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- Smith-Paredes D, Núñez-León D, Soto-Acuña S, O’Connor J, Botelho JF, Vargas AO. Dinosaur ossification centres in embryonic birds uncover developmental evolution of the skull. Nature Ecology & Evolution. 2018;2(12):1966-73.
- Faunes M, Botelho JF, Wild JM. Innervation of the syrinx of the zebra finch (Taeniopygia guttata). J Comp Neurol. 2017;525:2847–2860.
- Botelho JF, Smith-Paredes D, Soto-Acuña S, Núñez-León D, Palma V, Vargas AO (2017). Greater Growth of Proximal Metatarsals in Bird Embryos and the Evolution of Hallux Position in the Grasping Foot. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
- Faunes, M., & Wild, J. M. (2017). The ascending projections of the nuclei of the descending trigeminal tract (nTTD) in the zebra finch (Taeniopygia guttata). Journal of Comparative Neurology, 525(13), 2832-2846.
- Faunes, M., & Wild, J. M. (2017). The sensory trigeminal complex and the organization of its primary afferents in the zebra finch (Taeniopygia guttata). Journal of Comparative Neurology, 525(13), 2820-2831.
- Botelho JF, Smith-Paredes D, Soto-Acuña S, O'Connor J, Palma V, Vargas AO. Molecular development of fibular reduction in birds and its evolution from dinosaurs. Evolution. 2016;70(3):543-54.
- Faunes, M., Oñate‐Ponce, A., Fernández‐Collemann, S., & Henny, P. (2016). Excitatory and inhibitory innervation of the mouse orofacial motor nuclei: A stereological study. Journal of Comparative Neurology, 524(4), 738-758.
- Wild JM, Botelho JF. (2015). Involvement of the avian song system in reproductive behaviour. Biol Lett.11(12):20150773.
- Botelho, J., Smith-Paredes, D., & Vargas, A. (2015). Altriciality and the Evolution of Toe Orientation in Birds. Evolutionary Biology, 1-9. 10.1007/s11692-015-9334-7
- Botelho, J. F., & Faunes, M. (2015). The evolution of developmental modes in the new avian phylogenetic tree. Evolution & Development, 17(4), 221-223. 10.1111/ede.12126
- Faunes, M., Botelho, J. F., Ahumada Galleguillos, P., & Mpodozis, J. (2015). On the hodological criterion for homology. Frontiers in Neuroscience, 9, 223. 10.3389/fnins.2015.00223
- Botelho, J. F., Smith-Paredes, D., Soto-Acuña, S., Mpodozis, J., Palma, V., & Vargas, A. O. (2015). Skeletal plasticity in response to embryonic muscular activity underlies the development and evolution of the perching digit of birds. Scientific Reports, 5. 10.1038/srep0
- Botelho, J. F., Ossa-Fuentes, L., Soto-Acuña, S., Smith-Paredes, D., Nunez-Leon, D., Salinas-Saavedra, M., et al. (2014). New Developmental Evidence Clarifies the Evolution of Wrist Bones in the Dinosaur–Bird Transition. PLoS Biology, 12(9), e1001957, doi:10.1371/journal.pbio.1001957.
- Botelho, J. F., Smith-Paredes, D., & Palma, V. A. (2015). Efficient detection of Indian hedgehog during endochondral ossification by whole mount immunofluorescence. In N. A. Riobo (Ed.), Hedgehog signaling protocols Vol. 2: Springer.
- Botelho, J. F., Smith-Paredes, D., Nuñez-Leon, D., Soto-Acuña, S., & Vargas, A. O. (2014). The developmental origin of zygodactyl feet and its possible loss in the evolution of Passeriformes. Proceedings of the Royal Society B: Biological Sciences, 281(1788), doi:10.1098/rspb.2014.0765.
- Salinas-Saavedra, M., Gonzalez-Cabrera, C., Ossa-Fuentes, L., Botelho, J. F., Ruiz-Flores, M., & Vargas, A. O. (2014). New developmental evidence supports a homeotic frameshift of digit identity in the evolution of the bird wing. Frontiers in zoology, 11(1), 33.
- Henny, P., Brown, M. T., Northrop, A., Faunes, M., Ungless, M. A., Magill, P. J., & Bolam, J. P. (2012). Structural correlates of heterogeneous in vivo activity of midbrain dopaminergic neurons. Nature neuroscience, 15(4), 613.
- Faunes, M., Fernández, S., Gutiérrez‐Ibáñez, C., Iwaniuk, A. N., Wylie, D. R., Mpodozis, J., ... & Marín, G. (2013). Laminar segregation of GABAergic neurons in the avian nucleus isthmi pars magnocellularis: a retrograde tracer and comparative study. Journal of Comparative Neurology, 521(8), 1727-1742.
- Gutiérrez-Ibáñez, C., Iwaniuk, A. N., Lisney, T. J., Faunes, M., Marin, G. J., & Wylie, D. R. (2012). Functional implications of species differences in the size and morphology of the isthmo optic nucleus (ION) in birds. PloS one, 7(5).
- Rapacioli, M., Botelho, J. F., Cerda, G., Duarte, S., Elliot, M., Palma, V., et al. (2012). Sonic hedgehog (Shh)/Gli modulates the spatial organization of neuroepithelial cell proliferation in the developing chick optic tectum. BMC neuroscience, 13(1), 117.
- Botelho, J. F. Sobre Gêmulas, Genes e DNA Investigações Filosóficas Vol E1 (2011)
- Vaz, N; Mpodozis, J; Botelho J.F.; Ramos, G. Onde está o Organismo? Ed. UFSC. Florianópolis, 2011.
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