Preprint
1. Rivera-Rivera, Carlos J., Feuda,R, and Pisani,D. 2025. Molecular Characterisation of Neurons across Animals Identifies Conserved Gene Expression. bioRxiv. https://doi.org/10.1101/2025.06.04.657789
2. Aleotti, A., Flaviano G., and Feuda, R. 2025. A Pre-Bilaterian Origin of Phototransduction Genes and Photoreceptor Cells. bioRxiv. https://doi.org/10.1101/2025.02.09.637293
3. Goldman, O.V., DeFoe A.E., Qi Y, Jiao Y., Weng S/, Leah Houri-Zeevi, Priyanka Lakhiani, … Feuda, R. … et al. 2025. Mosquito Cell Atlas: A Single-Nucleus Transcriptomic Atlas of the Adult Aedes Aegypti Mosquito. bioRxiv. https://doi.org/10.1101/2025.02.25.639765
4. De Vivo, G., Pelettier, E., Feuda, R., & D’Aniello, S. (2024). An ocean of opsins. bioRxiv. https://doi.org/10.1101/2024.11.07.622103
Peer Reviewed
5. Devilliers, J., Warren, B., Rosato, E., Kyriacou, C., and Feuda, R. (2025). Hematophagy generates a convergent genomic signature in mosquitoes and sandflies Genome Biology and Evolution 17 (3): evaf044. [https://doi.org/10.1093/gbe/evaf044]
6. Devilliers, J., Marshall, H., Warren, B., Kyriacou, C.P., Araripe, L.O., Bruno, R.V., Rosato, E., and Feuda, R. (2024). Molecular correlates of swarming behaviour in Aedes aegypti males. Biology Letters, 20, 20240245. https://doi.org/10.1098/rsbl.2024.0245
7. Aleotti, A., Goulty, M., Lewis, C., Giorgini, F., & Feuda, R. (2024). The origin evolution and molecular diversity of the chemokine system. Life Science Alliance, 7. https://doi.org/10.26508/lsa.202302471
8. Yu, D., Ren, Y., Uesaka, M., Beavan, A. J. S., Muffato, M., Shen, J., Li, Y., Sato, I., Wan, W., Clark, J. W., Keating, J. N., Carlisle, E. M., Dearden, R. P., Giles, S., Randle, E., Sansom, R. S., Feuda, R., Fleming, J. F., Sugahara, F., Cummins, C., Patricio, M., Akanni, W., D’Aniello, S., Bertolucci, C., Irie, N., Alev, C., Sheng, G., de Mendoza, A., Maeso, I., Irimia, M., Fromm, B., Peterson, K. J., Das, S., Hirano, M., Rast, J. P., Cooper, M. D., Paps, J., Pisani, D., Kuratani, S., Martin, F. J., Wang, W., Donoghue, P. C. J., & Zhang, Y. E., Pascual-Anaya, J. (2024). Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nature Ecology & Evolution, 1–17. https://doi.org/10.1038/s41559-023-02299-z
9. Zadra, N., Tatti, A., Silverj, A., Piccinno, R., Devilliers, J., Lewis, C., Arnoldi, D., Montarsi, F., Escuer, P., Fusco, G., De Sanctis, V., Feuda, R., Sánchez-Gracia, A., Rizzoli, A., & Rota-Stabelli, O. (2023). Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding. Insects, 14, 904. https://doi.org/10.3390/insects14120904
10. Rzasa, P., Whelan, S., Farahmand, P., Cai, H., Guterman, I., Palacios-Gallego, R., Undru, S. S., Sandford, L., Green, C., Andreadi, C., Mintseva, M., Parrott, E., Jin, H., Hey, F., Giblett, S., Sylvius, N. B., Allcock, N. S., Straatman-Iwanowska, A., Feuda, R., Tufarelli, C., Brown, K., Pritchard, C., & Rufini, A. (2023). BRAFV600E-mutated serrated colorectal neoplasia drives transcriptional activation of cholesterol metabolism. Communications Biology, 6, 1–16. https://doi.org/10.1038/s42003-023-05331-x
11. Goulty, M., Botton-Amiot, G., Rosato, E., Sprecher, S. G., & Feuda, R. (2023). The monoaminergic system is a bilaterian innovation. Nature Communications, 14, 3284. https://doi.org/10.1038/s41467-023-39030-2
12. De Vivo, G., Crocetta, F., Ferretti, M., Feuda, R., & D’Aniello, S. (2023). Duplication and Losses of Opsin Genes in Lophotrochozoan Evolution. Molecular Biology and Evolution, 40, msad066. https://doi.org/10.1093/molbev/msad066
13. Pisani, D., Rossi, M. E., Marlétaz, F., & Feuda, R. (2022). Phylogenomics: Is less more when using large-scale datasets? Current Biology, 32, R1340–R1342. https://doi.org/10.1016/j.cub.2022.11.019
14. Feuda, R., & Peter, I. S. (2022). Homologous gene regulatory networks control development of apical organs and brains in Bilateria. Science Advances, 8, eabo2416. https://doi.org/10.1126/sciadv.abo2416
15. Giacomelli, M., Rossi, M. E., Lozano-Fernandez, J., Feuda, R., & Pisani, D. (2022). Resolving tricky nodes in the tree of life through amino acid recoding. iScience. https://doi.org/10.1016/j.isci.2022.105594
16. Feuda, R. (2022). The temporal dynamics of the sea urchin regulome. Biology Open. https://doi.org/10.1242/bio.059216
17. Feuda, R., Menon, A. K., & Göpfert, M. C. (2022). Rethinking Opsins. Molecular Biology and Evolution, 39. https://doi.org/10.1093/molbev/msac033
18. Musser, J. M., Schippers, K. J., Nickel, M., Mizzon, G., Kohn, A. B., Pape, C., Hammel, J. U., Wolf, F., Liang, C., Hernández-Plaza, A., Achim, K., Schieber, N. L., Francis, W. R., R. S. V., Kling, S., Renkert, M., Feuda, R., Gaspar, I., Burkhardt, P., Bork, P., Beck, M., Kreshuk, A., Wörheide, G., Huerta-Cepas, J., Schwab, Y., Moroz, L. L., & Arendt, D. (2021). Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science. https://doi.org/10.1126/science.abj2949
19. Almudi, I., Vizueta, J., Wyatt, C. D. R., de Mendoza, A., Marlétaz, F., Firbas, P. N., Feuda, R., Masiero, G., Medina, P., Alcaina-Caro, A., et al. (2020). Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications, 11, 2631. https://doi.org/10.1038/s41467-020-16284-8
20. Feuda, R., Goulty, M., Zadra, N., Gasparetti, T., Rosato, E., Segata, N., Rizzoli, A., Pisani, D., Ometto, L., & Stabelli, O. R. (2020). Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evab170
21. Pisani, D., Rota-Stabelli, O., & Feuda, R. (2020). Sensory Neuroscience: A Taste for Light and the Origin of Animal Vision. Current Biology, 30, R773–R775. https://doi.org/10.1016/j.cub.2020.05.009
22. Fleming, J. F., Feuda, R., Roberts, N. W., & Pisani, D. (2020). A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans. Genome Biology and Evolution, 12, 3906–3916. https://doi.org/10.1093/gbe/evaa015
23. Valencia, J. E., Feuda, R., Mellott, D. O., Burke, R. D., & Peter, I. S. (2021). Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation. BMC Biology, 19, 257. https://doi.org/10.1186/s12915-021-01194-y
24. Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D. (2017). Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals. Current Biology, 27, 3864-3870.e4. https://doi.org/10.1016/j.cub.2017.11.008
25. Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N., & Wörheide, G. (2016). Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets. Proceedings of the National Academy of Sciences, 113, E948–E949. https://doi.org/10.1073/pnas.1525718113
26. Feuda, R., Marletaz, F., Bentley, M. A., & Holland, P. W. (2016). Conservation duplication and divergence of five opsin genes in insect evolution. Genome Biology and Evolution, 8, 579–587. https://doi.org/10.1093/gbe/evw015
27. Xu, P., Feuda, R., Lu, B., Xiao, H., Graham, R. I., & Wu, K. (2016). Functional opsin retrogene in nocturnal moth. Mobile DNA, 7, 18. https://doi.org/10.1186/s13100-016-0074-8
28. Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N., & Wörheide, G. (2015). Genomic data do not support comb jellies as the sister group to all other animals. Proceedings of the National Academy of Sciences, 112, 15402–15407.
29. Feuda, R., Bannikova, A. A., Zemlemerova, E. D., Febbraro, M. D., Loy, A., Hutterer, R., Aloise, G., Zykov, A. E., Annesi, F., & Colangelo, P. (2015). Tracing the evolutionary history of the mole Talpa europaea through mitochondrial DNA phylogeography and species distribution modelling. Biological Journal of the Linnean Society, 114, 495–512. https://doi.org/10.1111/bij.12459
30. Feuda, R., & Smith, A. B. (2015). Phylogenetic Signal Dissection Identifies the Root of Starfishes. PLoS One. https://doi.org/10.1371/journal.pone.0123331
31. Feuda, R., Rota-Stabelli, O., Oakley, T. H., & Pisani, D. (2014). The comb jelly opsins and the origins of animal phototransduction. Genome Biology and Evolution, 6, 1964–1971. https://doi.org/10.1093/gbe/evu154
32. Feuda, R., Hamilton, S. C., McInerney, J. O., & Pisani, D. (2012). Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences, 109, 18868–72. https://doi.org/10.1073/pnas.1204609109
33. Pisani, D., Feuda, R., Peterson, K. J., & Smith, A. B. (2012). Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships. Molecular Phylogenetics and Evolution, 62, 27–34. https://doi.org/10.1016/j.ympev.2011.08.028
