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Dr Dave Ferrier

Dr Dave Ferrier
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Research Overview. We aim to understand how the diversity of form in the animal kingdom evolved. The focus of our research is the connection between the evolution of animal genome organisation and development, with a particular concentration on the homeobox-containing genes. The Hox gene cluster is established as a corner-stone of Evolutionary Developmental Biology, but much about the evolution of its organisation and mode of operation remains unknown. Also the Hox cluster is not unique as a homeobox gene cluster controlling animal development, further clusters being the ParaHox and NK clusters, all of which evolved within larger arrays of homeobox genes (the Mega-cluster and Super-Hox cluster). We utilize a variety of organisms in our research (including amphioxus, sea squirts, polychaetes and priapulids), chosen from key points in the phylogeny of the animals to enable reconstruction of the ancestral conditions at major nodes in the animal kingdom; the origin of bilaterians, protostomes, deuterostomes, chordates and vertebrates.

source: symbiosis

 

Recent publications listed in research@st-andrews
Plöschner, M, Kollárová, V, Dostál, Z, Nylk, J, Barton-Owen, T, Ferrier, DEK, Chmelík, R, Dholakia, K & Čižmár, T 2015, 'Multimode fibre: light-sheet microscopy at the tip of a needle' Scientific Reports, vol 5, 18050. DOI: 10.1038/srep18050
Chipman, AD, Ferrier, DEK, Brena, C, Qu, J, Hughes, DST, Schröder, R, Torres-Oliva, M, Znassi, N, Jiang, H, Almeida, FC, Alonso, CR, Apostolou, Z, Aqrawi, P, Arthur, W, Barna, JCJ, Blankenburg, KP, Brites, D, Capella-Gutiérrez, S, Coyle, M, Dearden, PK, Du Pasquier, L, Duncan, EJ, Ebert, D, Eibner, C, Erikson, G, Evans, PD, Extavour, CG, Francisco, L, Gabaldón, T, Gillis, WJ, Goodwin-Horn, EA, Green, JE, Griffiths-Jones, S, Grimmelikhuijzen, CJP, Gubbala, S, Guigó, R, Han, Y, Hauser, F, Havlak, P, Hayden, L, Helbing, S, Holder, M, Hui, JHL, Hunn, JP, Hunnekuhl, VS, Jackson, L, Javaid, M, Jhangiani, SN, Jiggins, FM, Jones, TE, Kaiser, TS, Kalra, D, Kenny, NJ, Korchina, V, Kovar, CL, Kraus, FB, Lapraz, F, Lee, SL, Lv, J, Mandapat, C, Manning, G, Mariotti, M, Mata, R, Mathew, T, Neumann, T, Newsham, I, Ngo, DN, Ninova, M, Okwuonu, G, Ongeri, F, Palmer, WJ, Patil, S, Patraquim, P, Pham, C, Pu, L-L, Putman, NH, Rabouille, C, Ramos, OM, Rhodes, AC, Robertson, HE, Robertson, HM, Ronshaugen, M, Rozas, J, Saada, N, Sánchez-Gracia, A, Scherer, SE, Schurko, AM, Siggens, KW, Simmons, D, Stief, A, Stolle, E, Telford, MJ, Tessmar-Raible, K, Thornton, R, van der Zee, M, von Haeseler, A, Williams, JM, Willis, JH, Wu, Y, Zou, X, Lawson, D, Muzny, DM, Worley, KC, Gibbs, RA, Akam, M & Richards, S 2014, 'The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima' PLoS Biology, vol 12, no. 11, e1002005. DOI: 10.1371/journal.pbio.1002005
Fortunato, S, Adamski, M, Mendivil Ramos, O, Leininger, S, Liu, J, Ferrier, DEK & Adamska, M 2014, 'Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes' Nature, vol 514, pp. 620-623. DOI: 10.1038/nature13881
Ferrier, DEK 2012, Evolution of the Hox gene cluster. in eLS. John Wiley and Sons, Chichester. DOI: 10.1002/9780470015902.a0023989
Hui, JHL, McDougall, C, Monteiro, AS, Holland, PWH, Arendt, D, Balavoine, G & Ferrier, DEK 2012, 'Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization' Molecular Biology and Evolution, vol 29, no. 1, pp. 157-165. DOI: 10.1093/molbev/msr175
Shigenobu, S, Bickel, RD, Brisson, JA, Butts, T, Chang, C-C, Christiaens, O, Davis, GK, Duncan, EJ, Ferrier, DEK, Iga, M, Janssen, R, Lin, G-W, Lu, H-L, McGregor, AP, Miura, T, Smagghe, G, Smith, JM, van der Zee, M, Velarde, RA, Wilson, MJ, Dearden, PK & Stern, DL 2010, 'Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes' Insect Molecular Biology, vol 19, pp. 47-62. DOI: 10.1111/j.1365-2583.2009.00944.x
Ferrier, DEK & The International Aphid Genomics Consortium 2010, 'Genome sequence of the pea aphid Acyrthosiphon pisum' PLoS Biology, vol 8, no. 2, e1000313. DOI: doi:10.1371/journal.pbio.1000313
Ferrier, DEK 2010, Evolution of Hox complexes. in J Deutsch (ed.), Hox Genes: studies from the 20th to the 21st century.: Advances in experimental medicine and biology. vol. 689, Landes Bioscience, pp. 91-100.
Takahashi, T, McDougall, C, Troschianko, J, Chen, W-C, Nagarajan, AJ, Shimeld, SM & Ferrier, DEK 2009, 'An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals.' BMC Evolutionary Biology, vol 9, 240. DOI: 10.1186/1471-2148-9-240
Hui, JHL, Raible, F, Korchagina, N, Dray, N, Samain, S, Magdelenat, G, Jubin, C, Segurens, B, Balavoine, G, Arendt, D & Ferrier, DEK 2009, 'Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes' BMC Biology, vol 7, 43. DOI: 10.1186/1741-7007-7-43
McDougall, C, Hui, JHL, Monteiro, A, Takahashi, T & Ferrier, DEK 2008, 'Annelids in evolutionary developmental biology and comparative genomics.' Parasite, vol 15, no. 3, pp. 321-328. DOI: 10.1051/parasite/2008153321
Amemiya, CT, Prohaska, SJ, Hill-Force, A, Cook, A, Wasserscheid, J, Ferrier, DEK, Pascual-Anaya, J, Garcia-Fernandez, J, Dewar, K & Stadler, PF 2008, 'The amphioxus Hox cluster: characterization, comparative genomics, and evolution' Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol 310B, no. 5, pp. 465 - 477. DOI: 10.1002/jez.b.21213
Holland, LZ, Albalat, R, Azumi, K, Benito-Gutierrez, E, Blow, MJ, Bronner-Fraser, M, Brunet, F, Butts, T, Candiani, S, Dishaw, LJ, Ferrier, DEK, Garcia-Fernandez, J, Gibson-Brown, JJ, 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, GW, McHardy, AC, Meulemans, D, Nonaka, M, Olinski, RP, Pancer, Z, Pennacchio, LA, Pestarino, M, Rast, JP, Rigoutsos, I, Robinson-Rechavi, M, Roch, G, Saiga, H, Sasakura, Y, Satake, M, Satou, Y, Schubert, M, Sherwood, N, Shiina, T, Takatori, N, Tello, J, Vopalensky, P, Wada, S, Xu, A, Ye, Y, Yoshida, K, Yoshizaki, F, Yu, J-K, Zhang, Q, Zmasek, CM, de Jong, PJ, Osoegawa, K, Putnam, NH, Rokhsar, DS, Satoh, N & Holland, PWH 2008, 'The amphioxus genome illuminates vertebrate origins and cephalochordate biology' Genome Research, vol 18, pp. 1100-1111. DOI: 10.1101/gr.073676.107
Putnam, NH, Butts, T, Ferrier, DEK, Furlong, RF, Hellsten, U, Kawashima, T, Robinson-Rechavi, M, Shoguchi, E, Terry, A, Yu, J-K, Benito-Gutierrez, E, Dubchak, I, Garcia-Fernandez, J, Gibson-Brown, JJ, Grigoriev, IV, Horton, AC, de Jong, PJ, Jurka, J, Kapitonov, VV, Kohara, Y, Kuroki, Y, Lindquist, E, Lucas, S, Osoegawa, K, Pennacchio, LA, Salamov, AA, Satou, Y, Sauka-Spengler, T, Schmutz, J, Shin-I, T, Toyoda, A, Bronner-Fraser, M, Fujiyama, A, Holland, LZ, Holland, PWH, Satoh, N & Rokhsar, DS 2008, 'The amphioxus genome and the evolution of the chordate karyotype.' Nature, vol 453, pp. 1064 - 1071. DOI: 10.1038/nature06967
Butts, T, Holland, PWH & Ferrier, DEK 2008, 'The Urbilaterian Super-Hox cluster.' Trends in Genetics, vol 24, no. 6, pp. 259 - 262. DOI: 10.1016/j.tig.2007.09.006
Ferrier, DEK 2008, When is a Hox gene not a Hox gene? The importance of gene nomenclature. in A Minelli & G Fusco (eds), Evolving Pathways: key themes in Evolutionary Developmental Biology.. Cambridge University Press, pp. 175-193.
Tribolium Sequencing Consortium, Richards et al., S & Ferrier, DEK 2008, 'The genome of the developmental model beetle and pest Tribolium castaneum' Nature, vol 452, pp. 949 - 955. DOI: 10.1038/nature06784
Denes, AS, Jekely, G, Steinmetz, PRH, Raible, F, Snyman, H, Prud'homme, B, Ferrier, DEK, Balavoine, G & Arendt, D 2007, 'Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria.' Cell, vol 129, no. 2, pp. 277-288. DOI: 10.1016/j.cell.2007.02.040
Ferrier, DEK 2007, Evolution of Hox gene clusters. in S Papageorgiou (ed.), HOX gene expression. Landes Bioscience, pp. 53-67.

Contact

The Secretary
Scottish Oceans Institute
Institiud Chuantan na h-Alba
Gatty Marine Laboratory
East Sands St Andrews
KY16 8LB
Scotland
UK

tel: +44 (0) 1334 463472
fax: +44 (0) 1334 463443
email: soi@st-andrews.ac.uk

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