Chambery A*, Parente A, D’Aniello A, Tope E, Ferrandino, G, Garcia-Fernàndez J, D’Aniello S* The presence and ancestral role of mammalian-GnRH in the reproductive system of chordates. Endocrinology, (in press)

Pascual-Anaya, J, D’Aniello, S, Garcia-Fernàndez J*. Unexpectedly large number of conserved non-coding regions within the ancestral chordate Hox cluster. Dev. Genes Evol. , (in press)

Bertrand, S, Campo-Paysa F, Camasses, A, Garcia-Fernandez J, Escrivà, H* RTKs downstream signalling pathways in amphioxus. Evolution & Development (in press)

Irimia M*, Rukov JL, , Roy SW, Vinther J, Garcia-Fernàndez J*, Quantitaive regulation of alternative splicing in devlopment and evolution. BioEssays (in press)

Roy, SW*, Irimia M, When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. BioEssays 30:601-605 (2008)

Irimia M*, Roy, SW*, Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acid Res. 36:1703-1712 (2008)

Roy, SW*, Irimia M*, Intron mis-splicing : no alternative? Genome Biology 9:208 (2008)

Roy, SW*, Irimia M, Rare genomic characters do not support Coelomata: intron loss/gain. Mol Biol. Evol. 25, 375-382 (2008)

Roy, SW*, Irimia M, Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax. Mol Biol. Evol 25, 1841-1854 (2008)

Irimia M, Rukov, JK, Penny D., Vinther, J., Garcia-Fernàndez J, Roy, SW*. Origins of introns by « intronization » of exonic sequences. Trends in Genetics 24, 378-381 (2008)

Irimia M, Maeso I, Garcia-Fernàndez J*. Convergent evolution o Iroquois homeobox genes across metazoans. Mol Biol. Evol 25, 1521-1525 (2008)

D’Aniello S, Irimia M, Maeso I, Pascual-Anaya J, Jiménez-Delgado S, Bertrand S. Garcia-Fernàndez J*. Massive gene expansion but not loss leads to unprecedented Tyrosine kinase diversity and richness in amphioxus. Mol. Biol. Evol. 25, 1841-1854 (2008)

Amemiya CT*, Prohaska, SJ, Hill-Force A, Cooke A, Wasserschei J, Ferrier DEK, Pascual-Anaya J, Garcia-Fernandez J, Dewar K, Stadler PF. The amphioxus Hox cluster: comparative genomics and evolution. J. Exp. Zool. (Mol Evol Biol) 310, 465-477 (2008)

Holland LZ*, Satoh N*, Azumi K, Benito-Gutiérrez E, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LD, Ferrier DEK, Garcia-Fernàndez J et al. Primitive and derived characters in the amphioxus genome. Genome Research. 7, 1100-1111 (2008)

Garcia-Fernàndez J*, Jiménez-Delgado S, Pascual-Anaya J, Maeso I, Irimia M, Minguillón C , Benito-Gutiérrez E, Gardenyes J, Bertrand S., D’Aniello S. From the American to the European amphioxus: towards Experimental Evo-Devo at the origin of Chordates. Int J Dev Biol DOI 10.1387/ijdb.072436jg

Roy SW*, Irimia M. Rare genomic characters do not support Coelomata: RGC_CAMs. J. Mol. Evol. 66:308-315 (2008)

Putnam N, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez E, Dubchak I, Garcia-Fernàndez J, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-1071 (2008) cover and News&Views

Irimia M*, Rukov JL, Penny D, Garcia-Fernàndez J, Vinther J, Roy SW*. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol.Biol. Evol. 25: 3675-3682 (2008).

D'Aniello S,* Fisher GH, Topo E, Ferrandino, G, Garcia-Fernandez J,* D'Aniello A.* N-Methyl-D-aspartic Acid (NMDA) in the nervous system of the amphioxus Branchiostoma lanceolatum. BMC Neuroscience 8:109 (pp1-7) 2007

Garcia-Fernàndez J, D'Aniello S, Escrivà H. Organizing chordates with an organizer. Bioessays. Jul;29(7):619-624, 2007

Irimia M, Maeso I, Penny D, Garcia-Fernàndez J, Roy SW. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol. 24, 1604-1607, 2007

Fuentes M, Benito E, Bertrand S, Paris M, Mignardot A, Godoy L, Jimenez-Delgado S, Oliveri D, Candiani S, Hirsinger E, D'Aniello S, Pascual-Anaya J, Maeso I, Pestarino M, Vernier P, Nicolas JF, Schubert M, Laudet V, Geneviere AM, Albalat R, Garcia Fernandez J, Holland ND, Escriva H. Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum). J Exp Zoolog B Mol Dev Evol. 308, 484-493, 2007

D'Aniello S, Garcia-Fernàndez J. D-aspartic acid and L-amino acids in the neural system of the amphioxus Branchiostoma lanceolatum. Amino Acids. 32, 21-26, 2007

Irimia M, Rukov JL, Penny D, Roy SW. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol. 7, 188, 2007

Irimia M, Penny D, Roy SW. Coevolution of genomic intron number and splice sites. Trends Genet. 23, 321-325, 2007

Rukov JL, Irimia M, Mørk S, Lund VK, Vinther J, Arctander P. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae. Mol Biol Evol. 24, 909-917, 2007

Jimenez-Guri E, Paps J, Garcia-Fernandez* J, Salo E*. Hox and ParaHox genes in Nemertodermatida, a basal bilaterian clade. Int J Dev Biol 50, 675-679, 2006

Benito-Gutiérrez E. A gene catalogue of the amphioxus nervous system. Int J Biol Sci. 2,149-160, 2006

Pascual-Anaya J, D'Aniello S. Free amino acids in the nervous system of the amphioxus Branchiostoma lanceolatum. A comparative study. Int J Biol Sci . 2, 87-92, 2006

Jiménez-Delgado S, Crespo M, Permanyer J, Garcia-Fernàndez J, Manzanares M. Evolutionary genomics of the recently duplicated amphioxus Hairy genes. Int J Biol Sci. 2, 66-72, 2006

Garcia-Fernàndez, J. Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II). Int. J. Biol. Sci. 2: 93-94; 2006

Garcia-Fernàndez, J.Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (I). Int. J. Biol. Sci. 2: 30-31; 2006

Garcia-Fernàndez, J. (editor). Special Issue on amphioxus Genetics (1 & 2). Int. J. Biol. Sci. Vol2, num1-2; 2006

Garcia-Fernandez, J. Origin and evolution of the homeobox gene clusters, Nature Rev. Genetics 6, 881-892; 2005

Benito-Gutierrez, E, Garcia-Fernandez, J & Comella, JX. Origin and evolution of the Trk family of neurotrophic receptors. Mol. Cell. Neurosciences 31, 179-192; 2006

Benito-Gutiérrez, E., Illas, M., Comella, J.X. & Garcia-Fernàndez. J. Outlining the nascent nervous system of Branchiostoma floridae (amphioxus) by the pan-neural marker AmphiElav. Brain Res. Bull. 66, 518-21; 2005

Rosanas-Urgell, A. Marfany, G. & Garcia-Fernàndez. J. Pdx1-related homeodomain transcription factors are distinctly expressed in mouse adult pancreatic islets. Mol. Cell. Endocrinol. 237, 59-66; 2005

Benito-Gutiérrez, E., Nake, C., llovera, M., Comella, J.X. & Garcia-Fernàndez. J. The single AmphiTrk receptor highlights increased complexity of neurotrophin signalling in vertebrates and suggests an early role in developing sensory neuroepidermal cells. Development 132, 2191-2202; 2005

Minguillón, C., Gardenyes, J., Serra, E., Castro, L.C.F. Hill-Force, A., Holland, P.W.H., Amemiya, C.T.,  & Garcia-Fernàndez, J. No more than 14: the end of the amphioxus Hox cluster. Int. J. Biol. Sciences 1; 19-23; 2005

Garcia-Fernàndez, J. Hox,  ParaHox, ProtoHox: facts and guesses. Heredity 94; 145-152; 2005.

Fuentes M, Schubert M, Dalfo D, Candiani S, Benito E, Gardenyes J, Godoy L, Moret F, Illas M, Patten I, Permanyer J, Oliveri D, Boeuf G, Falcon J, Pestarino M, Garcia-Fernandez J., Albalat R, Laudet V, Vernier P, Escriva H. Preliminary observations on the spawning conditions of the European amphioxus (Branchiostoma lanceolatum) in captivity. J Exp Zoolog Part B Mol Dev Evol 302; 384-91; 2004

Baguñà, J. & Garcia-Fernàndez, J. Evo-Devo : the long and winding road. Int. J. Dev. Biol. 4; 705-713; 2003

Baguñà, J. & Garcia-Fernàndez, J. (eds). Evolution and Development. Int. J. Dev. Biol 47, n.6-7; 2003

Minguillón, C., Jiménez-Delgado, S., Panopoulou, G. &Garcia-Fernàndez, J. The amphioxus hairy family: differential fate after duplication. Development 130; 5903-5914; 2003

Minguillón, C. & Garcia-Fernàndez, J. (2003). Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters. Genome Biology 4: R12.1-R12.8

Bayascas, J. R., Yuste, V.J., Benito, E, Garcia-Fernàndez, J & Comella, J.X (2002). Isolation of AmphiCASP-3/7, an ancestral caspase from amphioxus (Branchiostoma floridae). Evolutionaryconsiderations for vertebrate caspases. Cell Death and Differentiation 9:1078-1089

Minguillón, C. & Garcia-Fernàndez, J. (2002). The single amphioxus Mox gene: insights into the functional evolution of Mox genes, somites, and the assimetry of amphioxus somitogenesis. Dev. Biol. 246, 455–465

Minguillón, C, Ferrier, D.E.K., Cebrián, C. & Garcia-Fernàndez, J. (2002). Gene duplications in the prototypical cephalochordate amphioxus. Gene 287 121–128

Solé, R.V., Salazar-Ciudad, I. & Garcia-Fernàndez, J. (2002). Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis. Physica A 305, 640-647

Garcia-Fernàndez, J., Ferrier, D.E.K., Minguillón, C. & Cebrián, C. (2001). The amphioxus genome in Evo-Devo: archetype or “cul de sac”? Int. J. Dev. Biol. 45(S1), S137-S138

Ferrier, D.E.K., Minguillón, C, Cebrián, C. & Garcia-Fernàndez, J. (2001). Amphioxus Evx genes: implications for the evolution of the Midbrain-Hindbrain Boundary and the chordate tailbud. Dev. Biol. 237, 270-281

Saló, E., Tauler, J., Jimenez, E., Bayascas, J. R., González-Linares, J., Garcia-Fernàndez, J. & Baguñà, J. (2001). Hox and paraHox genes in flatworms. Characterization and expression. Amer. Zool. 41, 652-663.

Garcia-Fernàndez, J., Ferrier, D:E.K., Minguillón, C. Holland, P.W.H. & Wada, H. (2001). The amphioxus genome has both archetypal and derived features. Zool. Sci.18, 454-455

Cañestro, C., Hjelmqvist, L., Albalat, R., Garcia-Fernàndez, J., Gonzalez-Duarte, R. & Jörnvall, H. Amphioxus alcohol dehidrogensase: a class 3 form of single type and structural conservation but with unique developmental expression. Eur. J. Biochem. 267;pp.6511-6518, 2000

Ferrier, D:E.K., Minguillón, C. Holland, P.W.H. & Garcia-Fernàndez, J. The amphioxus Hox cluster: deuterostome Posterior Flexibility and Hox 14. Evolution &  Development2;pp.284-293; 2000

Salazar-Ciudad, I., Garcia-Fernàndez, J. & Solé, R. V. Gene networks capable of pattern formation: from induction to reaction-difussion. J. theor. Biol. 205;pp.587-603; 2000

Solé, R. V., Salazar-Ciudad, I. &  Garcia-Fernàndez, J. Landscapes, gene networks and pattern formation: on the Cambrian Explosion. Adv. Complex Systems4;pp.313-337; 1999

Wada, H.; Garcia-Fernàndez, J.  & Holland, P. W. H. Colinear and segmental expression of amphioxus Hox genes. Dev. Biol. 213; pp131-141; 1999

Brooke, N. M., Garcia-Fernàndez, J. & Holland, P. W. H. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature392, 920-922; 1998

Collet, J., Garcia-Fernàndez, J. & Marfany, G. Plasmid DNA small-scale preparation based on nuclease inactivation by diethylpyrocarbonate. Trends in Genetics Technical Tips on lineT01207; 1997

Garcia-Fernàndez, J. & Holland, P. W. H. Amphioxus Hox genes: insigths into evolution and development. Int. J. Dev. Biol. supp1; pp 71S-72S; 1996

Tauler, J., Baguñà, J., Saló, E. & Garcia-Fernàndez, J. Distox genes: a milestone in the evolution of Hox clusters? Int. J. Dev. Biol. supp1; pp 69S-70S; 1996

Garcia-Fernàndez, J. & Holland, P. W. H. Hox genes and the origin of vertebrates. Cell. Biol. Int. 20; pp 306-308; 1996

Holland, P. W. H. & Garcia-Fernàndez, J. Hox genes, developmental evolution and vertebrate origins. Ontogenez (Russian J. Dev. Biol.) 27; pp 273-279; 1996

Holland, P. W. H., Garcia-Fernàndez, J., Hox genes and chordate evolution. Dev. Biol. 173; pp 382-395; 1996

Saló E, Muñoz-Marmol, A.M., Bayascas-Ramirez J.R., Garcia-Fernàndez J., Casali, A., Corominas, M., & Baguñà J. The freshwater planarian Dugesia(G)tigrinacontains a great diversity of homeobox genes. Hydrobiologia305; pp 269-275; 1995

Garcia-Fernàndez, J., Bayascas-Ramírez, J. R., Marfany, G., Muñoz-Mármol, A. M., Casali,  A., Baguñà, J.  & Saló, E. High copy number of highly conserved mariner-like transposons in planarian (Platyhelminthe): Evidence for a trans-phyla horizontal transfer. Mol. Biol. Evol. 12; pp 421-431; 1995

Baguñà, J., Saló, E., Romero, R., Garcia-Fernàndez, J., Bueno, D., Muñoz-Mármol, A. M., Bayascas-Ramírez, J. R. & Casali, A. Regeneration and pattern formation in planarians: Cells, molecules and genes. Zool. Sci.11; pp 781-795; 1994

Holland, P. W. H., Garcia-Fernàndez, J., Williams, N. A. & Sidow, A. Gene duplications and the origin of vertebrate development. DevelopmentSuppl; pp 125-133; 1994

Garcia-Fernàndez, J. & Holland, P. W. H. Archetypal organization of the amphioxus Hox gene cluster. Nature370; 563-566; 1994

Burgaya F., Garcia-Fernàndez J., Riutort M., Baguñà J., & Saló E. Structure and expression of spk-1, a src-related gene product found in the simple triblastic Dugesia(G)tigrina.Oncogene9; pp 1267-1272; 1994

Holland, P. W. H., Garcia-Fernàndez, J., Holland, L. Z., Williams, N. A. & Holland, N. D. The molecular control of spatial paterning in amphioxus. J. Mar. Biol. Ass. U. K. 74; pp 49-60; 1993

Garcia-Fernàndez J., Marfany, G., Baguñà J.,  Saló E. Infiltration of mariner elements. Nature364, pp 109-110; 1993.

Garcia-Fernàndez J., Baguñà J.,  Saló E. Genomic organization and expression of the planarian homeobox genes Dth-1 and Dth-2. Development118; pp. 241-253; 1993

Garcia-Fernàndez, J., Baguñà, J. & Saló E. Planarian Homeobox genes: Cloning, sequence analysis, and expression. Proc. Natl. Acad. Sci. 88; pp. 7338-7342; 1991