Publications

Gasparini, F., Shimeld, S.M., Ruffoni, E., Burighel, P. and Manni^, L. (2011). Expression of a Musashi-like gene in sexual and asexual development of the colonial chordate Botryllus schlosseri and phylogenetic analysis of the protein group. J. Exp. Zool. B. In Press.

Gasparini, F. and Shimeld, S.M. (2011) Analysis of a botryllid enriched-full-lenght cDNA library: insight into the evolution of splice leader trans-splicing in tunicates. Dev. Genes Evol.220: 329-336.

Shimeld, S.M., Boyle, M.J., Brunet, T., Luke, G.N. and Seaver, E.C. (2010). Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster. Dev. Biol. 240: 234-348.

Shimeld, S.M., Degnan, B. and Luke, G.N. (2010). Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters. Genomics. 95: 256-260.

Shimeld, S.M. (2009) Models for the Future. Development. 136: 4068-4069.

Takahashi, T., McDougall, C., Troscianko, J., Chen, W.C., Jayaraman-Nagarajan, A., Shimeld, S.M. and Ferrier, D.E.K. (2009) An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals. BMC Evol. Biol. 9: 240. See a review of this paper in the Journal of Biology

Degasperi V, Gasparini F, Shimeld S.M., Sinigaglia, C., Burighel, P. and Manni, L. (2009) Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations. BMC Dev. Biol. 9: 48.

Shimeld, S.M., Degnan, B. and Luke, G.N. (2009). Evolutionary genomics of the Fox genes: Origin of gene families and the ancestry of gene clusters. Genomics. In Press. doi:10.1016/j.ygeno.2009.08.002

Shimeld, S.M. (2008). C2H2 zinc finger genes of the Gli, Zic, KLF, SP, Wilms’ tumour, Huckebein, Snail, Ovo, Spalt, Odd, Blimp-1, Fez and related gene families from Branchiostoma floridae. Dev Genes Evol 218: 639-649.

Yu, J.-K., Mazet, F., Chen, Y.-T., Huang, S.-W., Jung, K.-C. and Shimeld, S.M. (2008) The Fox genes of Branchiostoma floridae. Dev Genes Evol 218: 629-638.

Wotton, K, Mazet, F. and Shimeld, S.M. (2008). Expression of FoxC, FoxF, FoxL1, and FoxQ1 genes in the dogfish Scyliorhinus canicula defines ancient and derived roles for Fox genes in vertebrate development. Dev Dynamics 237:1590-1603.

Larroux, C., Luke, G.N., Koopman, P., Rokhsar, D.S., Shimeld, S.M. and Degnan, B.M. (2008). Genesis and expansion of metazoan transcription factor gene classes Mol Biol Evol 25:980-96.

Shimeld, S.M., van den Heuvel, M., Dawber, R. and Brisco, J. (2007). An Amphioxus Gli Gene Reveals Conservation of Midline Patterning and the Evolution of Hedgehog Signalling Diversity in Chordates. PLoS One.

Wotton, K., French, K.E.M.. and Shimeld, S.M. (2007). The developmental expression of foxl2 in the dogfish Scyliorhinus canicula. Gene Expression Patterns 7: 793-797.

Riyahi, K. and Shimeld, S.M. (2007). Chordate beta-gamma crystallins and the evolutionary developmental biology of the vertebrate lens. Comp Biochem Physiol B 147: 347-357.

Wotton, K. and Shimeld, S.M. (2006). Comparative genomics of vertebrate Fox cluster loci. BMC Genomics 7: 271. PDF.

McDougall, C., Chen, W.-C., Shimeld, S.M. and Ferrier, D.E.K. (2006). The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes. Frontiers in Zoology doi:10.1186/1742-9994-3-16. PDF.

Mazet, F., Amemiya, C. and Shimeld, S. M. (2006). An ancient Fox gene cluster in the Bilateria. Current Biology 16: R314-R316. PDF. Supplementary.

Shimeld, S. M. and Levin, M. (2006). Evidence for the regulation of left-right asymmetry in Ciona by ion flux. Dev Dynamics 235: 1543-1553. PDF.

Shimeld, S.M., Purkiss, A.G., Dirks, R.P.H., Bateman, O.A, Slingsby, C. and Lubsen, N.H. (2005). Urochordate βγ-crystallin and the evolutionary origin of the vertebrate eye lens. Current Biology, 15: 1684-1689. PDF. Supplementary.

Mazet, F. and Shimeld, S.M. (2005) Evolutionary origin of vertebrate cranial sensory placodes. J Exp Zool B Mol Dev Evol 304B: 340-346. PDF

Shimeld, S.M. and Holland, N.D. (2005) Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms. Can J Zool 83: 90-100. PDF

Mazet, F., Hutt, J.A., Milloz, J., Millard, J., Graham, A. and Shimeld, S.M. (2005). Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev Biol 282: 494-508. PDF.

Mazet, F., Luke, G.N. and Shimeld, S.M. (2005) An amphioxus FoxQ1 gene is expressed in the developing endostyle. Gene Expression Patterns 5: 313-315. PDF.

Mazet, F. Masood, S., Luke, G.N., Holland, N.D. and Shimeld, S.M. (2004) Expression of AmphiCoe, an amphioxus COE/EBF gene, in the developing central nervous system and epidermal sensory neurons. Genesis 38: 58-65. PDF.

Shimeld, S.M. (2004) Calcium turns sinister in left-right asymmetry. Trends. Genet. 20: 277-280. PDF

Mazet, F. Hutt, J.A., Millard, J. and Shimeld, S.M. (2003). Pax gene expression in the developing central nervous system of Ciona intestinalis. Gene Exp. Patterns. 3: 743-745. PDF

Mazet, F. and Shimeld, S.M. (2003) Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock. Dev Genes Evol.213: 505-509. PDF

Mazet, F., Yu, J.-K., Liberles, D., Holland, L.Z. and Shimeld, S.M. (2003). Phylogenetic relationships of the Fox (forkhead) gene family in the Bilateria. Gene. 316: 79-89. PDF

Yagi, K., Satou, Y, Mazet, F., Shimeld, S.M., Degnan, B., Rokhsar, D, Levine, M., Kohara, Y. and Satoh, N. (2003). A genomewide survey of developmentally relevant genes in Ciona intestinalis III. Genes for Fox, ETS, nuclear receptors and III NFκB. Dev. Genes Evol. 213: 235-244.

Gostling, N.J. and Shimeld, S.M. (2003) Protochordate Zic genes define primitive somite compartments and highlight molecular changes underlying neural crest evolution. Evol Dev. 5: 136-144. PDF

Boorman, C.J. and Shimeld, S.M. (2002) The evolution of chordate left right asymmetry. Bioessays 24: 1004-1011. PDF

Ferrier, D.E.K. and Shimeld, S.M. (2002) The evolution of developmental mechanisms. Genome Biology 3: 4020.1-4020.3

Mazet, F. and Shimeld, S.M. (2002) Gene duplication and divergence in the early evolution of vertebrates. Curr Opin Genet Dev 12: 393-396. PDF

Mazet, F. and Shimeld, S.M. (2002) The evolution of chordate neural segmentation Dev Biol 251: 258-270. PDF

Boorman, C.J. and Shimeld, S.M. (2002) Cloning and expression of a Pitx homeobox gene from the lamprey, a jawless vertebrate. Dev Genes Evol 212: 349-353. PDF

Boorman, C.J. and Shimeld, S.M. (2002) Pitx homeobox genes in Ciona and amphioxus show left-right asymmetry is a conserved chordate character and define the ascidian adenohypophysis. Evol Dev 4: 354-365. PDF

Knight, R.D. and Shimeld, S.M. (2001). Identification of conserved C2H2 zinc finger gene families in the Bilateria. Genome Biology 2: 0016.1-0016.8. PDF

Shimeld, S.M. and Holland, P.W.H. (2000). Vertebrate Innovations. Proc Natl Acad Sci USA 97: 4492-4452. PDF

Knight, R.D., Panopoulou, G.D., Holland, P.W.H. and Shimeld, S.M. (2000). An amphioxus Krox gene: Insights into vertebrate hindbrain evolution. Dev Genes Evol 210: 518-521. PDF

Shimeld, S.M. (2000). An amphioxus netrin gene is expressed in midline structures during embryonic and larval development. Dev Genes Evol 210: 337-344. PDF

Sedlacek, Z., Shimeld, S.M., Münstermann, E. and Poustka, A. (1999). The amphioxus rabGDI gene is neural specific: Implications for the evolution of chordate rabGDI genes. Mol Biol Evol 16: 1231-1237. PDF

Shimeld, S.M. (1999). Gene function, gene networks and the fate of duplicated genes. Seminars Cell Dev Biol 10: 549-553. PDF

Shimeld, S.M. (1999). The Evolution of Dorsoventral Patterning in the Chordate Neural Tube. Amer Zool 39: 641-649.

Sharman, A.S., Shimeld, S.M. and Holland, P.W.H. (1999) An amphioxus Msx gene expressed predominantly in the dorsal neural tube. Dev Genes Evol 209: 260-263. PDF

Shimeld, S.M. (1999). The evolution of the hedgehog gene family in chordates: Insights from amphioxus hedgehog. Dev Genes Evol 209: 40-47. PDF

Shimeld, S.M. (1998). Characterisation of AmphiF-spondin reveals the modular evolution of chordate F-spondin genes. Mol Biol Evol 15: 1218-122. PDF

Johnstone, C., Shimeld, S.M. and Sharpe, P.T. (1998). Molecular evolution of the Zfx and ZNF6 gene families. Mol Biol Evol 15: 129-137. PDF

Shimeld, S.M. (1997). Characterisation of amphioxus HNF-3 genes: Conserved expression in the notochord and floor plate. Dev Biol 183: 74-85. PDF

Shimeld, S.M. (1997). A transcriptional modification motif encoded by homeobox and fork head genes. FEBS letters 410: 124-125.

Shimeld, S.M. (1996). Retinoic acid, HOX genes and the anterior posterior axis in chordates. Bioessays 18: 613-616.

Shimeld, S.M., McKay, I.J. and Sharpe, P.T. (1996). The murine homeobox gene Msx-3 shows highly restricted expression in the developing neural tube. Mech Dev 55: 201-210.

Coriat, A-M., Barnett, M. and Shimeld, S.M. (1994). Sex in the swamps: Temperature dependent sex determination in the American alligator. Biol Sci Rev 7: 7-9.

Coletta, P.L., Shimeld, S.M. and Sharpe, P.T. (1994). The molecular anatomy of Hox gene expression. J Anat 184: 15-22.

Shimeld, S.M. and Sharpe, P.T. (1993) Ectopic expression of Hox-3.3 induces changes in cell surface properties. Biochem Biophys Acta 1136: 253-258.

Shimeld, S.M., Gaunt, S.J., Coletta, P.C., Geada, A.M.C., and Sharpe, P.T. (1993). Spatial localisation of transcripts of the Hoxc-6 gene. J Anat 183: 515-523.

Geada, A.M.C., Gaunt, S.J., Azzawi, M., Shimeld, S.M., Pearce, J. and Sharpe, P.T. (1992). Sequence and embryonic expression of the murine Hox-3.5 gene. Development 116: 497-506.

Coletta, P.L., Shimeld, S.M., Chaudhuri, C., Müller, U., Clarke, J.P. and Sharpe, P.T. (1991). Characterisation of the murine Hox-3.3 gene and its promoter. Mech Dev 35: 129-142.

Book Chapters and Abstracts

Mazet, F. and Shimeld, S.M. (2005). Variation and Conservation in the Development of Animal Bodies: Evolutionary Developmental Biology. In Encyclopaedia of Molecular Cell Biology and Molecular Medicine. Ed. R. A Myers Wile-VCH, Weinheim.

Shimeld, S.M. (2003) Evolutionary aspects of vertebrate patterning. In Patterning in Vertebrate Development: Frontiers in Molecular Biology. Ed C. Tickle. Oxford University Press.

Shimeld, S.M. (2001) Axial signalling and the evolution of dorsoventral pattern in neurectoderm and mesoderm. Zool Sci 18: 459-460.

Holland, P.W.H., Wada, H., Manzanares, M., Krumlauf, R. and Shimeld, S.M. (2001). The origin of the neural crest. In Major Events in Early Vertebrate Evolution. Ed. P.E. Ahlberg. Systematics Association Special Volume Series 61, Taylor & Francis, London.

Coletta, P.L., Shimeld, S.M., Clarke, J.P. and Sharpe, P.T. (1992). The murine Hox-3.3 gene. In Development and Regeneration of the Nervous System. Chapmann and Hall, London.