Maeso, I*,Irimia M, Tena2 JJ, González-Pérez E, Tran D, Ravi V, Venkatesh B, Campuzano S, Gómez-Skarmeta JL*, Garcia-FernàndezJ* An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. Genome Research, in the press

Irimia M*, Denuc A, Ferrán JL, Pernaute B, Puelles L, Roy SW, , Garcia-Fernàndez J*, Marfany G*. Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1. RNA Biol , in the press

Somorjai I*, Somorjai R, Garcia-Fernàndez J*, Escrivà E*. Vertebrate-like regeneration in the invertebrate chordate amphioxus. Proc. Natl Acad. Sci. USA , in the press

Irimia M, Denuc A, Burguera D, Somorjai I Martí-Durán J, Genikhovich G, Jimenez-Delgado S, Roy S*, Marfany G*, Garcia-Fernàndez J* Stepwise Assembly of the Nova-regulated Alternative Splicing Network in the Vertebrate Brain. Proc. Natl Acad. Sci. USA 108:5319-24, 2011

Royo JL, Maeso I, Irimia M, Gao F, D’Aniello S, Technau U, Davidson E*, Casares F, Garcia-Fernàndez J*, Gómez-Skarmeta JL*. Transphyletic conservation of developmental regulatory state in animal evolution. Proc. Natl Acad. Sci. USA 108:14186-91, 2011

Irimia M, Maeso I, Burguera D, Hidalgo-Sánchez M, Puelles L, Roy SW, Garcia-Fernàndez J, Ferrán JL. Contrasting 5' and 3' Evolutionary Histories and Frequent evolutionary convergence in Meis/hth gene structures. Genome Biol Evol, 113:505-12, 2011

Sánchez-Guardado LO, Irimia M, Sánchez-Arrones L, Burguera D, Rodríguez-Gallardo L, Garcia-FernàndezJ, Puelles L, Ferrán JL, Hidalgo-Sánchez M. Distinct and redundant expression and transcriptional diversity of Meis paralogs during chiken development. Dev. Dynamics 240:1475-92, 2011

D'Aniello S, Somorjai I, Garcia-Fernàndez J, Topo E, D'Aniello A.* D-Aspartic acid is a novel endogenous neurotransmitter. FASEB J. 25(3):1014-27, 2011

Andreakis N, D'Aniello S, Albalat R, Patti FP, Garcia-Fernàndez J, Procaccini G, Sordino P, Palumbo A*. Evolution of the Nitric Oxide Synthase family in metazoans. Mol Biol Evol. 28: 1. 163-179; 2011

Irimia M* , Piñeiro C, Maeso I , Gómez-Skarmeta J*, Casares F*, Garcia-Fernàndez J*. Conserved developmental expression of Fezf in bilaterians and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer. EvoDevo 1: 7; 2010,

Punnamoottil B, Herrmann C, Pascual-Anaya J, D'Aniello S, Garcia-Fernàndez J, Akalin A, Becker TS, Rinkwitz S*. Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Dev Biol. 340(2):269-82; 2010

Irimia M, Maeso I, Gunning PW, Garcia-Fernàndez J*, Roy SW*. Internal and external paralogy in the evolution of Tropomyosin genes in metazoans. Mol Biol Evol. 27, 269-82; 2010

Irimia M*, Roy SW*, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Research. 19(11):2021-7; 2009

Jiménez-Delgado S, Pascual-Anaya J, Garcia-Fernàndez J*. Implications of duplicated cis-regulatory elements in the evolution of metazoans: the DDI model or how simplicity begets novelty. Brief Funct Genomic Proteomic. 8(4):266-75; 2009.

Bertrand S, Somorjai I, Garcia-Fernandez J, Lamonerie T, Escriva H*. HYPERLINK "http://www.ncbi.nlm.nih.gov/pubmed/19740411"FGFRL1 is a neglected putative actor of the FGF signalling pathway present in all major metazoan phyla. BMC Evol Biol 9:226; 2009

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 53(8-10): 2021-7; 2009

Bertrand S, Campo-Paysaa F, Camasses A, García-Fernàndez J, Escrivà H. Actors of the tyrosine kinase receptor downstream signaling pathways in amphioxus. Evolution & Development.11(1):13-26; 2009.

Garcia-Fernàndez* J, Benito-Gutiérrez E*. It's a long way from amphioxus: descendants of the earliest chordate. BioEssays. 31(6):665-7; 2009., includes cover

Irimia M*, Rukov JL, , Roy SW, Vinther J, Garcia-Fernàndez J*, Quantitative regulation of alternative splicing in devlopment and evolution. BioEssays;31(1):40-5; 2009.

Chambery A*, Parente A, D’Aniello A, Tope E, Ferrandino, G, Garcia-Fernàndez J, D’Aniello S*. Characterization and putative role of a type I gonadotropin-releasing hormone in the cephalochordate amphioxus. Endocrinology 150(2):812-820; 2009

Chambery A*, Parente A, D’Aniello A, Tope E, Ferrandino, G, Garcia-Fernàndez J, D’Aniello S*. Characterization and putative role of a type I gonadotropin-releasing hormone in the cephalochordate amphioxus. Endocrinology 150(2):812-820; 2009

Roy, S.W., Irimia, M. Splicing in the eukaryotic ancestor: form, function and dysfunction. Trends Ecol Evol 24(8):447-55; 2009

Irimia, M., Rukov, J.L., Roy, S.W Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates. PLoS One 24(8):447-55; 2009

Roy, S.W., Irimia, M. Mystery of intron gain: new data and new models. Trends Genet 25(2):67-7; 2009

Rosanas-Urgell A, Garcia-Fernàndez J, Marfany G*. ParaHox genes in pancreatic cell cultures: effects on the insulin promoter regulation. Int J Biol Sci. 4(1):48-57; 2008.

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 218, 591-597 (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, 378-38; 2008.

Irimia M, Maeso I, Garcia-Fernàndez J*. Convergent evolution of 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*. Gene expansion and retention leads to a diverse tyrosine superfamily on 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, Gibson-BrownJJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GV, Mchardy AC, MeulemansD, Nonaka M, Olinski RP, Pancer Z, Pestarino M, Rast JP, Rigoutsos I, Roch G, Saiga H, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Ye Y, Yoshida K, Yoshizaki F, Yu Jr-K, Xu A, Zhang Q, Zmasek CM,, Putnam N, Rokhsar D, Holland PWH*. Primitive and derived characters in the amphioxus genome. Genome Research. 7, 1100-1111; 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, Grigoriev IV, Horton AV, de Jong PJ, Jurka J, Kapitonov V, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Asaf Salamov A, Satou Y, Sauka-Spengler T, Schmutz T, Shin-I T, Toyoda A, Gibson-Brown JJ, Bronner-Fraser M, Fujiyama M, Holland LZ*, Holland PWH, Satoh N*, Rokhsar DS*. The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-1071 (2008) Includes cover, News&Views, TV and press.

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.

Irimia, M., Roy, S.W Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genetics; 2008

Roy, S.W., Irimia, M When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. Bioessays 30(6):601-5; 2008

Roy, S.W., 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 P. vivax. Mol Biol Evol 25(6):1192-8; 2008

Roy, S.W., Irimia, M Rare Genomic Characters do not Support Coelomata: RGC_CAMs. J Mol Evol 66(3):308-15; 2008

Irimia, M., Roy, S.W Spliceosomal introns as tools for genomic and evolutionary analysis. Nucl Acids Res 36(5):1703-12; 2008

Roy, S.W., Irimia, M Rare Genomic Characters do not Support Coelomata: Intron Loss/Gain. Mol Biol Evol 25(4):620-3; 2008

Roy, S.W., Irimia, M Intron mis-splicing: no alternative? Genome Biol 9(2):208; 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