Profile

Dr Dave Ferrier

Dr Dave Ferrier
Reader in Biology and Deputy Director of the Scottish Oceans Institute


 

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, Giga-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, as well as the origin of the entire animal kingdom. Knowledge of such ancestors is vital in understanding subsequent diversification.

source: symbiosis

 

50 (of 80 published available) for dekf (source: University of St Andrews PURE)
Please click title of any item for full details

Space and time in Hox/ParaHox gene cluster evolution. David Ellard Keith Ferrier
2019 pp.245-258
Transcriptional regulation of the Ciona Gsx gene in the neural plate Clare Hudson, Rosaria Esposito, Antonio Palladino, Leopoldo Staiano, David Ellard Keith Ferrier, Emmanuel Faure, Patrick Lemaire, Hitoyoshi Yasuo, Antonietta Spagnuolo
Developmental Biology 2019 vol.448 pp.88-100
A revised spiralian homeobox gene classification incorporating new polychaete transcriptomes reveals a diverse TALE class and a divergent Hox gene Ildiko Maureen Lara Somorjai, David Ellard Keith Ferrier
Genome Biology and Evolution 2018 vol.10 pp.2151–2167
Amphioxus SYCP1 David Ellard Keith Ferrier
Development Genes and Evolution 2018 vol.228 pp.13-30
Amphioxus functional genomics and the origins of vertebrate gene regulation Ferdinand Marletaz, Panos Firbas, Ignacio Maeso, Juan Tena, Ozren Bogdanovic, Malcolm Perry, Chris Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael Acemel, Simon van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna Kozmikova, Jon Permanyer, Alexandra Louis, Beatriz Albuixech-Crespo, Yann Le Petillon, Anthony Leon Florian, Lucie Subirana, Piotr J. Balwierz, Paul Duckett, Ensieh Farahani, Jean Marc Aury, Sophie Mangenot, Patrick Wincker, Ricard Albalat, Elia Benito-Gutierrez, Cristian Canestro, Filipe Castro, Salvatore D'Aniello, David Ellard Keith Ferrier, Shengfeng Huang, Vincent Laudet, Gabriel Marais, Pierre Pontarotti, Michael Schubert, Herve Seitz, Ildiko Maureen Lara Somorjai, Tokiharu Takahashi, Olivier Mirabeau, Anlong Xu, Jr-Kai Yu, Piero Carninci, Juan Martinez-Morales, Hugues Crollius, Zbynek Kozmik, Matt Weirauch, Jordi Garcia-Fernandez, Ryan Lister, Boris Lenhard, Peter Holland, Hector Escriva, Jose Luis Gomez-Skarmeta, Manuel Irimia
Nature 2018 vol.564 pp.64-70
Genes for de novo biosynthesis of omega-3 polyunsaturated fatty acids are widespread in animals Naoki Kabeya, Miguel Fonseca, David Ellard Keith Ferrier, Juan Navarro, Line Bay, David Francis, Douglas Tocher, Filipe Castro, Oscar Monroig
Science Advances 2018 vol.4
Genome biology David Ellard Keith Ferrier, Shunsuke Sogabe
Current Biology 2018 vol.28 pp.R1208-R1210
Horizons in evolutionary genomics David Ellard Keith Ferrier
BMC Biology 2018 vol.16
Light-sheet microscopy with attenuation-compensated propagation-invariant beams Jonathan Nylk, Miguel Preciado, Michael Mazilu, Zhengyi Yang, Frank J Gunn-Moore, Javier Ananda Tello, David Ellard Keith Ferrier, Kishan Dholakia
Science Advances 2018 vol.4
Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage David Ellard Keith Ferrier, Ildiko Maureen Lara Somorjai
Scientific Reports 2018 vol.8
Two more Posterior Hox genes and Hox cluster dispersal in echinoderms David Ellard Keith Ferrier
BMC Evolutionary Biology 2018 vol.18
Recent advances in understanding the roles of whole genome duplications in evolution Carol MacKintosh, David Ellard Keith Ferrier
F1000Research 2017 vol.2017
Evolution of homeobox gene clusters in animals David Ellard Keith Ferrier
Frontiers in Ecology and Evolution 2016 vol.4
TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates Peter Osborne, David Ellard Keith Ferrier
BMC Evolutionary Biology 2016 vol.16
The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal David Ellard Keith Ferrier
Briefings in Functional Genomics 2016 vol.15 pp.333-341
Macro-optical trapping for sample confinement in light sheet microscopy Zhengyi Yang, Peeter Piksarv, David Ellard Keith Ferrier, Frank J Gunn-Moore, Kishan Dholakia
Biomedical Optics Express 2015 vol.6 pp.2778-2785
Multimode fibre Martin Plöschner, Vera Kollarova, Zbyněk Dostál, Jonathan Nylk, Thomas Barton-Owen, David Ellard Keith Ferrier, Radim Chmelík, Kishan Dholakia, Tomas Cizmar
Scientific Reports 2015 vol.5
A compact Airy beam light sheet microscope with a tilted cylindrical lens Zhengyi Yang, Martynas Prokopas, Jonathan Nylk, Frank J Gunn-Moore, David Ellard Keith Ferrier, Tom Vettenburg, Kishan Dholakia
Biomedical Optics Express 2014 vol.5 pp.3434-3442
Biomineralisation during operculum regeneration in the polychaete Spirobranchus lamarcki Angus Calder, David Ellard Keith Ferrier
Marine Biology 2014 vol.161 pp.2621-2629
Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes Sofia Fortunato, Marcin Adamski, Sven Leininger, Jing Liu, David Ellard Keith Ferrier, Maja Adamska
Nature 2014 vol.514 pp.620-623
Cell proliferation dynamics in regeneration of the operculum head appendage in the annelid Pomatoceros lamarckii David Ellard Keith Ferrier
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 2014 vol.322B pp.257-268
Light-sheet microscopy using an Airy beam Tom Vettenburg, Heather Isla Campbell Dalgarno, Jonathan Nylk, Clara Coll-Lladó, David Ellard Keith Ferrier, Tomas Cizmar, Frank J Gunn-Moore, Kishan Dholakia
Nature Methods 2014 vol.11 pp.541-544
The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima Ariel D Chipman, David Ellard Keith Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C J Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome H L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra L Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh N Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Ling-Ling Pu, Nicholas H Putman, Catherine Rabouille, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna M Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, Stephen Richards
PLoS Biology 2014 vol.12
The Hox-TALE has been wagging for a long time David Ellard Keith Ferrier
eLife 2014 vol.3
The dynamics of alkaline phosphatase activity during operculum regeneration in the polychaete Pomatoceros lamarckii David Ellard Keith Ferrier
International Journal of Developmental Biology 2014 vol.58 pp.635-642
4273π Daniel Barker, David Ellard Keith Ferrier, Peter W.H. Holland, John B. O. Mitchell, Heleen Plaisier, Michael Gordon Ritchie,
BMC Bioinformatics 2013 vol.14
Time is of the essence for ParaHox homeobox gene clustering. David Ellard Keith Ferrier
BMC Biology 2013 vol.11
Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates Michele Tinti, Catherine Johnson, Rachel Toth, David Ellard Keith Ferrier, Carol MacKintosh
Open Biology 2012 vol.2
Evolution of the Hox gene cluster. David Ellard Keith Ferrier
2012
Evolutionary crossroads in developmental biology: annelids. David Ellard Keith Ferrier
Development 2012 vol.139 pp.2643-2653
Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization Jerome H.L. Hui, Carmel McDougall, Ana S. Monteiro, Peter W.H. Holland, Detlev Arendt, Guillaume Balavoine, David Ellard Keith Ferrier
Molecular Biology and Evolution 2012 vol.29 pp.157-165
Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals Daniel Barker, David Ellard Keith Ferrier
Current Biology 2012 vol.22 pp.1951-1956
Annelid Distal-less/Dlx duplications reveal varied post-duplication fates Carmel McDougall, Natalia Korchagina, Johnathan Tobin, David Ellard Keith Ferrier
BMC Evolutionary Biology 2011 vol.11 pp.241
Hox and ParaHox genes in evolution, development and genomics. David Ellard Keith Ferrier
Genomics Proteomics & Bioinformatics 2011 vol.9 pp.63-64
Integrated holographic system for all-optical manipulation of developing embryos Maciej Antkowiak, Hana Cizmarova, David Ellard Keith Ferrier, Kishan Dholakia, Frank J Gunn-Moore
Biomedical Optics Express 2011 vol.2 pp.1564-1575
Tunicates push the limits of animal evo-devo David Ellard Keith Ferrier
BMC Biology 2011 vol.9
Ancient homeobox gene loss and the evolution of chordate brain and pharynx development Thomas Butts, Peter W.H. Holland, David Ellard Keith Ferrier
Proceedings of the Royal Society B: Biological Sciences 2010 vol.277 pp.3381-3389
Chordate Hox and ParaHox Gene Clusters Differ Dramatically in Their Repetitive Element Content Peter W. Osborne, David Ellard Keith Ferrier
Molecular Biology and Evolution 2010 vol.27 pp.217-220
Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes S. Shigenobu, R. D. Bickel, J. A. Brisson, T. Butts, C-C. Chang, O. Christiaens, G. K. Davis, E. J. Duncan, David Ellard Keith Ferrier, M. Iga, R. Janssen, G. -W. Lin, H. -L. Lu, A. P. McGregor, T. Miura, G. Smagghe, J. M. Smith, M. van der Zee, R. A. Velarde, M. J. Wilson, P. K. Dearden, D. L. Stern
Insect Molecular Biology 2010 vol.19 pp.47-62
Evolution of Hox complexes. David Ellard Keith Ferrier
2010 vol.689 pp.91-100
Genome sequence of the pea aphid Acyrthosiphon pisum David Ellard Keith Ferrier,
PLoS Biology 2010 vol.8
An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals. T. Takahashi, C. McDougall, J. Troschianko, W-C. Chen, A.J. Nagarajan, S.M. Shimeld, David Ellard Keith Ferrier
BMC Evolutionary Biology 2009 vol.9
Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae). PW Osborne, G Benoit, V Laudet, M Schubert, David Ellard Keith Ferrier
Developmental Biology 2009 vol.327 pp.252-262
Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes JHL Hui, F Raible, N Korchagina, N Dray, S Samain, G Magdelenat, C Jubin, B Segurens, G Balavoine, D Arendt, David Ellard Keith Ferrier
BMC Biology 2009 vol.7
Annelids in evolutionary developmental biology and comparative genomics. C. McDougall, J.H.L. Hui, A. Monteiro, T. Takahashi, David Ellard Keith Ferrier
Parasite 2008 vol.15 pp.321-328
Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. N. Takatori, T. Butts, S. Candiani, M Pestariono, David Ellard Keith Ferrier, H. Saiga, P.W.H. Holland
Development Genes and Evolution 2008 vol.218 pp.579-590
Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster. J.H.L. Hui, P.W.H. Holland, David Ellard Keith Ferrier
Evolution and Development 2008 vol.10 pp.725-730

Contact

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

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