Key background papers from the RiboCode team

Chau, C., Mohanan, G., Macaulay, I., Actis, P., & Wälti, C. (2023). Automated Purification of DNA Origami with SPRI BeadsSmall, 2308776.

Murphy, J. C., Harrington, E. M., Schumann, S., Vasconcelos, E. J., Mottram, T. J., Harper, K. L., Aspden, J. L., & Whitehouse, A. (2023). Kaposi’s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs. Nature Communications, 14(1), 300.

Harper, K. L., Mottram, T. J., Anene, C. A., Foster, B., Patterson, M. R., McDonnell, E., Macdonald, A., Westhead, D., & Whitehouse, A. (2022). Dysregulation of the miR‐30c/DLL4 axis by circHIPK3 is essential for KSHV lytic replication. EMBO Reports, 23(5), e54117.

Causier, B., Hopes, T., McKay, M., Paling, Z., & Davies, B. (2022). Plants utilise ancient conserved peptide upstream open reading frames in stress‐responsive translational regulation. Plant, Cell & Environment, 45(4), 1229-1241.

Hopes, T., Norris, K., Agapiou, M., McCarthy, C. G., Lewis, P. A., O’Connell, M. J., Fontana, J., & Aspden, J. L. (2022). Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Research, 50(4), 2240-2257.

Hyland, E. M., Webb, A. E., Kennedy, K. F., Gerek Ince, Z. N., Loscher, C. E., & O’Connell, M. J. (2021). Adaptive evolution in TRIF leads to discordance between human and mouse innate immune signaling. Genome Biology and Evolution, 13(12), evab268.

Bravo, J. P., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer, A., Davidovich, C., Lamb, D.C., Tuma, R., Calabrese, A. N., & Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences, 118(41), e2100198118.

Norris, K., Hopes, T., & Aspden, J. L. (2021). Ribosome heterogeneity and specialization in development. Wiley Interdisciplinary Reviews: RNA, 12(4), e1644.

Raveendran, M., Leach, A. R., Hopes, T., Aspden, J. L., & Actis, P. (2020). Ribosome fingerprinting with a solid-state nanopore. ACS Sensors, 5(11), 3533-3539.

Raveendran, M., Lee, A. J., Sharma, R., Wälti, C., & Actis, P. (2020). Rational design of DNA nanostructures for single molecule biosensing. Nature Communications, 11(1), 4384.

Patraquim, P., Mumtaz, M. A. S., Pueyo, J. I., Aspden, J. L., & Couso, J. P. (2020). Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biology, 21(1), 1-26.

Baquero-Perez, B., Antanaviciute, A., Yonchev, I. D., Carr, I. M., Wilson, S. A., & Whitehouse, A. (2019). The Tudor SND1 protein is an m6A RNA reader essential for replication of Kaposi’s sarcoma-associated herpesvirus. eLife, 8, e47261.

Siu-Ting, K., Torres-Sánchez, M., San Mauro, D., Wilcockson, D., Wilkinson, M., Pisani, D., O’Connell, M. J., & Creevey, C. J. (2019). Inadvertent paralog inclusion drives artifactual topologies and timetree estimates in phylogenomics. Molecular Biology and Evolution, 36(6), 1344-1356.

Lloyd, J. P. B., Lang, D., Zimmer, A. D., Causier, B., Reski, R., & Davies, B. (2018). The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Research, 46(11), 5822-5836.

Bravo, J. P., Borodavka, A., Barth, A., Calabrese, A. N., Mojzes, P., Cockburn, J. J., Lamb, D. C., & Tuma, R. (2018). Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research, 46(15), 7924-7937.

Causier, B., Li, Z., De Smet, R., Lloyd, J. P., Van de Peer, Y., & Davies, B. (2017). Conservation of nonsense-mediated mRNA decay complex components throughout eukaryotic evolution. Scientific Reports, 7(1), 16692.

Webb, A. E., Walsh, T. A., & O’Connell, M. J. (2017). VESPA: very large-scale evolutionary and selective pressure analyses. PeerJ Computer Science, 3, e118.

Schumann, S., Jackson, B. R., Yule, I., Whitehead, S. K., Revill, C., Foster, R., & Whitehouse, A. (2016). Targeting the ATP-dependent formation of herpesvirus ribonucleoprotein particle assembly as an antiviral approach. Nature Microbiology, 2(2), 1-11.

Thoms, M., Thomson, E., Baßler, J., Gnädig, M., Griesel, S., & Hurt, E. (2015). The exosome is recruited to RNA substrates through specific adaptor proteins. Cell, 162(5), 1029-1038.

Aspden, J. L., Eyre-Walker, Y. C., Phillips, R. J., Amin, U., Mumtaz, M. A. S., Brocard, M., & Couso, J. P. (2014). Extensive translation of small open reading frames revealed by Poly-Ribo-Seq. eLife, 3, e03528.

Rogulja-Ortmann, A., Picao-Osorio, J., Villava, C., Patraquim, P., Lafuente, E., Aspden, J., Thomsen, S., Technau, G. M., & Alonso, C. R. (2014). The RNA-binding protein ELAV regulates Hox RNA processing, expression and function within the Drosophila nervous system. Development, 141(10), 2046-2056.

McInerney, J. O., O’Connell, M. J., & Pisani, D. (2014). The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology, 12(6), 449-455.

Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O’Connell, M. J. (2013). Heterogeneous models place the root of the placental mammal phylogeny. Molecular Biology and Evolution, 30(9), 2145-2156.