David E K Ferrier

David E K Ferrier

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David E K Ferrier

David E K Ferrier

Publications by authors named "David E K Ferrier"

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Two more Posterior Hox genes and Hox cluster dispersal in echinoderms.

BMC Evol Biol 2018 12 27;18(1):203. Epub 2018 Dec 27.

The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1186/s12862-018-1307-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307216PMC
December 2018

Horizons in evolutionary genomics: an interview with David Ferrier.

BMC Biol 2018 11 1;16(1):124. Epub 2018 Nov 1.

The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK.

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http://dx.doi.org/10.1186/s12915-018-0587-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211512PMC
November 2018

Genome Biology: Unconventional DNA Repair in an Extreme Genome.

Curr Biol 2018 10;28(20):R1208-R1210

The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews KY16 8LB, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2018.09.004DOI Listing
October 2018

A Revised Spiralian Homeobox Gene Classification Incorporating New Polychaete Transcriptomes Reveals a Diverse TALE Class and a Divergent Hox Gene.

Genome Biol Evol 2018 09 1;10(9):2151-2167. Epub 2018 Sep 1.

Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evy144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6118893PMC
September 2018

Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage.

Sci Rep 2018 06 20;8(1):9414. Epub 2018 Jun 20.

University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1038/s41598-018-27700-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010424PMC
June 2018

Genes for de novo biosynthesis of omega-3 polyunsaturated fatty acids are widespread in animals.

Sci Adv 2018 05 2;4(5):eaar6849. Epub 2018 May 2.

Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.

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http://dx.doi.org/10.1126/sciadv.aar6849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931762PMC
May 2018

Light-sheet microscopy with attenuation-compensated propagation-invariant beams.

Sci Adv 2018 04 6;4(4):eaar4817. Epub 2018 Apr 6.

Scottish Universities Physics Alliance, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK.

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http://dx.doi.org/10.1126/sciadv.aar4817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938225PMC
April 2018

Amphioxus SYCP1: a case of retrogene replacement and co-option of regulatory elements adjacent to the ParaHox cluster.

Dev Genes Evol 2018 01 2;228(1):13-30. Epub 2018 Jan 2.

The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1007/s00427-017-0600-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803294PMC
January 2018

Recent advances in understanding the roles of whole genome duplications in evolution.

F1000Res 2017 31;6:1623. Epub 2017 Aug 31.

The Scottish Oceans Institute, University of St Andrews, Scotland, KY16 8LB, UK.

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http://dx.doi.org/10.12688/f1000research.11792.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590085.2PMC
August 2017

The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal.

Brief Funct Genomics 2016 Sep 4;15(5):333-41. Epub 2015 Dec 4.

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http://dx.doi.org/10.1093/bfgp/elv056DOI Listing
September 2016

TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates.

BMC Evol Biol 2016 Mar 3;16:57. Epub 2016 Mar 3.

The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1186/s12862-016-0614-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776371PMC
March 2016

Multimode fibre: Light-sheet microscopy at the tip of a needle.

Sci Rep 2015 Dec 14;5:18050. Epub 2015 Dec 14.

Ewing Building, School of Engineering, Physics &Mathematics, University of Dundee, Dundee, DD1 4HN, Scotland.

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http://dx.doi.org/10.1038/srep18050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4677299PMC
December 2015

The dynamics of alkaline phosphatase activity during operculum regeneration in the polychaete Pomatoceros lamarckii.

Int J Dev Biol 2014 ;58(6-8):635-42

The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, Fife, UK.

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http://www.intjdevbiol.com/paper.php?doi=140116df
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http://dx.doi.org/10.1387/ijdb.140116dfDOI Listing
October 2015

Another biomineralising protostome with an msp130 gene and conservation of msp130 gene structure across Bilateria.

Evol Dev 2015 May-Jun;17(3):195-7

The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://doi.wiley.com/10.1111/ede.12122
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http://dx.doi.org/10.1111/ede.12122DOI Listing
August 2015

Macro-optical trapping for sample confinement in light sheet microscopy.

Biomed Opt Express 2015 Aug 8;6(8):2778-85. Epub 2015 Jul 8.

SUPA, School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, KY16 9SS, UK.

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http://dx.doi.org/10.1364/BOE.6.002778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541507PMC
August 2015

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Authors:
Ariel D Chipman David E K 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 Peter D Evans 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 Olivia Mendivil Ramos 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 Biol 2014 Nov 25;12(11):e1002005. Epub 2014 Nov 25.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043PMC
November 2014

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes.

Nature 2014 Oct;514(7524):620-3

Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.

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http://dx.doi.org/10.1038/nature13881DOI Listing
October 2014

A compact Airy beam light sheet microscope with a tilted cylindrical lens.

Biomed Opt Express 2014 Oct 5;5(10):3434-42. Epub 2014 Sep 5.

SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK.

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http://dx.doi.org/10.1364/BOE.5.003434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206314PMC
October 2014

Light-sheet microscopy using an Airy beam.

Nat Methods 2014 May 6;11(5):541-4. Epub 2014 Apr 6.

School of Physics and Astronomy, University of St Andrews, St Andrews, UK.

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http://dx.doi.org/10.1038/nmeth.2922DOI Listing
May 2014

The Hox-TALE has been wagging for a long time.

Elife 2014 Mar 18;3:e02515. Epub 2014 Mar 18.

David EK Ferrier is at the Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, United Kingdom

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957476PMC
http://dx.doi.org/10.7554/eLife.02515DOI Listing
March 2014

Time is of the essence for ParaHox homeobox gene clustering.

BMC Biol 2013 Jun 26;11:72. Epub 2013 Jun 26.

The Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1186/1741-7007-11-72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694477PMC
June 2013

Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals.

Curr Biol 2012 Oct 27;22(20):1951-6. Epub 2012 Sep 27.

The Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK.

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http://dx.doi.org/10.1016/j.cub.2012.08.023DOI Listing
October 2012

Evolutionary crossroads in developmental biology: annelids.

Development 2012 Aug;139(15):2643-53

The Scottish Oceans Institute, the Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, UK.

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http://dev.biologists.org/content/develop/139/15/2643.full.p
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http://dev.biologists.org/cgi/doi/10.1242/dev.074724
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http://dx.doi.org/10.1242/dev.074724DOI Listing
August 2012

Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution.

Int J Evol Biol 2012 7;2012:846421. Epub 2012 Aug 7.

The Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, Fife KY16 8LB, UK.

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https://www.hindawi.com/archive/2012/846421/
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http://dx.doi.org/10.1155/2012/846421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420103PMC
August 2012

Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates.

Open Biol 2012 Jul;2(7):120103

MRC Protein Phosphorylation Unit, College of Life Sciences, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH , UK.

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http://dx.doi.org/10.1098/rsob.120103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411107PMC
July 2012

Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization.

Mol Biol Evol 2012 Jan 4;29(1):157-65. Epub 2011 Jul 4.

Department of Zoology, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msr175DOI Listing
January 2012

Tunicates push the limits of animal evo-devo.

BMC Biol 2011 Jan 20;9. Epub 2011 Jan 20.

The Scottish Oceans Institute, University of St Andrews, East Sands, UK.

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http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-
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http://dx.doi.org/10.1186/1741-7007-9-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024270PMC
January 2011

Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression.

Proc Biol Sci 2010 Nov 16;277(1699):3381-9. Epub 2010 Jun 16.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1098/rspb.2010.0647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982225PMC
November 2010

Evolution of Hox complexes.

Adv Exp Med Biol 2010 ;689:91-100

The Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.

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http://dx.doi.org/10.1007/978-1-4419-6673-5_6DOI Listing
September 2010

Chordate Hox and ParaHox gene clusters differ dramatically in their repetitive element content.

Mol Biol Evol 2010 Feb 5;27(2):217-20. Epub 2009 Oct 5.

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http://dx.doi.org/10.1093/molbev/msp235DOI Listing
February 2010

Hox genes are not always Colinear.

Int J Biol Sci 2006 5;2(3):95-103. Epub 2006 May 5.

Department of Zoology, University of Oxford, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458434PMC
http://dx.doi.org/10.7150/ijbs.2.95DOI Listing
September 2009

Differential regulation of ParaHox genes by retinoic acid in the invertebrate chordate amphioxus (Branchiostoma floridae).

Dev Biol 2009 Mar 7;327(1):252-62. Epub 2008 Dec 7.

Zoology Department, Oxford University, South Parks Road, Oxford, OX1 3PS, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S001216060801378
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http://dx.doi.org/10.1016/j.ydbio.2008.11.027DOI Listing
March 2009

Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster.

Evol Dev 2008 Nov-Dec;10(6):725-30

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1111/j.1525-142X.2008.00286.xDOI Listing
January 2009

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.

Dev Genes Evol 2008 Dec 17;218(11-12):579-90. Epub 2008 Sep 17.

Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, Japan.

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http://dx.doi.org/10.1007/s00427-008-0245-9DOI Listing
December 2008

The amphioxus Hox cluster: characterization, comparative genomics, and evolution.

J Exp Zool B Mol Dev Evol 2008 Jul;310(5):465-77

Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA.

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http://dx.doi.org/10.1002/jez.b.21213DOI Listing
July 2008

The urbilaterian Super-Hox cluster.

Trends Genet 2008 Jun 9;24(6):259-62. Epub 2008 May 9.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1016/j.tig.2007.09.006DOI Listing
June 2008

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Review of the 4th UK evolutionary developmental biology meeting.

Evol Dev 2004 Mar-Apr;6(2):65-6

University of Oxford, Department of Zoology, Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK.

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October 2004

Evolution of the Hox/ParaHox gene clusters.

Int J Dev Biol 2003 ;47(7-8):605-11

Department of Zoology, University of Oxford, UK.

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August 2004

Hox genes: Did the vertebrate ancestor have a Hox14?

Curr Biol 2004 Mar;14(5):R210-1

Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S096098220400125
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http://dx.doi.org/10.1016/j.cub.2004.02.025DOI Listing
March 2004

Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity.

Mol Phylogenet Evol 2002 Sep;24(3):412-7

School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, RG6 6AJ, UK.

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September 2002

Evolution of developmental mechanisms.

Genome Biol 2002 Jun 27;3(7):REPORTS4020. Epub 2002 Jun 27.

School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139381PMC
http://dx.doi.org/10.1186/gb-2002-3-7-reports4020DOI Listing
June 2002

Gene duplications in the prototypical cephalochordate amphioxus.

Gene 2002 Apr;287(1-2):121-8

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona., Avenida Diagonal 645, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1016/s0378-1119(01)00828-9DOI Listing
April 2002