short of it. Briefings in Functional Genomics and Proteomics, 8 (6). pp. 472-481. ISSN 1473-9550

Szittya, György, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Santos, Dulce M., Jing, Runchan, Fevereiro, Manuel P. S., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9. ISSN 1471-2164

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Jing, Runchan, Szittya, Gyorgy, Schwach, Frank, Rusholme Pilcher, Rachel L., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research, 18 (10). pp. 1602-1609. ISSN 1088-9051

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Kim, Jan T. (2008) A scoring matrix approach to detecting miRNA target sites. Algorithms for Molecular Biology, 3 (3). ISSN 1748-7188

Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Schwach, Frank, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429, MacLean, Dan, Studholme, David J. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24 (19). pp. 2252-2253. ISSN 1367-4803

Rusholme Pilcher, Rachel, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Pakseresht, Nima, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Manning, Kenneth, Seymour, Graham and Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 (2007) Identification of novel short RNAs in tomato (Solanum lycopersicum). Planta, 226 (3). pp. 709-717. ISSN 0032-0935

Finn, Robert D, Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Marshall, Mhairi, Khanna, Ajay, Durbin, Richard, Eddy, Sean R, Sonnhammer, Erik L L and Bateman, Alex (2006) Pfam: clans, web tools and services. Nucleic Acids Research, 34 (Suppl 1). D247-D251. ISSN 0305-1048

Griffiths-Jones, Sam, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R and Bateman, Alex (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research, 33 (Suppl 1). D121-D124. ISSN 0305-1048

Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D, Hollich, Volker, Griffiths-Jones, Sam, Khanna, Ajay, Marshall, Mhairi, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Sonnhammer, Erik L L, Studholme, David J, Yeats, Corin and Eddy, Sean R (2004) The Pfam protein families database. Nucleic Acids Research, 32 (Suppl 1). D138-D141. ISSN 0305-1048

Book Section

Bradley, Thomas and Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 (2017) An assessment of the next generation of animal miRNA target prediction algorithms. In: MicroRNA Detection and Target Identification. Methods in Molecular Biology . Springer, pp. 175-191. ISBN 978-1-4939-6864-0

Pais, Helio, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2011) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. In: RNA Infrastructure and Networks. Advances in Experimental Medicine and Biology, 722 . Springer, pp. 239-254. ISBN 978-1-4939-4254-1

Pais, H, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816, Dalmay, T ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, V ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Small RNA Discovery and Characterisation in Eukaryotes Using High-Throughput Approaches. In: Non-coding RNA networks. Landes Bioscience. ISBN 978-1-4614-0331-9

Monograph

Bagnall, Anthony, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816 and Studholme, David (2007) Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana. Working Paper. University of East Anglia.

Conference or Workshop Item

Bagnall, A, Moxon, S ORCID: https://orcid.org/0000-0003-4644-1816 and Studholme, D (2008) Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana. In: 2008 International Conference on Bioinformatics and Computational Biology, 2008-01-01.