Baguña, J.; Martinez, P.; Paps, J.; Riutort, M. (2008) Back in time: a new systematic proposal for the Bilateria. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 363: 1481-1491

Álvarez-Presas, M.; Baguñà, J.; Riutort, M. (2008) Molecular phylogeny of land and freshwater planarians (Tricladida, Platyhelminthes): From freshwater to land and back. Molecular Phylogenetics and Evolution, 47: 555 -568

Jaume Baguñà i Marta Riutort. (2004) The dawn of bilaterian animals: the case of acoelomorph flatworms. BioEssays 26: 1046-1057. Review

Iñaki Ruiz-Trillo, Marta Riutort, H. Matthew Fourcade, Jaume Baguñà, Jeffrey L. Boore (2004) Mitochodrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. Molecular phylogenetics and evolution 33: 321-332

Baguñà J., Riutort M. (2004) Molecular phylogeny of Platyhelminthes. Canadian Journal of Zoology 82: 168-193. Review

Ruiz-Trillo I., Paps J., Loukota M., Ribera C., Jondelius U., Baguñà J., Riutort M. (2002) A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. PNAS 99(17): 11246-11251

Littlewood D.T.J., Olson P.D., Telford M.J., Herniou E.A., Riutort M. (2001) Elongation Factor 1-alpha sequences alone do not assist in resolving the position of the Acoela within the Metazoa. Molecular Biology and Evolution 18(3): 437-442

Carranza S., Baguñà J., Riutort M. (1999) Origin and evolution of paralogous rRNA gene clusters within the flatworm family Dugesiidae (Platyhelminthes, Tricladida). Journal of Molecular Evolution 49:250-259

Ruiz-Trillo I., Riutort M., Littlewood D.T.J., Herniou E.A., Baguñà J. (1999) Acoel flatworms: earliest extant bilaterian metazoans, not members of Platyhelminthes. Science 283: 1919-1923

Carranza S., Littlewood D.T.J., Clough K.A., Ruiz I., Baguñà J., Riutort M. (1998) A robust molecular phylogeny of the Tricladida (Platyhelminthes, Seriata) and a reassessment of morphological synapomorphies. Proc. R. Soc. Lond. B. 265: 631-640

Carranza S., Baguñà J., Riutort M. (1997) Are the Platyhelminthes a monophyletic primitive group?. An assesment using 18S rDNA sequences Molecular Biology and Evolution 14(5): 485-497

Carranza S., Giribet G., Ribera C., Baguñà J., Riutort M. (1996) Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida) Molecular Biology and Evolution 13(6): 824-832