Publications (or see these in Google Scholar)

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A link to downloadable data related to publications will appear HERE in due course

2017   2016   2015   2014   2013   2012   2011   2010   1009   2008   2007   2006   2005   2004   Pre-2004


Lara-Ramirez, R., Poncelet, G., Patthey, C. and Shimeld, S,M. (2017). The structure, splicing, synteny and expression of lamprey COE genes and the evolution of the COE gene family in chordates. Dev Genes Evol 5: 319-338.
Bao, Y., Xu, F. and Shimeld, S.M. (2017). Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates. Genome biology and evolution 9 (4), 869-886
Li, G., Liu, X., Xing, C., Zhang, H., Shimeld, S.M. and Wang, Y. (2017). Cerberus–Nodal–Lefty–Pitx signaling cascade controls left–right asymmetry in amphioxus. Proceedings of the National Academy of Sciences, 201620519


Sutton, E.R., Yu, Y., Shimeld, S.M., White-Cooper, H. and Alphey, L. (2016). Identification of genes for engineering the male germline of Aedes aegypti and Ceratitis capitata. BMC genomics 17, 948.
Gregory, M., Morrison, N.I., Shimeld, S.M. and Alphey, L. (2016). Insect transformation with piggyBac: getting the number of injections just right. Insect Mol. Biol. 25: 259-271.
Patthey, C., Clifford, H., Haerty, W., Ponting, C.P., Shimeld, S.M. and Begbie, J. (2016). Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick. Neural Dev. 2016; 11: 3


Sato A, Kawashima T, Fujie M, Hughes S, Satoh N, and Shimeld, S.M. (2015). Molecular basis of canalization in an ascidian species complex adapted to different thermal conditions. Scientific Reports, 5:16717.
Kenny, N. Namigai, E., Marletaz, F. Hui, J, Shimeld, S,M. (2015). Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics. doi:10.1016/j.margen.2015.07.004.
Lara-Ramirez, R. Patthey, C. and Shimeld, S.M. (2015) Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system. Developmental Dynamics. 244: 1096–1108.
Thomson, H. and Shimeld, S.M. (2015) Transmission and scanning electron microscopy of the accessory cells and chorion during development of Ciona intestinalis type B embryos and the impact of their removal on cell morphology. Zoological Science 32:217-222..


Kenny, N.J., Namigai, E.K.O., Dearden, P.K., Hui, J.H.L., Grande, C. and Shimeld, S.M. (2014) The Lophotrochozoan TGF-β signalling cassette-diversification and conservation in a key signalling pathway. Int. J. Dev. Biol 58: 533-549
Sato, A., Shimeld, S.M. and Bishop, J.D.D. (2014). Symmetrical reproductive compatibility of two species in the Ciona intestinalis (Ascidiacea) species complex, a model for marine genomics and developmental biology. Zool. Sci. 39: 369-374.
Chen, W.-C., Pauls, S., Elgar, G. Bacha, J., Loose, M. and Shimeld, S.M. (2014) Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Dev. Biol. 390: 261-272.
Kenny, N.J., Sin, Y.W., Shen, X., Zhe, Q., Chan, T.F., Tobe, S.S., Shimeld, S.M., Chu, K.H. and Hui, J. (2014). Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Marine Drugs. 12, 1419-1437.
Patthey, C., Schlosser, G. and Shimeld, S,M. (2014). The evolutionary history of vertebrate cranial placodes-I: Cell type evolution. Dev. Biol. 389: 82-97.
Schlosser, G., Patthey, C. and Shimeld, S,M. (2014). The evolutionary history of vertebrate cranial placodes-II: Evolution of ectodermal patterning. Dev. Biol. 389: 98-118.
Namigai, E.O., Kenny, N.J. and Shimeld, S.M. (2014). Right across the tree of life: the evolution of left right asymmetry in the Bilateria. Genesis 52: 458-470.


Doglio, L,. Goode, D.K., Pelleri, M.C., Pauls, S., Frabetti, F., Shimeld, S.M., Vavouri, T., Elgar, G. (2013). Parallel Evolution of Chordate Cis-Regulatory Code for Development. PLOS Genetics DOI: 10.1371/journal.pgen.1003904.
Holland, L.Z., Carvalho, J.E., Escriva, H., Laudet, V., Schubert, M., Shimeld, S.M. and Yu, J.-K. (2013), Evolution of bilaterian central nervous systems: a single origin? EvoDevo  4:27.
Graham, A. and Shimeld, S.M. (2013). The origin and evolution of the ectodermal placodes. J. Anat. 222: 32-40.


Werner, G.A., Gemmell, P., Grosser, S., Hamer, R. and Shimeld, S.M. (2012). Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda:Patellidae) reveals candidate biomineralising genes. Mar. Biotechnol. DOI 10.1007/s10126-012-9481-0.
Kenny, N. and Shimeld, S.M. (2012). Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette. Dev. Genes. Evol. DOI 10.1007/s00427-012-0416-6.
Shimeld, S.M. and Donoghue, P.J. (2012) Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish). Development 139: 2091-2099.
Thompson, H., Shaw, M.K., Dawe, H. and Shimeld, S.M. (2012). The formation and positioning of cilia in Ciona intestinalis embryos in relation to the generation and evolution of chordate left-right asymmetry. Dev. Biol. 364: 214-223.
Paps, J., Holland, P.W.H., Shimeld, S.M. (2012). A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus? Briefings in Functional Genomics 11: 177-186.
Wotton, K. And Shimeld, S.M. (2011).  Analysis of lamprey clustered Fox genes: Insight into Fox gene evolution and expression in vertebrates. Gene 489: 30-40.
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. 316B: 562-573.
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: 234-248.
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.
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.
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. (2009). Book review: Models for the future. Development 136: 4068-4069
Shimeld, S.M. (2008). Peter Holland, homeobox genes and the developmental basis of animal diversity. Int. J. Dev Biol. 52: 3-7. Also reprinted in Russian in Ontogenez (2008) 39: 1-7.
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 Briscoe, J. (2007). An Amphioxus Gli Gene Reveals Conservation of Midline Patterning and the Evolution of Hedgehog Signalling Diversity in Chordates. PLoS One  9: e864.
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.
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.
Mazet, F., Amemiya, C. and Shimeld, S. M. (2006). An ancient Fox gene cluster in the Bilateria. Current Biology 16: R314-R316.
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.
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.
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.
Mazet, F. and Shimeld, S.M. (2005) Molecular evidence from ascidians for the evolutionary origin of vertebrate cranial sensory placodes. J Exp Zool B Mol Dev Evol 304B: 340-346.
Shimeld, S.M. and Holland, N.D. (2005) Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms. Can J Zool 83: 90-100.
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.
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.
Shimeld, S.M. (2004) Calcium turns sinister in left-right asymmetry. Trends Genet 20: 277-280
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.
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.
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.
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.
Mazet, F. and Shimeld, S.M. (2002) The evolution of chordate neural segmentation Dev Biol 251: 258-270.
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.
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.
Boorman, C.J. and Shimeld, S.M. (2002) The evolution of chordate left right asymmetry. Bioessays 24: 1004-1011.
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
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.
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.
Shimeld, S.M. (2000). An amphioxus netrin gene is expressed in midline structures during embryonic and larval development. Dev Genes Evol 210: 337-344.
Shimeld, S.M. and Holland, P.W.H. (2000). Vertebrate Innovations. Proc Natl Acad Sci USA 97: 4492-4452.
Shimeld, S.M. (1999). Gene function, gene networks and the fate of duplicated genes. Seminars Cell Dev Biol 10: 549-553.
Shimeld, S.M. (1999). The Evolution of Dorsoventral Patterning in the Chordate Neural Tube. Amer Zool  39: 641-649
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.
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.
Shimeld, S.M. (1999). The evolution of the hedgehog gene family in chordates: Insights from amphioxus hedgehog. Dev Genes Evol 209: 40-47.
Shimeld, S.M. (1998). Characterisation of AmphiF-spondin reveals the modular evolution of chordate F-spondin genes. Mol Biol Evol 15: 1218-1223.
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.
Shimeld, S.M. (1997). Characterisation of amphioxus HNF-3 genes: Conserved expression in the notochord and floor plate. Dev Biol 183: 74-85.
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.