Publications
Graham, A. and Shimeld, S.M.
(2012). The origin and evolution of the ectodermal
placodes. J.
Anat. In press.
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: 234-348.
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.