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Biologie du Développement de Villefranche-sur-Mer

Publications

 ## Selected Publications


 Li YI, Copley RR. Scaffolding low quality genomes using orthologous protein sequences. Bioinformatics. 2013 Jan 15;29(2):160-5.
doi: 10.1093/bioinformatics/bts661. Epub 2012 Nov 18. PubMed PMID: 23162087

Telford MJ, Copley RR. Improving animal phylogenies with genomic data. Trends* Genet. 2011 May;27(5):186-95.
doi: 10.1016/j.tig.2011.02.003. Epub 2011 Mar 15. Review. PubMed PMID: 21414681.

Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature. 2011 Feb 10;470(7333):255-8.
doi: 10.1038/nature09676. PubMed PMID: 21307940.

Copley RR
. The animal in the genome: comparative genomics and evolution. Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1453-61.
doi: 10.1098/rstb.2007.2235. Review. PubMed PMID: 18192189

 

Références (35)

2017

Costache V, Hebras C, Pruliere G, Besnardeau L, Failla M, Copley RR, Burgess D, Chenevert J, McDougall A. (2017) Kif2 localizes to a subdomain of cortical endoplasmic reticulum that drives asymmetric spindle position. Nat Commun. Oct 13;8(1):917. doi: 10.1038/s41467-017-01048-8.

Atilano ML, Glittenberg M, Monteiro A, Copley RR, Ligoxygakis P.(2017) MicroRNAs That Contribute to Coordinating the Immune Response in Drosophila melanogaster. Genetics. 2017 Sep;207(1):163-178. doi: 10.1534/genetics.116.196584. Epub 2017 Jul 13.

2016

Camps C, Petousi N, Bento C, Cario H, Copley R, McMullin M, Van wijk R, Ratcliffe P, Robbins P, Taylor J, WGS C (2016) Gene panel sequencing improves the diagnostic work-up of patients with idiopathic erythrocytosis and identifies new mutations. Haematologica 101: 1306-1318.

Leclère  L, Copley R, Momose T, Houliston E (2016) Hydrozoan insights in animal development and evolution. Curr Opin Genet Dev 39: 157-167 | doi: 10.1016/j.gde.2016.07.006

Karakostis K, Zanella-Cléon I, Immel F, Guichard N, Dru P, Lepage T, Plasseraud L, Matranga V, Marin F (2016) A minimal molecular toolkit for mineral deposition? Biochemistry and proteomics of the test matrix of adult specimens of the sea urchin Paracentrotus lividus. J Proteome 136: 133-144 | doi: 10.1016/j.jprot.2016.01.001

Ricci L, Chaurasia A, Lapébie  P, Dru P, Helm R, Copley R, Tiozzo S (2016) Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. Sci. Rep. 6 | doi: 10.1038/srep27357

Copley R (2016) The unicellular ancestry of Groucho mediated repression and the origins of metazoan transcription factors. Genome Biol Evol. 1-1 | doi: 10.1093/gbe/evw118

Telford M, Copley R (2016) Zoology: War of the Worms. Curr. Biol. 26 | doi: 10.1016/j.cub.2016.03.015

2015

Taylor J, Martin H, Lise S, Broxholme J, Cazier J-B, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle V, Bull K, Cais O, Cario H, Chapel H, Copley R, Cornall R, Craft J, Dahan K, Davenport E, Dendrou C, Devuyst O, Fenwick A, Flint J, Fugger L, Gilbert R, Goriely A, Green A, Greger I, Grocock R, Gruszczyk A, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight J, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan S, McMullin M, Miller K, Murray L, Nemeth A, Nesbit MA, Nutt D, Ormondroyd E, Oturai A, Pagnamenta A, Patel S, Percy M, Petousi N, Piazza P, Piret S, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins P, Robson K, Russo A, Sahgal N, van Schouwenburg P, Schuh A, Silverman E, Simmons A, Sørensen P, Sweeney S, Taylor J, Thakker R, Tomlinson I, Trebes A, Twigg S, Uhlig H, Vyas P, Vyse T, Wall S, Watkins H, Whyte M, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe P, Bell J, Wilkie A, Bentley D, Donnelly P, McVean G (2015) Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat. Genet. 47 | doi: 10.1038/ng.3304

Tiozzo S, Copley R (2015) Reconsidering regeneration in metazoans: an evo-devo approach. Front Ecol Evol

2014

Telford MJ, Lowe CJ, Cameron CB, Ortega-Martinez O, Aronowicz J, Oliveri P, Copley RR.(2014) Phylogenomic analysis of echinoderm class relationships supports Asterozoa. Proc Biol Sci. 2014 Jul 7;281(1786). pii: 20140479. | doi: 10.1098/rspb.2014.0479.

 

Petousi N, Copley RR, Lappin TR, Haggan SE, Bento CM, Cario H, Percy MJ; WGS Consortium, Ratcliffe PJ, Robbins PA, McMullin MF.(2014) Erythrocytosis associated with a novel missense mutation in the BPGM gene. Haematologica. 2014 Oct;99(10):e201-4. | doi: 10.3324/haematol.2014.109306. Epub 2014 Jul 11.

 

Martin HC, Kim GE, Pagnamenta AT, Murakami Y, Carvill GL, Meyer E, Copley RR, Rimmer A, Barcia G, Fleming MR, Kronengold J, Brown MR, Hudspith KA, Broxholme J, Kanapin A, Cazier JB, Kinoshita T, Nabbout R; WGS500 Consortium, Bentley D, McVean G, Heavin S, Zaiwalla Z, McShane T, Mefford HC, Shears D, Stewart H, Kurian MA, Scheffer IE, Blair E, Donnelly P, Kaczmarek LK, Taylor JC. (2014) Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis. Hum Mol Genet. 2014 Jun 15;23(12):3200-11. | doi: 10.1093/hmg/ddu030. Epub 2014 Jan 25.

 

Lapébie P, Ruggiero A, Barreau C, Chevalier S, Chang P, Dru P, Houliston E, Momose T.Differential responses to Wnt and PCP disruption predict expression and developmental function of conserved and novel genes in a cnidarian. (2014) PLoS Genet. 2014 Sep 18;10(9):e1004590. | doi: 10.1371/journal.pgen.1004590.

 

2013

 

ACL4.319 Shanks M., Downes S., Copley R., Lise S., Broxholme J., Hudspith K., Kwasniewska A., Davies W., Hankins M., Packham E., Clouston P., Seller A., Wilkie A., Taylor J., Ragoussis J., Nemeth A. (2013) Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. Eur. J. Hum. Genet. 21: 274-280 | doi: 10.1038/ejhg.2012.172.

ACL5.323 Li Y., Copley R. (2013) Scaffolding low quality genomes using orthologous protein sequences. Bioinformatics 29: 160-165| doi: 10.1093/bioinformatics/bts661.

ACL35.000 Sharma V., Fenwick A., Brockop M., McGowan S., Goos J., Hoogeboom A., Brady A., Jeelani N., Lynch S., Mulliken J., Murray D., Phipps J., Sweeney E., Tomkins S., Wilson L., Bennett S., Cornall R., Broxholme J., Kanapin A., 500 Whole-Genome Sequences (WGS500) Consortium _., Johnson D., Wall S., van der Spek P., Mathijssen I., Maxson R., Twigg S., Wilkie A. (2013) Mutations in {TCF12}, encoding a basic helix-loop-helix partner of {TWIST1}, are a frequent cause of coronal craniosynostosis. Nat. Genet. 45 | doi: 10.1038/ng.2531.

 

ACL35.000 Sharma V., Fenwick A., Brockop M., McGowan S., Goos J., Hoogeboom A., Brady A., Jeelani N., Lynch S., Mulliken J., Murray M., Phipps J., Sweeney S., Tomkins S., Wilson L., Bennett S., Cornall R., Broxholme J., Kanapin E., 500 Whole-Genome Sequences (WGS500) Consortium _., Johnson D., Wall S., van der Spek P., Mathijssen I., Maxson R., Twigg S., Wilkie A. (2013) Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis. Nat. Genet. 45: 304-307 | doi: 10.1038/ng.2531.

 

ACL8.000 Hosseini M., Goodstadt L., Hughes J., Kowalczyk M., de Gobbi M., Otto G., Copley R., Mott R., Higgs D., Flint J. (2013) Causes and Consequences of Chromatin Variation between Inbred Mice. PLoS Genet. 9 | doi: 10.1371/journal.pgen.1003570.

ACTI Ricci L., Dru P., Lotito S., Tiozzo S. (2013) Digging into non-embryonic development pathways: generating a toolbox to study Botryllus schlosseri vascular budding and blastogenesis.

AFF Andres G., Cormier A., Lorre-guidt M., Hoebeke M., Groc M., Dru P., Caron C. (2013) EMBRC-France e-infrastructure. JOBIM - Journées Ouvertes en Biologie Informatique et Mathématiques, Toulouse, 01 July-04 July 2014.

ACL5.560 Davies W., Downes S., Fu J., Shanks M., Copley R., Lise S., Ramsden S., Black G., Gibson K., Foster R., Hankins M., Nemeth A. (2012) Next generation sequencing (NGS) in healthcare delivery : lessons from the functionnal analysis of rhodopsin. Genet. Med. 14: 891-899.

 

2011

 

ACL10.000 Telford M., Copley R. (2011) Improving animal phylogeneis with genomic data. Trends Genet. 27: 186-195.

 

ACL36.000 Philippe H., Brinkmann H., Copley R., Moroz L., Nakano H., Poustka A., Wallberg A., Peterson K., Telford M. (2011) Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470: 255-258.

 

2010

 

ACL9.000 Goh F., Thomson S., Krausgruber T., Lafrancotti A., Copley R., Udalova I. (2010) Beyond the enhanceosome : cluster of novel kB sites downstream of the human IFN-B is essential for LPS-induced gene activation. Blood 116: 5580-5588.

 

2009

 

ACL4.000 Mole D., Blancher C., Copley R., Pollard P., Gleadle J., Ragoussis J., Ratcliffe P. (2009) Genome-wide chromatin-immunoprecipitation by the HIF-1a and HIF-2a transcription factors and its correlation with gene regulation. J. Biol. Chem. 284: 16727-16775.

 

ACL4.000 Taylor J., Street T., Hao L., Copley R., Taylor M., Hayden P., Stolper G., Mott R., Hein J., Moffatt M., Cookson W. (2009) Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes. PLoS ONE 4: 7651-7651.

 

ACL13.000 Johannesson M., Lopez-aumatell R., Diez M., Tuncel J., Blazquez G., Martinez E., Canete A., Vicens-Costa E., Graham D., Copley R., Hernandez-pliego P., Beyeen A., Stridh P., Ockinger J., Fernandez C., Tobena A., Guitart-Masip M., Gimenez-Llort L., Dominiczak A., Holmdahl R., Gauguier D., Olsson T., Mott R., Valdar W., Redei E., Fernandez-Teruel A., Flint J. (2009) A ressource for simultaneous high-resolution mapping of multiple quantitative trait loci in rats : the NIH heterogeneous stock. Genome Res. 19: 150-158.

 

AFF Paix A., Yamada L., Dru P., Lecordier H., Sardet C. (2009) Localization and corcical anchorage of ascidian postplasmic/PEM RNAs in eggs and embryos. Localization and corcical anchorage of ascidian postplasmic/PEM RNAs in eggs and embryos, Okinawa Japon.

 

2008

 

ACL6.000 Copley R. (2008) The animal in the genome : comparative genomics and evolution. Philos. Trans. R. Soc. B 363: 1453-1461.

 

ACL5.000 Juliusdottir T., Pettersson F., Copley R. (2008) POPE-a tool to aid high-throughput phylogenetic analysis. Bioinformatics 24: 2778-2779.

 

ACL8.000 Fullerton J., Willis-Owen S., Shifman S., Copley R., Miller S., Bhomra A., Davidson S., Oliver P., Mott R., Flint J. (2008) Human-Mouse quantitative trait locus concordance and the dissection of a human neuroticism locus. Biol. Psychiatry 63: 874-883.

 

ACL4.000 Paix A., Yamada L., Dru P., Lecordier H., Prulière G., Chenevert J., Satoh N., Sardet C. (2008) Cortical anchorages and cell type segregations of maternal postplasmic/PEM RNAs in ascidians. Dev. Biol. 336: 96-111.

 

2007

 

ACL8.000 Mulder N., Apweiler R., Attwood T., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Hunter S., Kahn D., Kanapin E., Kejariwal A., Labarga A., Langendijk-Genevaux P., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McAnulla C., Mcdowall J., Mistry J., Mitchell A., Nikolskaya A., Orchard R., Orengo C., Petryszak R., Selengut J., Sigrist C., Thomas P., Valentin F., Wilson D., Wu C., Yeast C. (2007) New developments in the InterPro datase. Nucleic Acids Res. 35: 224-228.

 

ACL2.000 Sardet C., Paix A., Prodon F., Dru P., Chenevert J. (2007) From oocyte to 16-cell stage : cytoplasmic and cortical reorganizations that pattern the ascidian embryo. Dev. Dynam. 236: 1716-1731.

 

ACL8.000 Hull J., Campino S., Rowlands K., Chan M.-S., Copley R., Taylor M., Rockett K., Elvidge G., Keating B., Knight J., Kwiatkowski D. (2007) Identification of common genetic variation which modulates alternative splicing. PLoS Genet. 3: 99-99.

 

ACL13.000 Copley R., Totrov M., Linnel J., Field S., Ragoussis J., Udalova I. (2007) Functional conservation of Rel binding sites in drosophilid genomes. Genome Res. 17: 1327-1335.

 

AFF Paix A., Dru P., Deshler J., Prodon F., Yamada L., Sardet S. (2007) Phosphoproteins of the translation-initiation machindery and postplasmic/PEM RNAs define the cER, a cortical subdomain of the rough endomplasmic reticulum network in ascidian oocytes and embryos. Phosphoproteins of the translation-initiation machindery and postplasmic/PEM RNAs define the cER, a cortical subdomain of the rough endomplasmic reticulum network in ascidian oocytes and embryos, St Jean Cap Ferrat.

 

 

 

 

 

 

 

Richard Copley - 16/11/17

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