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PublicaTIONS

Books & Monographs

Cooper DC, Spillane C, and Hodgkin T (Eds.) (2000) Broadening the Genetic Bases of Crop Production, IPGRI, FAO: Rome, CABI: Wallingford. 480pp.

Van Hintum ThJL., Brown AHD, Spillane C and Hodgkin T (2000) Core collections of Plant Genetic Resources. IPGRI Technical Bulletin No. 3, IPGRI:Rome, 48pp.

Thro AM and Spillane C (1999) Biotechnology assisted participatory plant breeding: Complement or contradiction? CGIAR Program on Participatory Research and Gender Analysis, Working Document No.4, CIAT: Cali. 150pp. http://www.prgaprogram.org/prga/

FAO (1997a) The State of the World's Plant Genetic Resources for Food and Agriculture, FAO: Rome, 336pp.

Spillane C, Engels J, Fassil F, Withers L, Gass T, and Cooper D (1999) Strengthening National Programmes for Plant Genetic Resources for Food and Agriculture. IPGRI:Rome, Issues in Genetic Resources No. 8. 65pp.

Spillane C & O’Mahony C (2006) “Plants for the Future in Ireland?”, Discussion document on EPSO/EUROPABIO national consultation on future of plant biotechnology in Ireland.

Research Papers, Reviews and Book Chapters

Duszynska D, McKeown P, Juenger TE, Pietraszewska A, Geelen D and Spillane C (2012) Gamete fertility and ovule number variation in selfed reciprocal F1 hybrid triploid plants are heritable and display epigenetic parent-of-origin effects. New Phytologist (in press) Impact factor: 6.645

McKeown P, Fort A and Spillane C (2012) Genomic imprinting: Parental control of gene expression in higher plants. In: Birchler J and Chen ZJ (Eds.) Plant Polyploidy and Hybrid Genomics, John Wiley & Sons Ltd (in press). [PDF]

O'Connell MJ, Doyle AM, Juenger TE, Donoghue MTA, Keshavaiah C, Tuteja R and Spillane C (2012) In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure. BMC Research Reports (in press). [PDF]

Selcuklu SD, Donoghue MTA, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ and Spillane C (2012) MicroRNA-9 inhibition of cell proliferation and identification of novel mir-9 targets by transcriptome profiling in breast cancer cells. Journal of Biological Chemistry July 2. [PDF] Impact factor: 5.328

Greenbiotech EU (2012) EU GMO Policies, Sustainable Farming and Public Research, Greenbiotech EU Briefing Paper, June 2012. www.greenbiotech.eu

Selcuklu D, Donoghue M, Kerin MJ and Spillane C (2012) Regulatory interplay between miR-21, JAG1 and 17beta-estradiol (E2) in breast cancer cells. Biochemical and Biophysical Research Communications. 2012 May 19. [PDF] Impact factor: 2.523

McKeown PC, Keshaviaiah C, Fort A, Tuteja R, Chatterjee M, Varshney RK and Spillane C (2012) Harnessing genomics to improve nutritional content and bioavailability of plant-derived foods. In: P.S. Panesar and S.S. Marwaha (Eds). Biotechnology in Agriculture and Food Processing: Opportunities and Challenges" CRC Press (Taylor & Francis Group), USA (in press).

Kohler C, Wolff P and Spillane C (2012) Epigenetic mechanisms underlying genomic imprinting in plants. Annual Review of Plant Biology 2012 Jan 30. Impact factor: 28.415

Berkowicz EW, Magee DA, Berry DP, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE. (2012) Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle. Animal Genetics. 43-7. Impact factor: 2.203

Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena, Jessica A Schlueter, Mark TA Donoghue, Sarwar Azam, Guangyi Fan, Adam M Whaley, Andrew D. Farmer, Jaime Sheridan, Reetu Tuetja, R Varma Penmetsa,Wei Wu, Hari D. Upadhyaya, Shiaw-Pyng Yang, Trushar Shah, KB Saxena, Eric Ward, Todd Michael, W Richard McCombie, Bicheng Yang, Gengyun Zhang, Jonathan DG Jones, Charles Spillane, Douglas R Cook, Greg D May, Xun Xu, Scott Jackson (2011) Decoding the genome of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor smallholder farmers in Asia and Africa. Nature Biotechnology 30:83-9. Impact factor: 31.1

McKeown PC, Laouielle-Duprat, Prins P, Wolff P, Schmid M, Donoghue MTA, Fort A, Duszynska D, Comte A, Lao NT, Wennblom TJ, Smant G, Kohler C, Grossniklaus U and Spillane C (2011) Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. BMC Plant Biology 11:113. Impact factor: 4.09

Sikora KM, Magee DA, Berkowicz EW, Lonergan P, Evans ACO, Carter F, Comte A, Waters SM, MacHugh DE and Charles Spillane C (2011) PHLDA2 is an imprinted gene in cattle. Animal Genetics Dec 2. doi: 10.1111/j.1365-2052.2011.02292.x. Impact factor: 2.203

Simrat Kaur, Mohan C. Kalita, Ravi B. Srivastava and Charles Spillane (2011) Eco-physiological Barriers and Technological Advances for Biodiesel Production from Microalgae. In: Biodiesel, eds. Stoytcheva M., Montero G., Intech Open Access Publisher, Croatia, ISBN 978-953-307-633-1.

Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MTA, Spillane C, Nordborg M, Rehmsmeier M and Köhler C (2011) High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm. PLOS Genetics Jun;7(6):e1002126 Impact factor: 9.5

Girum Azmach, Mosisa Worku, Legesse Wolde, Wende Abera, Birhanu Tadesse, Tolera Keno, Temesgen Chibsa, Charles Spillane and Abebe Menkir (2011) Development of Improved Yellow Maize Germplasm in Ethiopia. pp ...-... In B.M. Prasanna ... (ed.) Proceedings of the Third National Maize Workshop of Ethiopia. April 18-20, 2011. Addis Ababa, Ethiopia, EIAR/CIMMYT.

De Souza Gomes M, Kumar Muniyappa M, Gonçalves Carvalho S, Guerra-Sá R and Spillane C (2011) Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni. Genomics (May 26, in press). Impact factor: 3.327

Sikora KM, Magee DA, Berkowicz EW, Lonergan P, Evans ACO, Carter F, Comte A, Waters SM, MacHugh DE and Charles Spillane C (2011) Bovine PHLDA2 is a uniparentally expressed imprinted gene. Animal Genetics (in press). Impact factor: 2.203

Berkowicz EW, Magee DA, Berry DP, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane and MacHugh DE (2011) Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle. Animal Genetics (in press) Impact factor:

Donoghue, M.T., Keshavaiah, C., Swamidatta, S.H., and Spillane, C. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. (2011) BMC Evolutionary Biology 11, 47. Impact factor: 3.7

Sikora, K.M., Magee, D.A., Berkowicz, E.W., Berry, D.P., Howard, D.J., Mullen, M.P., Evans, R.D., Machugh, D.E., and Spillane, C. (2011) DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsalpha)-encoding (GNAS) genomic imprinting domain are associated with performance traits. BMC Genetics 12, 4. Impact factor: 2.49

Magee, D.A., Berry, D.P., Berkowicz, E.W., Sikora, K.M., Howard, D.J., Mullen, M.P., Evans, R.D., Spillane, C., and MacHugh, D.E. (2011) Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle. Journal of Heredity 102, 94-101. Impact factor: 2.396

Berkowicz, E.W., Magee, D.A., Sikora, K.M., Berry, D.P., Howard, D.J., Mullen, M.P., Evans, R.D., Spillane, C., and MacHugh, D.E. (2011) Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle. The Journal of Dairy Research 78, 1-8. Impact factor: 1.807

Morris SH and Spillane C (2010) EU GM Crop Regulation: A Road to Resolution or a Regulatory Roundabout? European Journal of Risk Regulation 4:359-369.

Atanassov, A., Gheysen, G., Murphy, D.J., Sanvido, O., Schiemann, J., Spillane, C., and Tuberosa, R. (2010) 1 out of 27-European politicians score poorly in agbiotech. Nature Biotechnology 28, 551-552. Impact factor: 31.1

Magee, D.A., Sikora, K.M., Berkowicz, E.W., Berry, D.P., Howard, D.J., Mullen, M.P., Evans, R.D., Spillane, C., and MacHugh, D.E. (2010) DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle. BMC Genetics 11, 93. Impact factor: 2.49

Magee, D.A., Berkowicz, E.W., Sikora, K.M., Sweeney, T., Kenny, D.A., Kelly, A.K., Evans, R.D., Wickham, B.W., Bradley, D.G., Spillane, C., and MacHugh, D.E. (2010) High concordance of bovine single nucleotide polymorphism genotypes generated using two independent genotyping strategies. Animal Biotechnology 21, 257-262. Impact factor: 0.818

O'Connell, M.J., Loughran, N.B., Walsh, T.A., Donoghue, M.T., Schmid, K.J., and Spillane, C. (2010) A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. Mammalian Genome 21, 486-498. Impact factor: 2.771

Schouest, K., Zitova, A., Spillane, C., and Papkovsky, D. (2009). Toxicological assessment of chemicals using Caenorhabditis elegans and optical oxygen respirometry. Environmental Toxicology and Chemistry 28, 791-799. Impact factor: 3.026

Selcuklu, S.D., Donoghue, M.T., and Spillane, C. (2009). miR-21 as a key regulator of oncogenic processes. Biochemical Society Transactions 37, 918-925. Impact factor: 3.378

Tessadori, F., van Zanten, M., Pavlova, P., Clifton, R., Pontvianne, F., Snoek, L.B., Millenaar, F.F., Schulkes, R.K., van Driel, R., Voesenek, L.A., Spillane, C., Pikaard, C.S., Fransz, P., and Peeters, A.J. (2009). Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genetics 5, e1000638. 38. Impact factor: 9.5

Garnier, O., Laoueille-Duprat, S., and Spillane, C. (2008a). Genomic imprinting in plants. Epigenetics 3, 14-20. [PDF]

Garnier, O., Laouielle-Duprat, S., and Spillane, C. (2008b). Genomic imprinting in plants. Advances in Experimental Medicine and Biology 626, 89-100.

Morris, S.H., and Spillane, C. (2008). GM directive deficiencies in the European Union. The current framework for regulating GM crops in the EU weakens the precautionary principle as a policy tool. EMBO Reports 9, 500-504. Impact factor: Impact factor: 7.822

Selcuklu, S.D., and Spillane, C. (2008). Translational epigenetics: clinical approaches to epigenome therapeutics for cancer. Epigenetics 3, 107-112.

Nembaware, V., Lupindo, B., Schouest, K., Spillane, C., Scheffler, K., and Seoighe, C. (2008). Genome-wide survey of allele-specific splicing in humans. BMC Genomics 9, 265. Impact factor: 4.206

Haun, W.J., Laoueille-Duprat, S., O'Connell M, J., Spillane, C., Grossniklaus, U., Phillips, A.R., Kaeppler, S.M., and Springer, N.M. (2007). Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs. Plant Journal 49, 325-337. Impact factor: 6.948

Fouhy, Y., Scanlon, K., Schouest, K., Spillane, C., Crossman, L., Avison, M.B., Ryan, R.P., and Dow, J.M. (2007). Diffusible signal factor-dependent cell-cell signaling and virulence in the nosocomial pathogen Stenotrophomonas maltophilia. Journal of Bacteriology 189, 4964-4968. Impact factor: 3.726

Spillane, C., Schmid, K.J., Laoueille-Duprat, S., Pien, S., Escobar-Restrepo, J.M., Baroux, C., Gagliardini, V., Page, D.R., Wolfe, K.H., and Grossniklaus, U. (2007). Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448, 349-352. Impact factor: 31.434

Gerlach JQ, Kilcoyne M, McKeown P, Spillane C and Joshi L (2009) Plant produced biopharmaceuticals. In: Kole C, Michler CH, Abbott AG and Hamm TC (Eds.) Biotech Plants: Development, Utilization and Deployment, Springer-Verlag (Berlin, Heidelberg, New York).

O’Brien M, Spillane C, Meade C, and Mullins E (2008) Impact of Arable Farming on Irish Biodiversity: A Scarcity of Studies Hinders a Rigorous Assessment. Biology & Environment (in press).

Schouest, K., Coghlan, A. and Spillane, C. (2008). Development of a C.elegans model system for genetic and molecular dissection of epigenetic mechanisms underlying trinucleotide expansion disorders. Ulster Medical Journal. 77(1): 70.

Martin G, Schouest K, Kovvuru P and Spillane C (2007) Prediction and validation of microRNA targets in animal genomes. J Biosci. 32:1049-52

Fouhy, Y., Scanlon, K., Schouest, K., Spillane C, Crossman, L., Avison M.B., Ryan, R.P., Dow, J.M. (2007). DSF-dependent cell-cell signaling and virulence in the nosocomial pathogen Stenotrophomonas maltophilia. Journal of Bacteriology. 189:4964-8.

Garnier O, Laouielle S and Spillane C (2006) Genomic imprinting in plants. In: Wilkins J (ed) Genomic Imprinting, Landes Biosciences: Georgetown, Texas.

Spillane C, Baroux C, Escobar-Restrepo J-M, Page DR, Laouielle S and Grossniklaus U (2005) Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. Cold Spring Harbor Symposia on Quantitative Biology, 69: 1-12.

Spillane C, Curtis MD, and Grossniklaus U (2004) Apomixis technology development – virgin births in farmers’ fields? Nature Biotechnology 22:687-691.

Collinge MA, Spillane C, Köhler C, Gheyselinck J and Grossniklaus U (2004) Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development. Plant Cell 16:1035-46.

Köhler C, Hennig L, Spillane C, Pien S, Gruissem W and Grossniklaus U (2003) The Polycomb group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes and Development 17:1540-53.

Grossniklaus, U. Moore, J.M., Brukhin, V., Gheyselinck, J., Baskar, R., Vielle-Calzada, J-P., Baroux, C., Page, D.R., and Spillane, C. (2002). Engineering of apomixis in crop plants: what can we learn from sexual model systems. In : Vasil IK (Ed) Plant Biotechnology 2002 & Beyond, Kluwer Academic Publishers: Dordrecht, pp. 309-314.

Baroux C, Spillane C and Grossniklaus U (2002) Evolutionary origins of the endosperm in flowering plants. Genome Biology 3:1026.1-1026.5.

Baroux C, Spillane C and Grossniklaus U (2002) Genomic imprinting during seed development. Advances in Genetics ;46:165-214

Spillane C, Steimer A and Grossniklaus U (2001) Apomixis in agriculture: the quest for clonal seeds. Sexual Plant Reproduction 14:179-187.

Spillane C, Vielle-Calzada JP and Grossniklaus U (2001) APO2001: A sexy apomixer in Como, Meeting Report, Plant Cell 13:1480-91.

Grossniklaus U, Spillane C, Page DR and Koehler C (2001) Genomic imprinting and seed development: endosperm formation with and without sex. Current Opinion in Plant Biology 4, 21-27

Spillane C, MacDougall C, Stock C, Koehler C, Vielle-Calzada JP, Nunes SM, Grossniklaus U and Goodrich J (2000) Interaction of the Arabidopsis polycomb group proteins FIE and MEA mediates their common phenotypes. Current Biology 10, 1535-1538.

Spillane C, Vielle-Calzada J-P and Grossniklaus U (2000) Parent-of-origin effects and seed development: Genetics and epigenetics. In: Hui TH, Khachatourians GG, McHughen A, Nip WK, Scorza R (Eds) Transgenic Plants and Crops, New York:Marcel-Dekker Inc.

Spillane C and Gepts P (2000) Evolutionary and genetic perspectives on the dynamics of crop genepools. In: Cooper DC, Spillane C and Hodgkin T (Eds.) (2000) Broadening the Genetic Bases of Crop Production, CABI:Wallingford.

Vielle-Calzada JP, Thomas J, Spillane C, Coluccio A, Hoeppner MA, and Grossniklaus U (1999) Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes and Development 13:2971-2982.

Brown AHD and Spillane C (1999) Implementing core collections - principles, procedures, progress, problems and promise. In: Johnson RC and Hodgkin T (Eds) Core Collections for Today and Tomorrow, Crop Science Society of America: Madison, Wisconsin, p1-10.

Spillane C, Baulcombe DC and Kavanagh TA (1998) Genetic engineering of the potato cultivar Glenroe for increased resistance to potato virus X. Irish Journal of Food and Agriculture 37: 173-182

Spillane C, Verchot J, Kavanagh TA and Baulcombe DC (1997) Concurrent suppression of virus replication and rescue of movement-defective virus in transgenic plants expressing the coat protein of potato virus X. Virology 236:76-84.

Gilbert J, Spillane C, Kavanagh TA and Baulcombe DC (1997) Elicitation of Rx-mediated resistance to PVX in potato does not require new RNA synthesis and may involve a latent hypersensitive response. Molecular Plant-Microbe Interactions 11: 833-835.

Spillane C (1995) Strategies for the Genetic Engineering of Resistance to Potato Virus X. Ph.D. thesis, Trinity College: Dublin, pp211.

Kavanagh TA and Spillane C (1995) Strategies for engineering virus resistance in transgenic plants, Euphytica 85:149-158.

Kavanagh TA and Spillane C (1992) Genes with your greens, Technology Ireland 24: 24-26.

Perspectives, Policy & Outreach-related Reviews and Book Chapters

Morris SH & Spillane C (2008) GM directive deficiencies in the European Union. The current framework for regulating GM crops in the EU weakens the precautionary principle as a policy tool. EMBO Reports. 9:500-4.

O’Mahony C & Spillane C (2004) Open-access publishers: Knowledge brokers in the electronic age. Irish Medical Times.

Spillane C and Doyle A (2004) Poverty alleviation, plant biotechnology and the CGIAR International Agricultural Research Centres. In: Christou P and Klee H (eds) Handbook of Plant Biotechnology, Wiley Europe. ISBN: 0-471-85199-X

Spillane C (2002), Agricultural Biotechnology and Developing Countries: Proprietary Knowledge and Diffusion of Benefits, in T. Swanson (ed.), Biotechnology, Agriculture and the Developing World, Cheltenham, UK and Northampton, MA, USA: Edward Elgar Publishing Ltd.

Thro AM and Spillane C (2005) Biotechnology-assisted Participatory Plant Breeding: Opportunity or Oxymoron?, In: Sperling L and Ashby JA (Eds) Participatory Plant Breeding and rural development. Cambridge:Cambridge University Press, (in press).

Spillane C and Pinto Y (2001) Biosafety in agricultural biotechnology: Balancing social and environmental impacts. In: Swanson T (ed). The Economics of Managing Biotechnologies, Springer:Netherlands, pp3-49..

Non-authored Government Commissioned Publications

NPBR (2007) Biodiversity Knowledge Programme for Ireland, Irish National Platform for Biodiversity Research, EPA/NPWS.

FAO (2000) Biotechnology, Biosafety and Biodiversity for Sustainable Agriculture. FAO Position paper for UN Commission on Sustainable Development review of Ch14 of Agenda 21, May 2000, UN, New York.

FAO (1996a) Draft Global Plan of Action for the Conservation and Sustainable Utilization of Plant Genetic Resources for Food and Agriculture, Document ITCPGR/96/5-Rev1 presented to, (and unanimously adopted by 150 governments), the 4th International Technical Conference on Plant Genetic Resources, Leipzig, Germany, June 17-23, 1996, p62.

FAO (1995a) Recent International Developments of Relevance to the Draft Code of Conduct for Plant Biotechnology, Document CPGR-6/95/15 of the Sixth Session of the FAO Commission on Plant Genetic Resources, June 19-39, 1995, p13.

Dept of Agriculture (1995) Country Report on the Status of Plant Genetic Resources in the Republic of Ireland, National Report submitted to the FAO by the Irish Department of Agriculture, Dublin, Ireland, p28 (invited contribution).

Persley GJ, Spillane C, Eggen A, Lehn-Jenszen H, Chiono C, Wagner H and Hammond K (2000) Modern biotechnology and the management of animal genetic resources: policy issues. FAO Animal Biotechnology Working Group, FAO: Rome.

Spillane C and Thro AM (2000) Farmer participatory research and pro-poor agricultural biotechnology. Centre for Development Research: Copenhagen, Den Ny Verden Vol 1 (In Danish), 45pp.

Spillane C (2000) Can agricultural biotechnology contribute to poverty alleviation? CABI AgBiotechNet, Vol 2 March ABN 042 .

Spillane C (1999) Recent developments in biotechnology as they relate to plant genetic resources for food and agriculture. FAO Commission on Genetic Resources:Rome, Backg round Study Paper No. 9., pp64.

http://www.fao.org/WAICENT/FAOINFO/AGRICULT/cgrfa/docs.htm#bsp

Cooper HD, Spillane C, Anishetty M, Griffee P (1998) Promoting the identification, conservation and use of wild food plant for food and agriculture: the FAO Global Plan of Action, Cahiers Options Mediterraneenes, vol 38. ISSN 1022-1379.

Cooper HD, Spillane C, Kermali I and Anishetty M (1996) Harnessing plant genetic resources for sustainable agriculture. Plant Genetic Resources Newsletter 114.

Esquinas JT, Spillane C and Stannard C (1997) Biodiversity and biotechnology for food and agriculture. International action for the conservation and utilization of plant genetic resources for food and agriculture, Chapter in book on UN Earth Charter.

Brown AHB and Spillane C (1998) Implementing core collections - principles, procedure, progress, problems and promise, In: CSSA/IPGRI (1998) Core collections ’98, Proceedings of Crop Science Society of America Core Collections Workshop, October 1998.

Cooper HD, Spillane C and Anishetty NM (1997) The Global Plan of Action for the Conservation and Sustainable Use of Plant Genetic Resources for Food and Agriculture. Paper presented at BRG/Solagral/IER International Forum on “Sustainable management of plant genetic resources in the African Savannah, Bamako, Mali, 26-28 February, 1997.

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