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

 

Recent publications


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

2019
pp.245-258
(Chapter)
2018 (1)
Development Genes and Evolution
vol.228 pp.13-30
(Article)
2018 (21/11)
Nature
vol.564 pp.64-70
(Article)
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 
2018 (2/5)
Science Advances
vol.4 
(Article)
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 
2018 (22/10)
Current Biology
vol.28 pp.R1208-R1210
(Review article)
Genome biology
David Ellard Keith Ferrier, Shunsuke Sogabe 
2018 (1/11)
BMC Biology
vol.16 
(Article)
2018 (6/4)
Science Advances
vol.4 
(Article)
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 
2018 (20/6)
Scientific Reports
vol.8 
(Article)
Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage
David Ellard Keith Ferrier, Ildiko Maureen Lara Somorjai 

Developmental Biology
vol.In press 
(Article)
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 
Keywords: Ascidian, Ciona, Gsx, Transcriptional regulation, Promoter, Neural patterning, Para-hox
2018 (27/12)
BMC Evolutionary Biology
vol.18 
(Article)
2017 (31/8)
F1000Research
vol.2017 
(Review article)
2016 (14/4)
Frontiers in Ecology and Evolution
vol.4 
(Review article)
2016 (3/3)
BMC Evolutionary Biology
vol.16 
(Article)
2016 (5/9)
Briefings in Functional Genomics
vol.15 pp.333-341
(Review article)
2015 (5)
Evolution and Development
vol.17 pp.195-197
(Article)
2015 (1/8)
Biomedical Optics Express
vol.6 pp.2778-2785
(Article)
Macro-optical trapping for sample confinement in light sheet microscopy
Zhengyi Yang, Peeter Piksarv, David Ellard Keith Ferrier, Frank J Gunn-Moore, Kishan Dholakia 
2015 (14/12)
Scientific Reports
vol.5 
(Article)
Multimode fibre
Martin Plöschner, Vera Kollarova, Zbyněk Dostál, Jonathan Nylk, Thomas Barton-Owen, David Ellard Keith Ferrier, Radim Chmelík, Kishan Dholakia, Tomas Cizmar 
Keywords: Plane illumination microscopy, Optical fibers, Deep, Transmission, Beams
2014 (1/10)
Biomedical Optics Express
vol.5 pp.3434-3442
(Article)
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 
2014 (11)
Marine Biology
vol.161 pp.2621-2629
(Article)
2014 (30/10)
Nature
vol.514 pp.620-623
(Article)
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 
2014 (7)
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
vol.322B pp.257-268
(Article)
2014 (5)
Nature Methods
vol.11 pp.541-544
(Article)
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 
2014 (11)
PLoS Biology
vol.12 
(Article)
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 
2014 (18/3)
eLife
vol.3 
(Review article)
2014
International Journal of Developmental Biology
vol.58 pp.635-642
(Article)
2013 (12/8)
BMC Bioinformatics
vol.14 
(Article)
4273π
Daniel Barker, David Ellard Keith Ferrier, Peter W.H. Holland, John B. O. Mitchell, Heleen Plaisier, Michael Gordon Ritchie,  
Keywords: Bioinformatics education, Teaching material, Raspberry Pi, Linux
2013 (6)
BMC Biology
vol.11 
(Review article)
2012 (7)
Open Biology
vol.2 
(Article)
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 
Keywords: Branchiostoma, Ciona, Hereditary spastic paraplegia, RAB3GAP1, RAB3GAP2
2012 (8)

(Entry for encyclopedia/dictionary)
2012
Development
vol.139 pp.2643-2653
(Review article)
2012 (1)
Molecular Biology and Evolution
vol.29 pp.157-165
(Article)
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 
2012 (10)
Current Biology
vol.22 pp.1951-1956
(Article)
2012
International Journal of Evolutionary Biology
vol.2012 
(Review article)
2011 (16/8)
BMC Evolutionary Biology
vol.11 pp.241
(Article)
Annelid Distal-less/Dlx duplications reveal varied post-duplication fates
Carmel McDougall, Natalia Korchagina, Johnathan Tobin, David Ellard Keith Ferrier 
2011
Genomics Proteomics & Bioinformatics
vol.9 pp.63-64
(Editorial)
2011 (1/6)
Biomedical Optics Express
vol.2 pp.1564-1575
(Article)
Integrated holographic system for all-optical manipulation of developing embryos
Maciej Antkowiak, Hana Cizmarova, David Ellard Keith Ferrier, Kishan Dholakia, Frank J Gunn-Moore 
Keywords: Multiphoton processes, Lasers, Ultrafast lasers
2011 (20/1)
BMC Biology
vol.9 
(Comment/debate)
2010 (22/11)
Proceedings of the Royal Society B: Biological Sciences
vol.277 pp.3381-3389
(Article)
Ancient homeobox gene loss and the evolution of chordate brain and pharynx development
Thomas Butts, Peter W.H. Holland, David Ellard Keith Ferrier 
2010 (2)
Molecular Biology and Evolution
vol.27 pp.217-220
(Letter)
2010 (10/3)
Insect Molecular Biology
vol.19 pp.47-62
(Article)
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 
Keywords: aphid, genome analysis, signalling pathway, development, hemimetabolous insect, polyphenism, symbiosis, BEETLE TRIBOLIUM-CASTANEUM, GERM-CELL SPECIFICATION, ASYMMETRIC LOCALIZATION, NEMATOSTELLA-VECTENSIS, WING POLYMORPHISM, PATTERN-FORMATION, DROSOPHILA, EXPRESSION, SEGMENTATION, INSECT
2010
vol.689 pp.91-100
(Chapter)
Evolution of Hox complexes.
David Ellard Keith Ferrier 
2010 (2)
PLoS Biology
vol.8 
(Article)
2009 (25/9)
BMC Evolutionary Biology
vol.9 
(Article)
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 
2009 (23/7)
BMC Biology
vol.7 
(Article)
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 
2008 (11)
Evolution and Development
vol.10 pp.725-730
(Article)

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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