Publications

2017

• Antwis, R.E., Griffiths, S.M., Harrison, X.A., Aranega-Bou, P., Arce, A., Bettridge, A.S., Brailsford, F.L., de Menezes, A., Devaynes, A., Forbes, K.M. and Fry, E.L., 2017. Fifty important research questions in microbial ecology. FEMS Microbiology Ecology, 93(5).
• Auer, A., Vande Burgt, N. H., Abram, F., Barry, G., Fenton, O., Markey, B. K., ... & Gordon, S. V. (2017). Agricultural anaerobic digestion power plants in Ireland and Germany: policy and practice. Journal of the Science of Food and Agriculture, 97(3), 719-723.
• Bauer, P., Wedi, N., Baldauf, M., Benard, P., Fuhrer, O., Kulczewski, M., McKinstry, A., Messmer, P., New, N., HansenSass, B. and Szmelter, J., 2017. Energy-efficient SCalable Algorithms for weather Prediction at Exascale. Impact, 2017(1), pp.69-71.
• Braud M, David A. Magee, Stephen D.E. Park, Tad S. Sonstegard, Sinead M. Waters, David E. MacHugh, Charles Spillane (2017) Genome-wide microRNA binding site variation between extinct wild aurochs and modern cattle identifies candidate microRNA-regulated domestication genes. Frontiers in Genetics. 31 January 2017 | https://doi.org/10.3389/fgene.2017.00003
• Bralatei, E., Nekrosiute, K., Ronan, J., Raab, A., McGovern, E., Stengel, D.B., Krupp, E.M. and Feldmann, J., 2017. A field deployable method for a rapid screening analysis of inorganic arsenic in seaweed. Microchimica Acta, 184(6), pp.1701-1709.
• Cao, Yongfeng, Chaosheng Zhang, Hongwei Rong, Guilin Zheng, and Limin Zhao. "The effect of dissolved oxygen concentration (DO) on oxygen diffusion and bacterial community structure in moving bed sequencing batch reactor (MBSBR)." Water Research 108 (2017): 86-94.
• Chen, M., Ding, S., Zhang, L., Li, Y., Sun, Q. and Zhang, C., 2017. An investigation of the effects of elevated phosphorus in water on the release of heavy metals in sediments at a high resolution. Science of The Total Environment, 575, pp.330-337.
• Clarke, R., Peyton, D., Healy, M.G., Fenton, O. and Cummins, E., 2017. A quantitative microbial risk assessment model for total coliforms and E. coli in surface runoff following application of biosolids to grassland. Environmental Pollution, 224, pp.739-750.
• Daly, K., Breuil, M., Buckley, C., O’Donoghue, C., Ryan, M. and Seale, C., 2017. A review of water quality policies in relation to public good benefits and community engagement in rural Ireland. European Countryside, 9(1), pp.99-115.
• Dennehy, C., Lawlor, P.G., Jiang, Y., Gardiner, G.E., Xie, S., Nghiem, L.D. and Zhan, X., 2017. Greenhouse gas emissions from different pig manure management techniques: a critical analysis. Frontiers of Environmental Science & Engineering, 11(3), p.11.
• Dennehy, C., Lawlor, P.G., Gardiner, G.E., Jiang, Y., Cormican, P., McCabe, M.S. and Zhan, X., 2017. Process stability and microbial community composition in pig manure and food waste anaerobic co-digesters operated at low HRTs. Frontiers of Environmental Science & Engineering, 11(3), p.4.
• Doherty, E., Queally, M., Cullinan, J. and Gillespie, P., 2017. The Impact of Childhood Overweight and Obesity on Healthcare Utilisation. Economics & Human Biology.
• Domozych, D., Sørensen, I. and Popper, Z.A., 2017. Charophytes: Evolutionary Ancestors of Plants and Emerging Models for Plant Research. Frontiers in Plant Science, 8.
• Douthwaite, B. and Hoffecker, E., 2017. Towards a complexity-aware theory of change for participatory research programs working within agricultural innovation systems. Agricultural Systems, 155, pp.88-102.
• Douthwaite, B., Apgar, J.M., Schwarz, A.M., Attwood, S., Senaratna Sellamuttu, S. and Clayton, T., 2017. A new professionalism for agricultural research for development. International Journal of Agricultural Sustainability, pp.1-15.
• Duffy C, Murray U, Nowak A, Girvetz E, Corner-Dolloff C, Twyman J, Huyer S, Jarvis A and Spillane C. 2017. National level indicators for gender, poverty, food security, nutrition and health in Climate-Smart Agriculture (CSA) activities. CCAFS Working Paper no 195. Copenhagen, Denmark: CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS).
• Dussan, K. and Monaghan, R.F., 2017. Integrated Thermal Conversion and Anaerobic Digestion for Sludge Management in Wastewater Treatment Plants. Waste and Biomass Valorization, pp.1-21.
• Fhlatharta, A.M.N. and Farrell, M., 2017. Unravelling the strands of ‘patriarchy’ in rural innovation: A study of female innovators and their contribution to rural Connemara. Journal of Rural Studies, 54, pp.15-27.
• Finnegan, W., Goggins, J., Clifford, E. and Zhan, X., 2017. Environmental impacts of milk powder and butter manufactured in the Republic of Ireland. Science of The Total Environment, 579, pp.159-168.
• Finnegan, W., Goggins, J., Chyzheuskaya, A. and Zhan, X., 2017. Global warming potential associated with Irish milk powder production. Frontiers of Environmental Science & Engineering, 11(3), p.12.
• Girma, Gezahegn, Melaku Gedil, and Charles Spillane. "Morphological, SSR and ploidy analysis of water yam (Dioscorea alata L.) accessions for utilization of aerial tubers as planting materials." Genetic resources and crop evolution 64, no. 2 (2017): 291-305.
• Golden, N., Zhang, C., Potito, A.P., Gibson, P.J., Bargary, N. and Morrison, L., 2017. Impact of grass cover on the magnetic susceptibility measurements for assessing metal contamination in urban topsoil. Environmental research, 155, pp.294-306.
• Guihéneuf, F., & Stengel, D.B. (2017). Interactive effects of light and temperature on pigments and n-3 LC-PUFA-enriched oil accumulation in batch-cultivated Pavlova lutheri using high-bicarbonate supply. Algal Research, 23, 113-125.
• Glaubitz, U., Li, X., Schaedel, S., Erban, A., Sulpice, R., Kopka, J., Hincha, D.K. and Zuther, E., 2017. Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity‐and tolerance‐related profiles. Plant, Cell & Environment, 40(1), pp.121-137.
• Hamuda, E., Mc Ginley, B., Glavin, M. and Jones, E., 2017. Automatic crop detection under field conditions using the HSV colour space and morphological operations. Computers and Electronics in Agriculture, 133, pp.97-107.
• Ishihara, H., Moraes, T.A., Pyl, E.T., Schulze, W.X., Obata, T., Scheffel, A., Fernie, A.R., Sulpice, R. and Stitt, M., 2017. Growth rate correlates negatively with protein turnover in Arabidopsis accessions. The Plant Journal.
• Kumar APK, McKeown PC, Boualem A, Ryder P, Brychkova G, Bendahmane A, Sarkar A, Chatterjee M and Spillane C (2017) Tilling by Sequencing (TbyS) for targeted genome mutagenesis in crops. Molecular Breeding. 37:14. doi:10.1007/s11032-017-0620-1
• Leonard, B., Kinsella, A., O’Donoghue, C., Farrell, M. and Mahon, M., 2017. Policy drivers of farm succession and inheritance. Land Use Policy, 61, pp.147-159.
• Leonard, B., Mahon, M., Kinsella A., O’Donoghue, C, Farrell, M., Curran, T. and Hennessy, T., 2017. The Potential of Farm Partnerships to Facilitate Farm Succession and Inheritance. International Journal of Agricultural Management, 6(1), pp.4-19.
• Liu, H., Shi, J., Zhan, X., Zhang, L., Fu, B. and Liu, H., 2017. Selective acetate production with CO 2 sequestration through acetogen-enriched sludge inoculums in anaerobic digestion. Biochemical Engineering Journal, 121, pp.163-170.
• Martin, G., Selcuklu, S.D., Schouest, K., Nembaware, V., McKeown, P.C., Seoighe, C. and Spillane, C., 2017. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Gene, 598, pp.107-112.
• McDonagh, J., Farrell, M. and Conway, S., 2017. The Role of Small‐scale Farms and Food Security. Sustainability Challenges in the Agrofood Sector, pp.33-47.
• McGrory, E.R., Brown, C., Bargary, N., Williams, N.H., Mannix, A., Zhang, C., Henry, T., Daly, E., Nicholas, S., Petrunic, B.M. and Lee, M., 2017. Arsenic contamination of drinking water in Ireland: A spatial analysis of occurrence and potential risk. Science of The Total Environment, 579, pp.1863-1875.
• Meng, Y., Cave, M. and Zhang, C., 2017. Spatial distribution patterns of phosphorus in top-soils of Greater London Authority area and their natural and anthropogenic factors. Applied Geochemistry.
• Pathak, A., Morrison, L. and Healy, M.G., 2017. Catalytic potential of selected metal ions for bioleaching, and potential techno-economic and environmental issues: A critical review. Bioresource Technology.
• Paula, F.S., Tatti, E., Abram, F., Wilson, J. and O'Flaherty, V., 2017. Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment. Journal of Environmental Management, 196, pp.476-486.
• Pereiro, I., Bendali, A., Tabnaoui, S., Alexandre, L., Srbova, J., Bilkova, Z., Deegan, S., Joshi, L., Viovy, J.L., Malaquin, L. and Dupuy, B., 2017. A new microfluidic approach for the one-step capture, amplification and label-free quantification of bacteria from raw samples. Chemical Science.
• Prendergast-Miller, M.T., de Menezes, A.B., Macdonald, L.M., Toscas, P., Bissett, A., Baker, G., Farrell, M., Richardson, A.E., Wark, T. and Thrall, P.H., 2017. Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities. Soil Biology and Biochemistry, 109, pp.1-13.
• Raimundo, S.C., Pattathil, S., Eberhard, S., Hahn, M.G. and Popper, Z.A., 2017. β-1, 3-Glucans are components of brown seaweed (Phaeophyceae) cell walls. Protoplasma, 254(2), pp.997-1016.
• Ryder P, McHale M, Fort A and Spillane C (2017) Generation of stable nulliplex autopolyploid lines of Arabidopsis thaliana using CRISPR/Cas9 genome editing. Plant Cell Reports Mar 13. doi: 10.1007/s00299-017-2125-0.
• Salojärvi, J., Smolander, O.P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J. and Rastas, P., 2017. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics, 49(6), pp.904-912.
• Sanfo, S., Barbier, B., Dabiré, I.W., Vlek, P.L., Fonta, W.M., Ibrahim, B. and Barry, B., 2017. Rainfall variability adaptation strategies: An ex-ante assessment of supplemental irrigation from farm ponds in southern Burkina Faso. Agricultural Systems, 152, pp.80-89.
• Santos, Clelton A., Jaire A. Ferreira-Filho, Anthonia O’Donovan, Vijai K. Gupta, Maria G. Tuohy, and Anete P. Souza. "Production of a recombinant swollenin from Trichoderma harzianum in Escherichia coli and its potential synergistic role in biomass degradation." Microbial cell factories 16, no. 1 (2017): 83.
• Shore, M., Murphy, S., Mellander, P.E., Shortle, G., Melland, A.R., Crockford, L., O'Flaherty, V., Williams, L., Morgan, G. and Jordan, P., 2017. Influence of stormflow and baseflow phosphorus pressures on stream ecology in agricultural catchments. Science of The Total Environment, 590, pp.469-483.
• Shtein, Ilana, Yaniv Shelef, Ziv Marom, Einat Zelinger, Amnon Schwartz, Zoë A. Popper, Benny Bar-On, and Smadar Harpaz-Saad. "Stomatal cell wall composition: distinctive structural patterns associated with different phylogenetic groups." Annals of Botany (2017).
• Stack, J., Tobin, P.R., Gietl, A., Harnedy, P.A., Stengel, D.B. and FitzGerald, R.J., 2017. Seasonal variation in nitrogenous components and bioactivity of protein hydrolysates from Porphyra dioica. Journal of Applied Phycology, pp.1-12.
• Sun, Q., Ding, S., Zhang, L., Chen, M. and Zhang, C., 2017. A millimeter-scale observation of the competitive effect of phosphate on promotion of arsenic mobilization in sediments. Chemosphere, 180, pp.285-294.
• Sun, X.L., Wang, H.L., Zhao, Y.G., Zhang, C. and Zhang, G.L., 2017. Digital soil mapping based on wavelet decomposed components of environmental covariates. Geoderma, 303, pp.118-132.
• Tutwiler, A., Padulosi, S. and Hunter, D., 2017. Securing sustainable and nutritious food systems through mainstreaming agricultural biodiversity: an interdisciplinary study. The Lancet, 389, p.S22.
• Vero, S.E., Healy, M.G., Henry, T., Creamer, R.E., Ibrahim, T.G., Richards, K.G., Mellander, P.E., McDonald, N.T. and Fenton, O., 2017. A framework for determining unsaturated zone water quality time lags at catchment scale. Agriculture, Ecosystems & Environment, 236, pp.234-242.
• Wang, Y., Ding, S., Wang, D., Sun, Q., Lin, J., Chen, M. and Zhang, C., 2017. Static layer: a key to immobilization of phosphorus in sediments amended with lanthanum modified bentonite (Phoslock®). Chemical Engineering Journal.
• Xu, Y., Zhang, C., Zhao, M., Rong, H., Zhang, K. and Chen, Q., 2017. Comparison of bioleaching and electrokinetic remediation processes for removal of heavy metals from wastewater treatment sludge. Chemosphere, 168, pp.1152-1157.
• Xu, L., Sun, Q., Ding, S., Gong, M. and Zhang, C., 2017. Simultaneous measurements of arsenic and sulfide using diffusive gradients in thin films technique (DGT). Environmental Geochemistry and Health, pp.1-11.
• Zhang, L., Sun, Q., Ding, S., Cheng, X., Liu, Q. and Zhang, C., 2017. Characterization of arsenic availability in dry and flooded soils using sequential extraction and diffusive gradients in thin films (DGT) techniques. Environmental Science and Pollution Research, pp.1-8.

2016

1. Arendt, E.K., 2016. Gluten-Free. Annual Review of Food Science and Technology, 8(1).
2. Axel, C., Zannini, E. and Arendt, E.K., 2016. Mould spoilage of bread and its biopreservation: A review of current strategies for bread shelf life extension. Critical Reviews in Food Science and Nutrition, (accepted).
3. Axel, C., Brosnan, B., Zannini, E., Furey, A., Coffey, A. and Arendt, E.K., 2016. Antifungal sourdough lactic acid bacteria as biopreservation tool in quinoa and rice bread. International Journal of Food Microbiology.
4. Barrett, M., Khalil, M.I., Jahangir, M.M.R., Lee, C., Cardenas, L.M., Collins, G., Richards, K.G. and O’Flaherty, V., 2016. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils. Environmental Science and Pollution Research, pp.1-12.
5. Breen, B., Kelley, H. and Hynes, S., 2016. The impact of precautionary quota constraints on the composition of multispecies harvest portfolios. Marine Policy, 69, pp.13-23.
6. Chen, X., O’Halloran, J. and Jansen, M.A., 2016. The toxicity of zinc oxide nanoparticles to Lemna minor (L.) is predominantly caused by dissolved Zn. Aquatic Toxicology, 174, pp.46-53.
7. CIAT; BFS/USAID (2016) Climate-Smart Agriculture in Senegal. CSA Country Profiles for Africa Series. International Center for Tropical Agriculture (CIAT); Bureau for Food Security, United States Agency for International Development (BFS/USAID), Washington, D.C. 18 p. (in press).
8. Coffey, R., Benham, B., Wolfe, M. L., Dorai-Raj, S., Bhreathnach, N., O’Flaherty, V., ... & Cummins, E. Sensitivity of streamflow and microbial water quality to future climate and land use change in the West of Ireland. Regional Environmental Change, 1-18.
9. Conway, S.F., McDonagh, J., Farrell, M. and Kinsella, A., 2016. Cease agricultural activity forever? Underestimating the importance of symbolic capital. Journal of Rural Studies, 44, pp.164-176.
10. Craven, D., McGinley, B., Kilmartin, L., Glavin, M. and Jones, E., 2016. Energy-efficient Compressed Sensing for ambulatory ECG monitoring. Computers in biology and medicine, 71, pp.1-13.
11. Delêtre, M., Hodkinson, T. R., & McKey, D. Perceptual selection and the unconscious selection of ‘volunteer’seedlings in clonally propagated crops: an example with African cassava (Manihot esculenta Crantz) using ethnobotany and population genetics. Genetic Resources and Crop Evolution, 1-16.
12. Ding, S., Wang, Y., Wang, D., Li, Y.Y., Gong, M. and Zhang, C., 2016. In situ, high-resolution evidence for iron-coupled mobilization of phosphorus in sediments. Scientific Reports, 6.
13. Dussan K, Girisuta B, Lopes M, Leahy JJ, Hayes MH. Effects of Soluble Lignin on the Formic Acid‐Catalyzed Formation of Furfural: A Case Study for the Upgrading of Hemicellulose. ChemSusChem. 2016 Jan 1.
14. Fenton, O., Healy, M.G., Brennan, F.P., Thornton, S.F., Lanigan, G.J. and Ibrahim, T.G., 2016. Holistic evaluation of field-scale denitrifying bioreactors as a basis to improve environmental sustainability. Journal of Environmental Quality, 45(3), pp.788-795.
15. Flannelly, T., Lopes, M., Kupiainen, L., Dooley, S. and Leahy, J.J., 2016. Non-stoichiometric formation of formic and levulinic acids from the hydrolysis of biomass derived hexose carbohydrates. RSC Advances, 6(7), pp.5797-5804.
16. Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M. Photoperiod‐dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. Plant, Cell & Environment. 2016 Apr 1.
17. Flynn, R.M., Deakin, J., Archbold, M., Cushnan, H., Kilroy, K., O'Flaherty, V. and Misstear, B.D., 2016. Using microbiological tracers to assess the impact of winter land use restrictions on the quality of stream headwaters in a small catchment. Science of The Total Environment, 541, pp.949-956.
18. Fort, A., Ryder, P., McKeown, P. C., Wijnen, C., Aarts, M. G., Sulpice, R., & Spillane, C. (2016). Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New Phytologist, 209(2), 590-599.
19. Furey, E.M., O'Hora, D., McNamara, J., Kinsella, S. and Noone, C., 2016. The roles of financial threat, social support, work stress and mental distress in dairy farmers’ expectations of injury. Frontiers in Public Health, 4, p.126.
20. Goñi, O., Fort, A., Quille, P., McKeown, P. C., Spillane, C., & O’Connell, S. (2016). Comparative Transcriptome Analysis of Two Ascophyllum nodosum Extract Biostimulants: Same Seaweed but Different. Journal of Agricultural and Food Chemistry, 64(14), 2980-2989.
21. Guiheneuf, F., Khan, A., & Phan Tran, L. S. (2016). Genetic engineering: a promising tool to engender physiological, biochemical and molecular stress resilience in green microalgae. Frontiers in Plant Science, 7, 400.
22. Healy M. Carbon and nitrogen dynamics and greenhouse gas emissions in constructed wetlands treating wastewaters: a review. (2016) Hydrology And Earth System Sciences. 2016 Feb 17.
23. Healy, M. G., Fenton, O., Forrestal, P. J., Danaher, M., Brennan, R. B., & Morrison, L. (2016). Metal concentrations in lime stabilised, thermally dried and anaerobically digested sewage sludges. Waste Management, 48, 404-408.
24. Healy, M. G., Ryan, P. C., Fenton, O., Peyton, D. P., Wall, D. P., & Morrison, L. (2016). Bioaccumulation of metals in ryegrass (Lolium perenne L.) following the application of lime stabilised, thermally dried and anaerobically digested sewage sludge. Ecotoxicology and Environmental Safety, 130, 303-309.
25. Horstmann, S.W., Belz, M.C., Heitmann, M., Zannini, E. and Arendt, E.K., 2016. Fundamental Study on the Impact of Gluten-Free Starches on the Quality of Gluten-Free Model Breads. Foods, 5(2), p.30.
26. Horvat A, Kwapinska M, Xue G, Dooley S, Kwapinski W, Leahy JJ. Detailed Measurement Uncertainty Analysis of Solid-Phase Adsorption Total Gas Chromatography (GC)-Detectable Tar from Biomass Gasification. Energy & Fuels. 2016 Feb 17;30(3):2187-97.
27. Imamura, H., Downing, T., Van den Broeck, F., Sanders, M.J., Rijal, S., Sundar, S., Mannaert, A., Vanaerschot, M., Berg, M., De Muylder, G. and Dumetz, F., 2016. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife, 5, p.e12613.
28. Karnjanapratum, S., O'Callaghan, Y.C., Benjakul, S. and O'Brien, N.M., 2016. In vitro cellular bioactivities of Maillard reaction products from sugar-gelatin hydrolysate of unicorn leatherjacket skin system. Journal of Functional Foods, 23, pp.87-94.
29. Karnjanapratum S, O'Callaghan YC, Benjakul S, O'Brien N. Antioxidant, immunomodulatory and antiproliferative effects of gelatin hydrolysate from unicorn leatherjacket skin. Journal of the Science of Food and Agriculture. 2016 Jan 1.
30. Keating, C., Chin, J.P., Hughes, D., Manesiotis, P., Cysneiros, D., Mahony, T., Smith, C.J., McGrath, J.W. and O’Flaherty, V., 2016. Biological phosphorus removal during high-rate, low-temperature, anaerobic digestion of wastewater. Frontiers in microbiology, 7.
31. Kitavi, M., Downing, T., Lorenzen, J., Karamura, D., Onyango, M., Nyine, M., ... & Spillane, C. (2016). The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. Theoretical and Applied Genetics, 1-15.
32. Kongsager, R., Locatelli, B. and Chazarin, F., 2016. Addressing climate change mitigation and adaptation together: A global assessment of agriculture and forestry projects. Environmental management, 57(2), pp.271-282.
33. Leskow, C.C., Kamenetzky, L., Dominguez, P.G., Zirpolo, J.A.D., Obata, T., Costa, H., Martí, M., Taboga, O., Keurentjes, J., Sulpice, R. and Ishihara, H., 2016. Allelic differences in a vacuolar invertase affect Arabidopsis growth at early plant development. Journal of Experimental Botany, p.erw185.
34. Li, R., Morrison, L., Collins, G., Li, A. and Zhan, X., 2016. Simultaneous nitrate and phosphate removal from wastewater lacking organic matter through microbial oxidation of pyrrhotite coupled to nitrate reduction. Water Research, 96, pp.32-41.
35. Liao, Q.N., Ji, F., Li, J.C., Zhan, X. and Hu, Z.H., 2016. Decomposition and mineralization of sulfaquinoxaline sodium during UV/H 2 O 2 oxidation processes. Chemical Engineering Journal, 284, pp.494-502.
36. Liu, X., Wolfe, R., Welch, L. R., Domozych, D. S., Popper, Z. A., & Showalter, A. M. (2016). Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom. PloS one, 11(2), e0150177.
37. Liu, X., Sheng, H., Jiang, S., Yuan, Z., Zhang, C., & Elser, J. J. (2016). Intensification of phosphorus cycling in China since the 1600s. Proceedings of the National Academy of Sciences, 113(10), 2609-2614.
38. Lynch KM, Zannini E, Guo J, Axel C, Arendt EK, Kildea S, Coffey A. Control of Zymoseptoria tritici cause of septoria tritici blotch of wheat using antifungal Lactobacillus strains. Journal of Applied Microbiology. 2016 May 1.
39. Manton, R., Hynes, S. and Clifford, E., 2016. Greenways as a tourism resource: a study of user spending and value. Tourism Planning & Development, pp.1-22.
40. Mäkinen, O.E., Zannini, E., Koehler, P. and Arendt, E.K., 2016. Heat-denaturation and aggregation of quinoa (Chenopodium quinoa) globulins as affected by the pH value. Food chemistry, 196, pp.17-24.
41. Mina-Vargas A.M., McKeown P.C., Flanagan N.S., Debouck D.G., Kilian A., Hodkinson T.R., Spillane C (2016)  Origin of year-long bean (Phaseolus dumosus Macfady, Fabaceae) from reticulated hybridisation events between multiple Phaseolus species. Annals of Botany (in press).
42. Murray, U., Gebremedhin, Z., Brychkova, G. and Spillane, C., 2016. Smallholder Farmers and Climate Smart Agriculture Technology and Labor-productivity Constraints amongst Women Smallholders in Malawi. Gender, Technology and Development, p.0971852416640639.
43. Nguyen, V., Karunakaran, E., Collins, G. and Biggs, C.A., 2016. Physicochemical analysis of initial adhesion and biofilm formation of Methanosarcina barkeri on polymer support material. Colloids and Surfaces B: Biointerfaces, 143, pp.518-525.
44. Nitschke, U., & Stengel, D. B. (2016). Quantification of iodine loss in edible Irish seaweeds during processing. Journal of Applied Phycology, 1-7.
45. Nunes-Nesi, A., de Laia Nascimento, V., de Oliveira Silva, F. M., Zsögön, A., Araújo, W. L., & Sulpice, R. (2016). Natural genetic variation for morphological and molecular determinants of plant growth and yield. Journal of Experimental Botany, erw124.
46. O'Flaherty, V. and McCay P (2016). Antimicrobial compositions and methods for their  production. U.S. Patent 20,160,074,436, issued March 17, 2016.
47. O’Hagan CP, O’Brien BJ, Leen SB, Monaghan RF. (2016) A microstructural investigation into the accelerated corrosion of P91 steel during biomass co-firing. Corrosion Science. 2016 Mar 26.
48. Olsen, S., Popper, Z.A. and Krause, K., 2016. Two sides of the same coin: Xyloglucan endotransglucosylases/hydrolases in host infection by the parasitic plant Cuscuta. Plant signaling & behavior, 11(3), p.e1145336.
49. Pandey, D.S., Kwapinska, M., Gómez-Barea, A., Horvat, A., Fryda, L.E., Rabou, L.P., Leahy, J.J. and Kwapinski, W., 2016. Poultry litter gasification in a fluidized bed reactor: effects of gasifying agent and limestone addition. Energy & Fuels, 30(4), pp.3085-3096.
50. Peyer LC, Zannini E, Arendt EK. Lactic Acid Bacteria as Sensory Biomodulators for Fermented Cereal-Based Beverages. Trends in Food Science & Technology. 2016 May 14.
51. Peyton, D.P., Healy, M.G., Fleming, G.T.A., Grant, J., Wall, D., Morrison, L., Cormican, M. and Fenton, O., 2016. Nutrient, metal and microbial loss in surface runoff following treated sludge and dairy cattle slurry application to an Irish grassland soil. Science of The Total Environment, 541, p.218.
52. Pires, N. D., Bemer, M., Müller, L. M., Baroux, C., Spillane, C., & Grossniklaus, U. (2016). Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development. PLoS Genet, 12(1), e1005806.
53. Porwol L, Ojo A, Breslin JG. (2016) An ontology for next generation e-Participation initiatives. Government Information Quarterly. 2016 Feb 28.
54. Porwol L, Ojo A, Breslin JG. (2016) Social Software Infrastructure for e-Participation. Government Information Quarterly. 2016 Feb 28.
55. Raimundo, S. C., Avci, U., Hopper, C., Pattathil, S., Hahn, M. G., & Popper, Z. A. (2016). Immunolocalization of cell wall carbohydrate epitopes in seaweeds: presence of land plant epitopes in Fucus vesiculosus L.(Phaeophyceae). Planta, 243(2), 337-354.
56. Roba, K.T., O’Connor, T.P., Belachew, T. and O’Brien, N.M., 2016. Infant and Young Child Feeding (IYCF) Practices Among Mothers of Children Aged 6–23 Months in Two Agro-ecological Zones of Rural Ethiopia. Sciences, 5(3), pp.185-194.
57. Ross, S.A., Lane, J.A., Kilcoyne, M., Joshi, L. and Hickey, R.M., 2016. Defatted bovine milk fat globule membrane inhibits association of enterohaemorrhagic Escherichia coli O157: H7 with human HT-29 cells. International Dairy Journal, 59, pp.36-43.
58. Ross SA, Gerlach JQ, Gill SK, Lane JA, Kilcoyne M, Hickey RM, Joshi L. (2016) Temporal alterations in the bovine buttermilk glycome from parturition to milk maturation. Food Chemistry. 2016 May 6.
59. Robertson, R.C., Mateo, M.R.G., O'Grady, M.N., Guihéneuf, F., Stengel, D.B., Ross, R.P., Fitzgerald, G.F., Kerry, J.P. and Stanton, C., 2016. An assessment of the techno-functional and sensory properties of yoghurt fortified with a lipid extract from the microalga Pavlova lutheri. Innovative Food Science & Emerging Technologies.
60. Rubiano M, J.E., Cook, S., Rajasekharan, M. and Douthwaite, B., 2016. A Bayesian method to support global out-scaling of water-efficient rice technologies from pilot project areas. Water International, 41(2), pp.290-307.
61. Sae-leaw, T., Benjakul, S. and O'Brien, N.M., 2016. Effects of defatting and tannic acid incorporation during extraction on properties and fishy odour of gelatin from seabass skin. LWT-Food Science and Technology, 65, pp.661-667.
62. Sae‐leaw, T., O'Callaghan, Y.C., Benjakul, S. and O'Brien, N.M., 2016. Antioxidant, immunomodulatory and antiproliferative effects of gelatin hydrolysates from seabass (Lates calcarifer) skins. International Journal of Food Science & Technology.
63. Schmid, M., Guihéneuf, F., & Stengel, D. B. (2016). Evaluation of food grade solvents for lipid extraction and impact of storage temperature on fatty acid composition of edible seaweeds Laminaria digitata (Phaeophyceae) and Palmaria palmata (Rhodophyta). Food Chemistry, 208, 161-168.
64. Schmidt, M., Horstmann, S., De Colli, L., Danaher, M., Speer, K., Zannini, E. and Arendt, E.K., 2016. Impact of fungal contamination of wheat on grain quality criteria. Journal of Cereal Science, 69, pp.95-103.
65. Schreiner, M., Mewis, I., Neugart, S., Zrenner, R., Glaab, J., Wiesner, M. and Jansen, M.A., 2016. UV-B Elicitation of Secondary Plant Metabolites. In III-Nitride Ultraviolet Emitters (pp. 387-414). Springer International Publishing.
66. Serrano D, Kwapinska M, Horvat A, Sánchez-Delgado S, Leahy JJ. Cynara cardunculus L. gasification in a bubbling fluidized bed: The effect of magnesite and olivine on product gas, tar and gasification performance. Fuel. 2016 Jan 22.
67. Sikora, K. S., McPolin, D. O., & Harte, A. M. (2016). Effects of the thickness of cross-laminated timber (CLT) panels made from Irish Sitka spruce on mechanical performance in bending and shear. Construction and Building Materials, 116, 141-150.
68. Stewart, D., Graciet, E., & Wellmer, F. (2016). Molecular and regulatory mechanisms controlling floral organ development. FEBS Journal.
69. Subedi, R., Taupe, N., Pelissetti, S., Petruzzelli, L., Bertora, C., Leahy, J.J. and Grignani, C., 2016. Greenhouse gas emissions and soil properties following amendment with manure-derived biochars: influence of pyrolysis temperature and feedstock type. Journal of environmental management, 166, pp.73-83.
70. Subedi, R., Taupe, N., Ikoyi, I., Bertora, C., Zavattaro, L., Schmalenberger, A., Leahy, J.J. and Grignani, C., 2016. Chemically and biologically-mediated fertilizing value of manure-derived biochar. Science of the Total Environment, 550, pp.924-933.
71. Sun, Q., Ding, S., Wang, Y., Xu, L., Wang, D., Chen, J. and Zhang, C., 2016. In-situ characterization and assessment of arsenic mobility in lake sediments. Environmental Pollution, 214, pp.314-323.
72. Taupe, N.C., Lynch, D., Wnetrzak, R., Kwapinska, M., Kwapinski, W. and Leahy, J.J., 2016. Updraft gasification of poultry litter at farm-scale–A case study. Waste Management, 50, pp.324-333.
73. Taylor JP, Arendt EK. A fundamental study on the relationship between barley cultivar and hordeins in single cultivar beers. Journal of the Institute of Brewing. 2016 Jun 1;122(2):243-50.
74. Trazzi, P.A., Leahy, J.J., Hayes, M.H.B. and Kwapinski, W., 2016. Adsorption and desorption of phosphate on biochars. Journal of Environmental Chemical Engineering, 4(1), pp.37-46.
75. Tuohy, S., Winterlich, A., McGinley, B., Glavin, M., Jones, E., Denny, P. and Kilmartin, L., 2016. Evaluating the influence of packet loss on visual quality of perception for high bandwidth automotive networks. Signal Processing: Image Communication, 43, pp.15-27.
76. Ulaszewska, M.M., Trost, K., Stanstrup, J., Tuohy, K.M., Franceschi, P., Chong, M.F.F., George, T., Minihane, A.M., Lovegrove, J.A. and Mattivi, F., 2016. Urinary metabolomic profiling to identify biomarkers of a flavonoid-rich and flavonoid-poor fruits and vegetables diet in adults: the FLAVURS trial. Metabolomics, 12(2), pp.1-22.
77. Yang, J., Xu, X., Liu, M., Xu, C., Luo, W., Song, T., Du, H. and Kiely, G., 2016. Effects of Napier grass management on soil hydrologic functions in a karst landscape, southwestern China. Soil and Tillage Research, 157, pp.83-92.
78. Zhao, M., Zhang, C., Zeng, G., Cheng, M. and Liu, Y., 2016. A combined biological removal of Cd 2+ from aqueous solutions using Phanerochaete chrysosporium and rice straw. Ecotoxicology and Environmental Safety, 130, pp.87-92.

2015

1. Abberton, M., Batley, J., Bentley, A., Bryant, J., Cai, H., Cockram, J., ... & Yano, M. (2015). Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal
2. Abram, F. (2015). Systems-based approaches to unravel multi-species microbial community functioning. Computational and Structural Biotechnology Journal, 13, 24-32.
3. APHALO, P. J., JANSEN, M. A., MCLEOD, A. R., & URBAN, O. (2015). Ultraviolet radiation research: from the field to the laboratory and back. Plant, Cell & Environment, 38(5), 853-855.
4. Babenko, O. N., Brychkova, G., Sagi, M., & Alikulov, Z. A. (2015). Molybdenum application enhances adaptation of crested wheatgrass to salinity stress. Acta Physiologiae Plantarum, 37(2), 1-13
5. Baerenfaller, K., Massonnet, C., Hennig, L., Russenberger, D., Sulpice, R., Walsh, S., ... & Gruissem, W. (2015). A long photoperiod relaxes energy management in Arabidopsis leaf six. Current Plant Biology, 2, 34-45.
6. Bayer, P. E., Ruperao, P., Mason, A. S., Stiller, J., Chan, C. K. K., Hayashi, S., ... & Edwards, D. (2015). High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics, 1-9.
7. Brychkova, G., Yarmolinsky, D., Batushansky, A., Grishkevich, V., Khozin-Goldberg, I., Fait, A., ... & Sagi, M. (2015). Sulfite Oxidase Activity Is Essential for Normal Sulfur, Nitrogen and Carbon Metabolism in Tomato Leaves. Plants, 4(3), 573-605.
8. Chen, H., Zhang, C., Deng, Y., Zhou, S., Zheng, Y., Ma, S., ... & Zhuang, W. (2015). Identification of low Ca2+ stress‐induced embryo apoptosis response genes in Arachis hypogaea by SSH‐associated library lift (SSHaLL). Plant Biotechnology Journal.
9. Cubry, P., Gallagher, E., O’Connor, E., & Kelleher, C. T. (2015). Phylogeography and population genetics of black alder (Alnus glutinosa (L.) Gaertn.) in Ireland: putting it in a European context. Tree Genetics & Genomes, 11(5), 1-15.
10. da Silva, R. P., Heiss, C., Black, I., Azadi, P., Gerlach, J. Q., Travassos, L. R., ... & Puccia, R. (2015). Extracellular vesicles from Paracoccidioides pathogenic species transport polysaccharide and expose ligands for DC-SIGN receptors. Scientific reports, 5, 14213.
11. Deokar, A. A., Kondawar, V., Kohli, D., Aslam, M., Jain, P. K., Karuppayil, S. M., ... & Srinivasan, R. (2015). The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor. Functional & integrative genomics, 15(1), 27-46.
12. Devkota, M., Gupta, R. K., Martius, C., Lamers, J. P. A., Devkota, K. P., Sayre, K. D., & Vlek, P. L. G. (2015). Soil salinity management on raised beds with different furrow irrigation modes in salt-affected lands. Agricultural Water Management, 152, 243-250.
13. Devkota, K. P., Hoogenboom, G., Boote, K. J., Singh, U., Lamers, J. P. A., Devkota, M., & Vlek, P. L. G. (2015). Simulating the impact of water saving irrigation and conservation agriculture practices for rice–wheat systems in the irrigated semi-arid drylands of Central Asia. Agricultural and Forest Meteorology, 214, 266-280.
14. Devkota, K. P., Lamers, J. P. A., Manschadi, A. M., Devkota, M., McDonald, A. J., & Vlek, P. L. G. (2015). Comparative advantages of conservation agriculture based rice–wheat rotation systems under water and salt dynamics typical for the irrigated arid drylands in Central Asia. European Journal of Agronomy, 62, 98-109
15. Deokar, A. A., Kondawar, V., Kohli, D., Aslam, M., Jain, P. K., Karuppayil, S. M., ... & Srinivasan, R. (2015). The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor. Functional & integrative genomics, 15(1), 27-46.
16. Farrell, N., O’Donoghue, C., & Morrissey, K. (2015). Quantifying the uncertainty of wave energy conversion device cost for policy appraisal: An Irish case study. Energy Policy, 78, 62-77.
17. Faye, I., Pandey, M. K., Hamidou, F., Rathore, A., Ndoye, O., Vadez, V., & Varshney, R. K. Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal. Euphytica, 1-17.
18. Fernández A., Grienke U, Soler-Vila A, Guihéneuf F, Stengel DB, Tasdemir D (2015). Seasonal and geographical variations in the biochemical composition of the blue mussel ( Mytilus edulis L.) from Ireland. Food Chemistry 77, 43-52. DOI 10.1016/j.foodchem.2014.12
19. Flis, A., Fernández, A. P., Zielinski, T., Mengin, V., Sulpice, R., Stratford, K., ... & Millar, A. J. (2015). Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biology, 5(10), 150042.
20. Fort, A., Ryder, P., McKeown, P. C., Wijnen, C., Aarts, M. G., Sulpice, R., & Spillane, C. (2015). Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New Phytologist
21. Fosu-Mensah, B. Y., Vlek, P. L., Manske, G., & Mensah, M. (2015). The Influenec of Azolla pinnata on Floodwater Chemistry, Grain Yield and Nitrogen Uptake of Rice in Dano, Southwestern Burkina Faso. Journal of Agricultural Science, 7(8), p118.
22. Gahan, J., & Schmalenberger, A. (2015). Arbuscular mycorrhizal hyphae in grassland select for a diverse and abundant hyphospheric bacterial community involved in sulfonate desulfurization. Applied Soil Ecology, 89, 113-121.
23. Grace, M. A., Healy, M. G., & Clifford, E. (2015). Use of industrial by-products and natural media to adsorb nutrients, metals and organic carbon from drinking water. Science of The Total Environment, 518, 491-497.
24. Guihéneuf, F., Mimouni, V., Tremblin, G., & Ulmann, L. (2015). Light intensity regulates the LC-PUFA incorporation into lipids of Pavlova lutheri and the final desaturase and elongase activities involved in their biosynthesis. Journal of agricultural and food chemistry.
25. Guihéneuf, F., & Stengel, D. B. (2015). Towards the biorefinery concept: Interaction of light, temperature and nitrogen for optimizing the co-production of high-value compounds in Porphyridium purpureum. Algal Research, 10, 152-163.
26. Gopalakrishnan, S., Srinivas, V., Alekhya, G., Prakash, B., Kudapa, H., Rathore, A., & Varshney, R. K. (2015). The extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum Streptomyces sp. in chickpea. SpringerPlus, 4(1), 31.
27. Gopalakrishnan, S., Srinivas, V., Alekhya, G., Prakash, B., Kudapa, H., & Varshney, R. K. (2015). Evaluation of Streptomyces sp. obtained from herbal vermicompost for broad spectrum of plant growth-promoting activities in chickpea. Organic Agriculture, 1-11.
28. Grace, M. A., Clifford, E., & Healy, M. G. A novel filtration configuration for targeted humic acid removal from drinking water.
29. Gunnigle, E., Siggins, A., Botting, C. H., Fuszard, M., O’Flaherty, V., & Abram, F. (2015). Low-temperature anaerobic digestion is associated with differential methanogenic protein expression. FEMS microbiology letters, fnv059
30. Haig, S. J., Quince, C., Davies, R. L., Dorea, C. C., & Collins, G. (2015). The Relationship between Microbial Community Evenness and Function in Slow Sand Filters. mBio, 6(5), e00729-15.
31. Healy, M. G., Barrett, M., Lanigan, G. J., Serrenho, A. J., Ibrahim, T. G., Thornton, S. F., ... & Fenton, O. (2015). Optimizing nitrate removal and evaluating pollution swapping trade-offs from laboratory denitrification bioreactors. Ecological Engineering, 74, 290-301
32. Heinemann, A. B., Barrios-Perez, C., Ramirez-Villegas, J., Arango-Londoño, D., Bonilla-Findji, O., Medeiros, J. C., & Jarvis, A. (2015). Variation and impact of drought-stress patterns across upland rice target population of environments in Brazil. Journal of experimental botany, erv126.
33. Hernandez‐Kantun, J. J., Rindi, F., Adey, W., Heesch, S., Peña, V., Le Gall, L., & Gabrielson, P. W. (2015). Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans, and related European species L. hibernicum and L. bathyporum (Corallinales, Rhodophyta). Journal of Phycology.
34. Hickey, J. M., Gorjanc, G., Varshney, R. K., & Nettelblad, C. (2015). Imputation of Single Nucleotide Polymorphism Genotypes in Biparental, Backcross, and Topcross Populations with a Hidden Markov Model. Crop Science
35. Higgins NF, Connan S and Stengel DB (2015). Factors influencing the distribution of coastal lichens Hydropunctaria maura and Wahlenbergiella mucosa. Marine Ecology doi: 10.1111/maec.12239
36. Huang, B. E., Verbyla, K. L., Verbyla, A. P., Raghavan, C., Singh, V. K., Gaur, P., ... & Cavanagh, C. R. (2015). MAGIC populations in crops: current status and future prospects. Theoretical and Applied Genetics, 1-19.
37. Ibrahim, T. G., Goutelle, A., Healy, M. G., Brennan, R., Tuohy, P., Humphreys, J., ... & Fenton, O. (2015). Mixed Agricultural Pollutant Mitigation Using Woodchip/Pea Gravel and Woodchip/Zeolite Permeable Reactive Interceptors. Water, Air, & Soil Pollution, 226(3), 1-11.
38. Ishihara, H., Obata, T., Sulpice, R., Fernie, A. R., & Stitt, M. (2015). Quantifying Protein Synthesis and Degradation in Arabidopsis by Dynamic 13 CO.
39. JADHAV, A., RAYATE, S., MHASE, L., THUDI, M., CHITIKINENI, A., HARER, P., ... & KULWAL, P. Marker-trait association study for protein content in chickpea (Cicer arietinum L.). Journal of Genetics, 1-8.
40. Janila, P., Pandey, M. K., Shasidhar, Y., Variath, M. T., Sriswathi, M., Khera, P., ... & Varshney, R. K. (2015). Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes. Plant Science.
41. Jenko, J., Gorjanc, G., Cleveland, M. A., Varshney, R. K., Whitelaw, C. B. A., Woolliams, J. A., & Hickey, J. M. (2015). Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs. Genetics Selection Evolution, 47(1), 1-14.
42. Kashiwagi, J., Krishnamurthy, L., Purushothaman, R., Upadhyaya, H. D., Gaur, P. M., Gowda, C. L. L., ... & Varshney, R. K. (2015). Scope for improvement of yield under drought through the root traits in chickpea (Cicer arietinum L.). Field Crops Research, 170, 47-54.
43. Khera, P., Saxena, R., Sameerkumar, C. V., Saxena, K., & Varshney, R. K. (2015). Mitochondrial SSRs and their utility in distinguishing wild species, CMS lines and maintainer lines in pigeonpea (Cajanus cajan L.). Euphytica, 1-10.
44. Khoury, C. K., Castañeda-Alvarez, N. P., Achicanoy, H. A., Sosa, C. C., Bernau, V., Kassa, M. T., ... & Struik, P. C. (2015). Crop wild relatives of pigeonpea [Cajanus cajan (L.) Millsp.]: Distributions, ex situ conservation status, and potential genetic resources for abiotic stress tolerance. Biological Conservation, 184, 259-270.
45. Klem, K., Holub, P., Štroch, M., Nezval, J., Špunda, V., Tříska, J., ... & Urban, O. (2015). Ultraviolet and photosynthetically active radiation can both induce photoprotective capacity allowing barley to overcome high radiation stress. Plant Physiology and Biochemistry.
46. Kole, C., Muthamilarasan, M., Henry, R., Edwards, D., Sharma, R., Abberton, M., ... & Prasad, M. (2015). Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects. Frontiers in Plant Science, 6, 563.
47. Korir, P. K., Geeleher, P., & Seoighe, C. (2015). Seq-ing improved gene expression estimates from microarrays using machine learning. BMC bioinformatics, 16(1), 286.
48. Lahive, E., O'Halloran, J., & Jansen, M. A. K. (2015). A marriage of convenience; a simple food chain comprised of Lemna minor (L.) and Gammarus pulex (L.) to study the dietary transfer of zinc. Plant Biology, 17(s1), 75-81.
49. Llorens, L., Badenes-Pérez, F. R., Julkunen-Tiitto, R., Zidorn, C., Fereres, A., & Jansen, M. A. (2015). The role of UV-B radiation in plant sexual reproduction. Perspectives in Plant Ecology, Evolution and Systematics.
50. Longphuirt, S. N., O'Boyle, S., & Stengel, D. B. (2015). Environmental response of an Irish estuary to changing land management practices. Science of The Total Environment, 521, 388-399.
51. Moynihan, E. L., Richards, K. G., Brennan, F. P., Tyrrel, S. F., & Ritz, K. (2015). Enteropathogen survival in soil from different land-uses is predominantly regulated by microbial community composition. Applied Soil Ecology, 89, 76-84.
52. Murnane, J. G., Brennan, R. B., Healy, M. G., & Fenton, O. (2015). Use of Zeolite with Alum and Polyaluminum Chloride Amendments to Mitigate Runoff Losses of Phosphorus, Nitrogen, and Suspended Solids from Agricultural Wastes Applied to Grassed Soils. Journal of Environmental Quality.
53. Murphy, S., Jordan, P., Mellander, P. E., & O'Flaherty, V. (2015). Quantifying faecal indicator organism hydrological transfer pathways and phases in agricultural catchments. Science of The Total Environment, 520, 286-299
54. Nielsen, M. M., Kumar, J. P., Soler-Vila, A., Johnson, M. P., & Bruhn, A. (2015). Early stage growth responses of Saccharina latissima spores and gametophytes. Part 1: inclusion of different phosphorus regimes. Journal of Applied Phycology, 1-7.
55. Nyarko, B. K., Diekkrüger, B., Van De Giesen, N. C., & Vlek, P. L. (2015). Floodplain wetland mapping in the White Volta River Basin of Ghana. GIScience & Remote Sensing, (ahead-of-print), 1-22.
56. O’Boyle, S., Wilkes, R., McDermott, G., Longphuirt, S. N., & Murray, C. (2015). Factors affecting the accumulation of phytoplankton biomass in Irish estuaries and nearshore coastal waters: A conceptual model. Estuarine, Coastal and Shelf Science.
57. O’Driscoll, A., Doohan, F., & Mullins, E. (2015). Exploring the utility of Brachypodium distachyon as a model pathosystem for the wheat pathogen Zymoseptoria tritici. BMC research notes, 8(1), 132.
58. O'Doherty A., MacHugh D., Spillane C., & Magee D. (2015). Genomic imprinting effects on complex traits in domesticated animal species. Frontiers in Genetics, 6, 156.
59. O’Donovan, P., Coburn, D., Jones, E., Hannon, L., Glavin, M., Mullins, D., & Clifford, E. (2015). A Cloud-based Distributed Data Collection System for Decentralised Wastewater Treatment Plants. Procedia Engineering, 119, 464-469.
60. O’Flynn, M. G., Finnan, J. M., Curley, E. M., & McDonnell, K. P. (2015). Annually repeated traffic in delayed Miscanthus× giganteus harvests; effects on crop response and mitigation measures. Soil and Tillage Research, 148, 133-141.
61. Ojiewo, C., Keatinge, D. J., Hughes, J., Tenkouano, A., Nair, R., Varshney, R., ... & Silim, S. (2015). The Role of Vegetables and Legumes in Assuring Food, Nutrition, and Income Security for Vulnerable Groups in Sub‐Saharan Africa. World Medical & Health Policy, 7(3), 187-210.
62. Ó’Maoiléidigh, D. S., Thomson, B., Raganelli, A., Wuest, S. E., Ryan, P. T., Kwaśniewska, K., ... & Wellmer, F. (2015). Gene network analysis in Arabidopsis thaliana flower development through dynamic gene perturbations. The Plant Journal.
63. Pazhamala, L., Saxena, R. K., Singh, V. K., Sameerkumar, C., Kumar, V., Sinha, P., ... & Varshney, R. K. (2015). Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan). Name: Frontiers in Plant Science, 6, 50.
64. Peyton, D. P., Healy, M. G., Fleming, G. T. A., Grant, J., Wall, D., Morrison, L., ... & Fenton, O. (2015). Nutrient, metal and microbial loss in surface runoff following treated sludge and dairy cattle slurry application to an Irish grassland soil. Science of The Total Environment, 541, 218-229.
65. Phelan, S., Fitzgerald, T., Grant, J., Byrne, S., Meade, C., & Mullins, E. (2015). Propensity for seed-mediated gene flow from potato crops and potential consequences for the coexistence of GM and non-GM potato systems. European Journal of Agronomy, 67, 52-60.
66. Pletsers, A., Caffarra, A., Kelleher, C. T., & Donnelly, A. (2015). Chilling temperature and photoperiod influence the timing of bud burst in juvenile Betula pubescens Ehrh. and Populus tremulaL. trees. Annals of Forest Science, 1-13.
67. Purushothaman, R., Thudi, M., Krishnamurthy, L., Upadhyaya, H. D., Kashiwagi, J., Gowda, C. L. L., & Varshney, R. K. (2015). Association of mid-reproductive stage canopy temperature depression with the molecular markers and grain yields of chickpea (Cicer arietinum L.) germplasm under terminal drought. Field Crops Research, 174, 1-11.
68. Pushpavalli, R., Krishnamurthy, L., Thudi, M., Gaur, P. M., Rao, M. V., Siddique, K. H., ... & Vadez, V. (2015). Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2× JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines. BMC Plant Biology, 15(1), 124.
69. Ratcliff, J. J., Wan, A. H. L., Edwards, M. D., Soler-Vila, A., Johnson, M. P., Abreu, M. H., & Morrison, L. (2015). Metal content of kelp (Laminaria digitata) co-cultivated with Atlantic salmon in an Integrated Multi-Trophic Aquaculture system. Aquaculture.
70. Rathore, D. S., Lopez-Vernaza, M. A., Doohan, F., Connell, D. O., Lloyd, A., & Mullins, E. (2015). Profiling antibiotic resistance and electro-transformation potential of Ensifer adhaerens OV14; a non-Agrobacterium species capable of efficient rates of plant transformation. FEMS Microbiology Letters, fnv126.
71. Rautenberger, R., Fernández, P. A., Strittmatter, M., Heesch, S., Cornwall, C. E., Hurd, C. L., & Roleda, M. Y. (2015). Saturating light and not increased carbon dioxide under ocean acidification drives photosynthesis and growth in Ulva rigida (Chlorophyta). Ecology and evolution, 5(4), 874-888.
72. Reddy, P. S., Jogeswar, G., Rasineni, G. K., Maheswari, M., Reddy, A. R., Varshney, R. K., & Kishor, P. K. (2015). Proline over-accumulation alleviates salt stress and protects photosynthetic and antioxidant enzyme activities in transgenic sorghum [Sorghum bicolor (L.) Moench]. Plant Physiology and Biochemistry.
73. Rosado-Souza, L., Scossa, F., Chaves, I. S., Kleessen, S., Salvador, L. F., Milagre, J. C., ... & Nunes-Nesi, A. (2015). Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions. Planta, 1-15.
74. Ryan, P. T., Ó’Maoiléidigh, D. S., Drost, H. G., Kwaśniewska, K., Gabel, A., Grosse, I., ... & Wellmer, F. (2015). Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation. BMC Genomics, 16(1), 488.
75. Samineni, S., Kamatam, S., Thudi, M., Varshney, R. K., & Gaur, P. M. Vernalization response in chickpea is controlled by a major QTL. Euphytica, 1-9.
76. Saxena, R. K., Saxena, K. B., Pazhamala, L. T., Patel, K., Parupalli, S., Sameerkumar, C. V., & Varshney, R. K. (2015). Genomics for greater efficiency in pigeonpea hybrid breeding. Frontiers in Plant Science, 6, 793.
77. Schmengler, A. C., & Vlek, P. L. (2015). Assessment of accumulation rates in small reservoirs by core analysis, 137Cs measurements and bathymetric mapping in Burkina Faso. Earth Surface Processes and Landforms.
78. Schmid, M and Stengel, DB. (2015). Intra-thallus differentiation of fatty acid and pigment profiles in some temperate Fucales and Laminariales. J. Phycol. DOI: 10.1111/jpy.12268 
79. Singh, V. K., Khan, A. W., Saxena, R. K., Kumar, V., Kale, S. M., Sinha, P., ... & Varshney, R. K. (2015). Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnology Journal.
80. Sinha, P., Saxena, K. B., Saxena, R. K., Singh, V. K., Suryanarayana, V., Sameer Kumar, C. V., ... & Varshney, R. K. (2015). Association of Gene with Cytoplasmic Male Sterility in Pigeonpea. The Plant Genome, 8(2).
81. Smýkal, P., Coyne, C. J., Ambrose, M. J., Maxted, N., Schaefer, H., Blair, M. W., ... & Varshney, R. K. (2015). Legume crops phylogeny and genetic diversity for science and breeding. Critical Reviews in Plant Sciences, 34(1-3), 43-104.
82. de Sousa Cardoso, T. C., Portilho, L. G., Oliveira, C. L., McKeown, P. C., Maluf, W. R., Gomes, L. A. A., ... & Souza Gomes, M. (2015). Genome‐wide identification and in silico characterization of microRNAs, their targets and processing pathway genes in Phaseolus vulgaris L. Plant Biology.
83. Srikanth, S., Saxena, R. K., Rao, M. V., Varshney, R. K., & Mallikarjuna, N. (2015). Development of a new CMS system in pigeonpea utilizing crosses with Cajanus lanceolatus (WV Fitgz) van der Maesen. Euphytica, 1-14.
84. Srivastava, S., Zheng, Y., Kudapa, H., Jagadeeswaran, G., Hivrale, V., Varshney, R. K., & Sunkar, R. (2015). High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. Plant Science, 235, 46-57.
85.  Sulpice R & McKeown PC (2015) Moving Toward a Comprehensive Map of Central Plant Metabolism. Annual review of plant biology. 63.
86. Varshney, R. K., Kudapa, H., Pazhamala, L., Chitikineni, A., Thudi, M., Bohra, A., ... & Ellis, N. (2015). Translational genomics in agriculture: some examples in grain legumes. Critical Reviews in Plant Sciences, 34(1-3), 169-194.
87. Varshney, R. K. (2015, July). Whole Genome Re-Sequencing for Pigeonpea Improvement. In PAG ASIA 2015. Plant and Animal Genome.
88. Varshney, R. K. (2015). Exciting journey of 10 years from genomes to fields and markets: some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut. Plant Science.
89. Váry, Z., Mullins, E., McElwain, J. C., & Doohan, F. M. (2015). The severity of wheat diseases increases when plants and pathogens are acclimatized to elevated carbon dioxide. Global Change Biology.
90. Wellmer, F., Stewart, D., & O’Maoileidigh, D. S. (2015). My favourite flowering image: floral organs with trichomes. Journal of Experimental Botany, 66(23), 9-10.
91. Yamaguchi, N., Winter, C. M., Wellmer, F., & Wagner, D. (2015). Identification of Direct Targets of Plant Transcription Factors Using the GR Fusion Technique. Plant Functional Genomics: Methods and Protocols, 123-138.
92. Zuniga-Soto, E., Mullins, E., & Dedicova, B. (2015). Ensifer-mediated transformation: an efficient non-Agrobacterium protocol for the genetic modification of rice. SpringerPlus, 4(1), 600.

2014

1. Asam, Z. U. Z., Nieminen, M., O’Driscoll, C., O’Connor, M., Sarkkola, S., Kaila, A., ... & Xiao, L. (2014). Export of phosphorus and nitrogen from lodgepole pine (Pinus contorta) brash windrows on harvested blanket peat forests. Ecological Engineering, 64, 161-170.
2. Axel, C., Zannini, E., Arendt, E. K., Waters, D. M., & Czerny, M. (2014). Quantification of cyclic dipeptides from cultures of Lactobacillus brevis R2Δ by HRGC/MS using stable isotope dilution assay. Analytical and bioanalytical chemistry, 406(9-10), 2433-2444.
3. Arrivault, S., Guenther, M., Florian, A., Encke, B., Feil, R., Vosloh, D., ... & Schulze, W. X. (2014). Dissecting the subcellular compartmentation of proteins and metabolites in Arabidopsis leaves using non-aqueous fractionation. Molecular & Cellular Proteomics, mcp-M114.
4. Baer, J., & Stengel, D. B. (2014, January). Can Native Epiphytes Affect Establishment Success of the Alien Seaweed Sargassum Muticum (Phaeophyceae)?. In Biology & Environment: Proceedings of the Royal Irish Academy (Vol. 114, No. 1, pp. 1-12). The Royal Irish Academy.
5. Beatty, G. E., Barker, L., Chen, P. P., Kelleher, C. T., & Provan, J. (2014). Cryptic introgression into the kidney saxifrage (Saxifraga hirsuta) from its more abundant sympatric congener Saxifraga spathularis, and the potential risk of genetic assimilation. Annals of botany, mcu226.
6. Beltman, M. E., Mullen, M. P., Elia, G., Hilliard, M., Diskin, M. G., Evans, A. C., & Crowe, M. A. (2014). Global proteomic characterization of uterine histotroph recovered from beef heifers yielding good quality and degenerate day 7 embryos. Domestic animal endocrinology, 46, 49-57.
7. Berry, D. P., McClure, M. C., & Mullen, M. P. (2014). Within‐and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium‐and low‐density genotypes. Journal of Animal Breeding and Genetics, 131(3), 165-172.
8. Berry, D. P., McParland, S., Kearney, J. F., Sargolzaei, M., & Mullen, M. P. (2014). Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes. Animal, 8(06), 895-903.
9. Brennan, F. P., Moynihan, E., Griffiths, B. S., Hillier, S., Owen, J., Pendlowski, H., & Avery, L. M. (2014). Clay mineral type effect on bacterial enteropathogen survival in soil. Science of the total environment, 468, 302-305.
10. Brennan, R. B., Wall, D. P., Fenton, O., Grant, J., Sharpley, A. N., & Healy, M. G. (2014). Impact of Chemical Amendment of Dairy Cattle Slurry on Soil Phosphorus Dynamics Following Application to Five Soils. Communications in Soil Science and Plant Analysis, 45(16), 2215-2233.
11. Bialek, K., Cysneiros, D., & O’Flaherty, V. (2014). Hydrolysis, acidification and methanogenesis during low-temperature anaerobic digestion of dilute dairy wastewater in an inverted fluidised bioreactor. Applied microbiology and biotechnology, 1-14.
12. Boualem, A., Fleurier, S., Troadec, C., Audigier, P., Kumar, A. P., Chatterjee, M., ... & Bendahmane, A. (2014). Development of a Cucumis sativus TILLinG Platform for Forward and Reverse Genetics. PloS one, 9(5), e97963.
13. Brosnan, B., Coffey, A., Arendt, E. K., & Furey, A. (2014). The QuEChERS approach in a novel application for the identification of antifungal Compounds produced by lactic acid bacteria cultures. Talanta.
14. Brosnan, B., Coffey, A., Arendt, E., & Furey, A. (2014). A Comprehensive Investigation into Sample Extraction and Method Validation for the Identification of Antifungal Compounds produced by Lactic Acid Bacteria using both HPLC-UV/DAD and LC-FTMS. Analytical Methods.
15. Capuani, A., Behr, J., Arendt, E. K., & Vogel, R. F. (2014). Impact of ‘oxidizing’and ‘reducing’ buckwheat sourdoughs on brown rice and buckwheat batter and bread. European Food Research and Technology, 238(6), 979-988.
16. Cerrone, F., Choudhari, S. K., Davis, R., Cysneiros, D., O’Flaherty, V., Duane, G., ... & O’Connor, K. (2014). Medium chain length polyhydroxyalkanoate (mcl-PHA) production from volatile fatty acids derived from the anaerobic digestion of grass. Applied microbiology and biotechnology, 98(2), 611-620.
17. Chen, X., Daniell, T. J., Neilson, R., O'Flaherty, V., & Griffiths, B. S. (2014). Microbial and microfaunal communities in phosphorus limited, grazed grassland change composition but maintain homeostatic nutrient stoichiometry. Soil Biology and Biochemistry, 75, 94-101.
18. Cott, G. M., Chapman, D. V., & Jansen, M. A. (2014). Differences in nitrogen‐assimilating enzyme activity in halophyte species are habitat‐related. Journal of Plant Nutrition and Soil Science, 177(5), 705-713.
19. Dasgupta, K., Khadilkar, A. S., Sulpice, R., Pant, B., Scheible, W. R., Fisahn, J., ... & Ayre, B. G. (2014). Expression of Sucrose Transporter cDNAs Specifically in Companion Cells Enhances Phloem Loading and Long-Distance Transport of Sucrose but Leads to an Inhibition of Growth and the Perception of a Phosphate Limitation. Plant physiology, 165(2), 715-731.
20. Devaney, J. L., Jansen, M. A., & Whelan, P. M. (2014). Spatial patterns of natural regeneration in stands of English yew (Taxus baccata L.); Negative neighbourhood effects. Forest Ecology and Management, 321, 52-60.
21. Donoghue MT, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinksi ML, Borevitz JO, Spillane C.(2014) C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants. DNA Research. 2014;21(2):141- 51.
22. Domozych DS, Sørensen I, Sacks C, Brechka H, Andreas A, Fangel JU, Rose JK, Willats WG, Popper ZA. (2014) Disruption of the microtubule network alters cellulose deposition and causes major changes in pectin distribution in the cell wall of the green alga, Penium margaritaceum 65:465-79.
23. Domozych DS, Sørensen I, Popper ZA, Ochs J, Andreas A, Fangel JU, Pielach A, Sacks C, Brechka H, Ruisi-Besares P, Willats WG, Rose JK. (2014) Pectin metabolism and assembly in the cell wall of the charophyte green alga Penium margaritaceum. Plant Physiol. 2014 May;165(1):105-18.
24. Dussan, K., Girisuta, B., Haverty, D., Leahy, J. J., & Hayes, M. H. B. (2014). The Effect of Hydrogen Peroxide Concentration and Solid Loading on the Fractionation of Biomass in Formic Acid. Carbohydrate Polymers.
25. Eeckhout S, Leroux O, Willats WG, Popper ZA, Viane RL. (2014) Comparative glycan profiling of Ceratopteris richardii 'C-Fern' gametophytes and sporophytes links cell-wall composition to functional specialization. Ann Bot. 2014 Apr 3.
26. Ernfors, M., Brennan, F. P., Richards, K. G., McGeough, K. L., Griffiths, B. S., Laughlin, R. J., ... & MÜLLER, C. (2014). The nitrification inhibitor dicyandiamide increases mineralization–immobilization turnover in slurry-amended grassland soil. The Journal of Agricultural Science, 152(S1), 137-149.
27. Faltermaier, A., Waters, D., Becker, T., Arendt, E., & Gastl, M. (2014). Common wheat (Triticum aestivum L.) and its use as a brewing cereal–a review. Journal of the Institute of Brewing, 120(1), 1-15.
28. Fatima A, Waters S, O'Boyle P, Seoighe C, Morris DG. (2014) Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle. BMC Genomics. 2014 Jan 15;15(1):28.
29. Fatima, A., Lynn, D. J., Padraic, O., Seoighe, C., & Morris, D. (2014). The miRNAome of the postpartum dairy cow liver in negative energy balance. BMC genomics, 15(1), 279.
30. Fenton, O., Healy, M. G., Brennan, F., Jahangir, M. M. R., Lanigan, G. J., Richards, K. G., ... & Ibrahim, T. G. (2014). Permeable reactive interceptors: blocking diffuse nutrient and greenhouse gases losses in key areas of the farming landscape. The Journal of Agricultural Science, 1-11.
31. Figueroa FL, Conde-Álvarez R, Bonomi Barufi J, Celis-Plá PSM, Flores P, Malta EJ, Stengel DB, Meyerhoff O, Pérez-Ruzafa A (2014). Continuous monitoring of  in vivo chlorophyll  a fluorescence in  Ulva rigida (Chlorophyta) submitted to different CO2, nutrient and temperature regimes. Aquatic Biology 22:195-212 doi: 10.3354/ab00593 
32. Figueroa FL, Bonomi Barufi J, Malta EJ, Conde-Álvarez R, Nitschke U, Arenas F, Mata M, Connan S, Abreu MH, Marquardt R, Vaz-Pinto F, Konotchick T, Celis-Plá PSM, Hermoso M, Ordoñez G, Ruiz E, Flores P, de los Ríos J, Kirke D, Chow F, Nassar CAG, Robledo D, Pérez-Ruzafa Á, Bañares-España E, Altamirano M, Jiménez C, Korbee N, Bischof K, Stengel DB. (2014). Short-term effects of increasing CO2, nitrate and temperature on three Mediterranean macroalgae: biochemical composition. Aquatic Biology 22:177-193 
33. Finnegan, J., Regan, J. T., Fenton, O., Lanigan, G. J., Brennan, R. B., & Healy, M. G. (2014). The short-term effects of management changes on watertable position and nutrients in shallow groundwater in a harvested peatland forest. Journal of environmental management, 142, 46-52.
34. Finnegan, J., Regan, J. T., O’Connor, M., Wilson, P., & Healy, M. G. (2014). Implications of applied best management practice for peatland forest harvesting. Ecological Engineering, 63, 12-26.
35. Fitzhenry, K., Barrett, M., O'Flaherty, V., Dore, W., Keaveney, S., Cormican, M., & Clifford, E. (2014). Detection and removal of pathogenic norovirus employing tertiary treatment in wastewater and water treatment facilities. Water Practice & Technology, 9(3), 370-376.
36. Florian, A., Nikoloski, Z., Sulpice, R., Timm, S., Araújo, W. L., Tohge, T., ... & Fernie, A. R. (2014). Analysis of short-term metabolic alterations in Arabidopsis following changes in the prevailing environmental conditions. Molecular Plant, ssu008.
37. Fox, A., Kwapinski, W., Griffiths, B. S., & Schmalenberger, A. (2014). The role of sulfur-and phosphorus-mobilizing bacteria in biochar-induced growth promotion of Lolium perenne. FEMS microbiology ecology, 90(1), 78-91.
38. Fu, W., Fu, Z., Zhao, K., Tunney, H., & Zhang, C. (2014). Variation of soil P and other nutrients in a long-term grazed grassland P experiment field. Archives of Agronomy and Soil Science, (jin press).
39. Gahan, J., & Schmalenberger, A. (2014). The role of bacteria and mycorrhiza in plant sulfur supply. Frontiers in plant science, 5.
40. Galle, Sandra, and Elke K. Arendt. "Exopolysaccharides from Sourdough Lactic Acid Bacteria." Critical reviews in food science and nutrition 54.7 (2014): 891-901.
41. Girma G, Hyma KE, Asiedu R, Mitchell SE, Gedil M, Spillane C. (2014) Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of guinea yams. Theor Appl Genet. 2014 Jul 1.
42. Graciet, E., Ó’Maoiléidigh, D. S., & Wellmer, F. (2014). Next-Generation Sequencing Applied to Flower Development: ChIP-Seq. In Flower Development (pp. 413-429). Springer New York.
43. Guihéneuf, F., Schmid, M., & Stengel, D. B. (2015). Lipids and Fatty Acids in Algae: Extraction, Fractionation into Lipid Classes, and Analysis by Gas Chromatography Coupled with Flame Ionization Detector (GC-FID). Natural Products From Marine Algae: Methods and Protocols, 173-190.
44. Hager, A. S., Taylor, J. P., Waters, D. M., & Arendt, E. K. (2014). Gluten free beer–A review. Trends in Food Science & Technology, 36(1), 44-54.
45. Hager, A. S., Mäkinen, O. E., & Arendt, E. K. (2014). Amylolytic activities and starch reserve mobilization during the germination of quinoa. European Food Research and Technology, 1-7.
46. Hectors, K., Van Oevelen, S., Geuns, J., Guisez, Y., Jansen, M. A., & Prinsen, E. (2014). Dynamic changes in plant secondary metabolites during UV acclimation in Arabidopsis thaliana. Physiologia plantarum.
47. Hincha, D. K., Schulz, E., Thalhammer, A., Tohge, T., Sulpice, R., Fernie, A. R., & Zuther, E. (2014, May). The Role of Secondary Metabolites and COR Proteins in Plant Freezing Tolerance. In IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL (Vol. 50, pp. S13-S13). 233 SPRING ST, NEW YORK, NY 10013 USA: SPRINGER.
48. Howley, P., Yadav, L., Hynes, S., Donoghue, C. O., & Neill, S. O. (2014). Contrasting the attitudes of farmers and the general public regarding the ‘multifunctional’role of the agricultural sector. Land Use Policy, 38, 248-256.
49. James, T. C., Gallagher, L., Titze, J., Bourke, P., Kavanagh, J., Arendt, E., & Bond, U. (2014). In situ production of human β defensin‐3 in lager yeasts provides bactericidal activity against beer‐spoiling bacteria under fermentation conditions. Journal of applied microbiology, 116(2), 368-379.
50. Jones, C. M., Spor, A., Brennan, F. P., Breuil, M. C., Bru, D., Lemanceau, P., ... & Philippot, L. (2014). Recently identified microbial guild mediates soil N2O sink capacity. Nature Climate Change, 4(9), 801-805.
51. Julkunen-Tiitto, R., Nenadis, N., Neugart, S., Robson, M., Agati, G., Vepsäläinen, J., ... & Jansen, M. A. (2014). Assessing the response of plant flavonoids to UV radiation: an overview of appropriate techniques. Phytochemistry Reviews, 1-25.
52. Kagale S, Koh C, Nixon J, Bollina V, Clarke WE, Tuteja R, Spillane C, Robinson SJ, Links MG, Clarke C, Higgins EE, Huebert T, Sharpe AG, Parkin IA. (2014) The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nature Communications 2014 Apr 23;5:3706.
53. Keegan, M., Kilroy, K., Nolan, D., Dubber, D., Johnston, P. M., Misstear, B. D., ... & Gill, L. W. (2014). Assessment of the impact of traditional septic tank soakaway systems on water quality in Ireland. Water Science & Technology, 70(4), 634-641.
54. Kehoe, J. J., Lišková, K., Mok, K. H., O'Brien, N., Kelly, A. L., & Brodkorb, A. (2014). Formation of cytotoxic α-lactalbumin/ sodium oleate complexes: Concentration and temperature effects. International Dairy Journal, 38(1), 65-73.
55. Kenny, O., Smyth, T. J., Walsh, D., Kelleher, C. T., Hewage, C. M., & Brunton, N. P. (2014). Investigating the potential of under-utilised plants from the Asteraceae family as a source of natural antimicrobial and antioxidant extracts. Food chemistry, 161, 79-86.
56. Killeen, A. P., Morris, D. G., Kenny, D. A., Mullen, M. P., Diskin, M. G., & Waters, S. M. (2014). Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle. BMC genomics, 15(1), 234.
57. Kleessen, Sabrina, Roosa Laitinen, Corina M. Fusari, Carla Antonio, Ronan Sulpice, Alisdair R. Fernie, Mark Stitt, and Zoran Nikoloski. "Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana." Nature Communications 5 (2014).
58. Korir PK, Seoighe C. (2014) Inference of Allele-Specific Expression from RNA-seq Data. Methods Mol Biol. 2014;1112:49-69.
59. Korir, P. K., Roberts, L., Ramesar, R., & Seoighe, C. (2014). A mutation in a splicing factor that causes retinitis pigmen-tosa has a transcriptome-wide effect on mRNA splicing. BMC research notes, 7(1), 401.
60. Kumar, P. A., Bhattacharya, A., Dutta, O. P., & Chatterjee, M. (2014). Allele Discovery Platform (ADP) in Papaya (Carica papaya L.). In Genetics and Genomics of Papaya (pp. 409-421). Springer New York.
61. Legg, J., Somado, E. A., Barker, I., Beach, L., Ceballos, H., Cuellar, W., ... & Fauquet, C. (2014). A global alliance declaring war on cassava viruses in Africa. Food Security, 6(2), 231-248.
62. Li, Z., Liu, Y., Kwapinski, W., & Leahy, J. J. (2014). ZrO2-modified TiO2 nanorod composite: Hydrothermal synthesis, characterization and application in esterification of organic acid. Materials Chemistry and Physics, 145(1), 82-89.
63. Liu, L., Farrona, S., Klemme, S., & Turck, F. K. (2014). Post-fertilization expression of FLOWERING LOCUS T suppresses reproductive reversion. Frontiers in Plant Science, 5, 164. doi:10.3389/fpls.2014.00164
64. Lucid, J. D., Fenton, O., Grant, J., & Healy, M. G. (2014). Effect of Rainfall Time Interval on Runoff Losses of Biosolids and Meat and Bone Meal when Applied to a Grassland Soil. Water, Air, & Soil Pollution, 225(8), 1-11.
65. Lynch, D., Low, F., Henihan, A. M., Garcia, A., Kwapinski, W., Zhang, L., & Leahy, J. J. (2014). Behavior of heavy metals during fluidized bed combustion of poultry litter. Energy & Fuels.
66. Lynch, K. M., Pawlowska, A. M., Brosnan, B., Coffey, A., Zannini, E., Furey, A., ... & Arendt, E. K. (2014). Application of Lactobacillus amylovorus as an antifungal adjunct to extend the shelf-life of Cheddar cheese. International Dairy Journal, 34(1), 167-173.
67. Lynch, K. M., McSweeney, P. L., Arendt, E. K., Uniacke-Lowe, T., Galle, S., & Coffey, A. (2014). Isolation and characterisation of exopolysaccharide-producing Weissella and Lactobacillus and their application as adjunct cultures in Cheddar cheese. International Dairy Journal, 34(1), 125-134.
68. Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. (2014) Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Animal Genetics. 2014 Jul 2. doi: 10.1111/age.12168.
69. McArdle, S., Leahy, J. J., Curtin, T., & Tanner, D. (2014). Hydrogenation of sunflower oil over Pt–Ni bimetallic supported catalysts: Preparation, characterization and catalytic activity. Applied Catalysis A: General, 474, 78- 86.
70. MacCarthy, D. S., Vlek, P. L., & Fosu, M. (2014). Assessing the influence of land-use change on the variability of soil chemical properties in semi-arid zone of Ghana. Ghana Journal of Agricultural Science, 47(1), 81-93.
71. McCarthy, A. L., O'Callaghan, Y. C., Connolly, A., Piggott, C. O., FitzGerald, R. J., & O'Brien, N. M. (2014). Phenolic‐enriched fractions from brewers' spent grain possess cellular antioxidant and immunomodulatory effects in cell culture model systems. Journal of the science of food and agriculture, 94(7), 1373-1379.
72. McKeown PC and Spillane C (Eds) (2014) Treasuring Exceptions: Plant Epigenetics and Epigenomics. Humana Press: New Jersey, USA. (in press).
73. McKeown PC, Fort A and Spillane C (2014) Analysis of genomic imprinting by quantitative allele-specific expression by pyrosequencing(®). Methods Mol Biol. 1112:85-104.
74. McKeown PC and Spillane C (2014) Landscaping plant epigenetics. Methods Mol Biol. 1112:1-24.
75. McKeown, P. C. (2014). Mechanisms of rDNA silencing and the Nucleolar Remodelling Complex (NoRC).
76. McPhillips, K., Waters, D. M., Parlet, C., Walsh, D. J., Arendt, E. K., & Murray, P. G. (2014). Purification and Characterisation of a β-1, 4-Xylanase from Remersonia thermophila CBS 540.69 and Its Application in Bread Making. Applied biochemistry and biotechnology, 172(4), 1747-1762.
77. Miller, A. C., Donnellan, T., Matthews, A., Hanrahan, K., & O’Donoghue, C. (2014). Expanding Agri-Food Production and Employment in the Presence of Climate Policy Constraints: Quantifying the Trade-Off in Ireland. In Agricultural Cooperative Management and Policy (pp. 223-242). Springer International Publishing.
78. Minguzzi S, Selcuklu SD, Spillane C, Parle-McDermott A. (2014) An NTD-associated polymorphism in the 3' UTR of MTHFD1L can affect disease risk by altering miRNA binding. Human Mutation. 2014 Jan;35(1):96-104.
79. Moreira C, Spillane C, Fathalli A, Vasconcelos V, Antunes A. (2014) African Origin and Europe-Mediated Global Dispersal of The Cyanobacterium Microcystis aeruginosa. Current Microbiology 2014 Jun 21.
80. Mullen, M. P., & Hanrahan, J. P. (2014). Direct Evidence on the Contribution of a Missense Mutation in GDF9 to Variation in Ovulation Rate of Finnsheep. PloS one, 9(4), e95251.
81. Mullen, M. P., Bazer, F. W., Wu, G., Parr, M. H., Evans, A. C., Crowe, M. A., & Diskin, M. G. (2014). Effects of systemic progesterone during the early luteal phase on the availabilities of amino acids and glucose in the bovine uterine lumen. Reproduction, Fertility and Development, 26(2), 282-292.
82. Mullins, E. (2014). Engineering for disease resistance: persistent obstacles clouding tangible opportunities. Pest management science.
83. Murray, H., Meunier, G., Stengel, D. B., & Cave, R. (2014). Metal complexation by organic ligands (L) in near-pristine estuarine waters: evidence for the identity of L. Environmental Chemistry, 11(2), 89-99.
84. Nieminen, M., Kaila, A., Laiho, R., Sarkkola, S., O’Connor, M., O’Driscoll, C., ... & Xiao, L. Nutrient and heavy metals in decaying harvest residue needles on drained blanket peat forests. European Journal of Forest Research, 1-14.
85. Nitschke, U., & Stengel, D. B. (2014). Iodine contributes to osmotic acclimatisation in the kelp Laminaria digitata (Phaeophyceae). Planta, 239(2), 521-530.
86. Nitschke, U., Karsten, U., & Eggert, A. (2014). Physiological performance of the red alga Stylonema alsidii (Stylonematophyceae) under varying salinities. Journal of Experimental Marine Biology and Ecology, 460, 170-176.
87. Oliveira, P. M., Zannini, E., & Arendt, E. K. (2014) . Cereal fungal infection, mycotoxins, and lactic acid bacteria mediated bioprotection: From crop farming to cereal products. Food microbiology, 37, 78-95.
88. O’Callaghan, Y., McCarthy, F. O., & O’Brien, N. M. (2014). Recent advances in phytosterol oxidation products. Biochemical and biophysical research communications, 446(3), 786-791.
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96. Pajoro, A., Madrigal, P., Muiño, J. M., Matus, J. T., Jin, J., Mecchia, M. A., ... & Kaufmann, K. (2014). Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome biology, 15(3), R41.
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114. Schmalenberger, A., & Noll, M. (2014). Bacterial communities in grassland turfs respond to sulphonate addition while fungal communities remain largely unchanged. European Journal of Soil Biology, 61, 12-19.
115. Schmid, M., Guihéneuf, F., & Stengel, D. B. (2014). Fatty acid contents and profiles of 16 macroalgae collected from the Irish Coast at two seasons. Journal of Applied Phycology, 26(1), 451-463.
116. Schnitzenbaumer, B., Kaspar, J., Titze, J., & Arendt, E. K. (2014). Implementation of commercial oat and sorghum flours in brewing. European Food Research and Technology, 238(3), 515-525.
117. Schnitzenbaumer, B., & Arendt, E. K. (2014). Effect of unmalted oats (Avena sativa L.) on the quality of high-gravity mashes and worts without or with exogenous enzyme addition. European Food Research and Technology, 238(2), 225-235.
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121. Stengel DB, Conde-Álvarez R, Connan S, Nitschke U, Arenas F, Abreu H, Bonomi Barufi J, Chow F, Robledo D, Malta EJ, Mata M, Konotchick T, Nassar C, Pérez-Ruzafa Á, López D, Marquardt R, Vaz-Pinto F, Celis-Plá PSM, Hermoso M, Ruiz E, Ordoñez G, Flores P, Zanolla M, Bañares-España E, Altamirano M, Korbee N, Bischof K, Figueroa FL (2014). Short-term effects of CO2, nutrients and temperature on three marine macroalgae under solar radiation. Aquatic Biology 22:159-175.
122. Sulpice, R., Flis, A., Ivakov, A. A., Apelt, F., Krohn, N., Encke, B., ... & Stitt, M. (2014). Arabidopsis coordinates the diurnal regulation of carbon allocation and growth across a wide range of photoperiods. Molecular plant, 7(1), 137-155.
123. Sulpice, R., Ishihara, H., Schlereth, A., Cawthray, G. R., Encke, B., Giavalisco, P., ... & Lambers, H. (2014). Low levels of ribosomal RNA partly account for the very high photosynthetic phosphorus‐use efficiency of Proteaceae species. Plant, Cell & Environment, 37(6), 1276-1298.
124. Tamene, L., Le, Q. B., & Vlek, P. L. (2014). A landscape planning and management tool for land and water resources management: an example application in northern Ethiopia. Water Resources Management, 28(2), 407-424.
125. Troy, S. M., Lawlor, P. G., O’Flynn, C. J., & Healy, M. G. (2014). The Impact of Biochar Addition on Nutrient Leaching and Soil Properties from Tillage Soil Amended with Pig Manure. Water, Air, & Soil Pollution, 225(3), 1-15.
126. Upton, V., O'Donoghue, C., & Ryan, M. (2014). The physical, economic and policy drivers of land conversion to forestry in Ireland. Journal of environmental management, 132, 79-86.
127. Valcarcel, J., Reilly, K., Gaffney, M., & O'Brien, N. (2014). Effect of Genotype and Environment on the Glycoalkaloid Content of Rare, Heritage, and Commercial Potato Varieties. Journal of food science, 79(5), T1039-T1048.
128. Vallons, K. J., Ryan, L. A., & Arendt, E. K. (2014). Pressure-Induced Gelatinization of Starch in Excess Water. Critical reviews in food science and nutrition, 54(3), 399-409.
129. Vero, S. E., Ibrahim, T. G., Creamer, R. E., Grant, J., Healy, M. G., Henry, T., ... & Fenton, O. (2014). Consequences of varied soil hydraulic and meteorological complexity on unsaturated zone time lag estimates. Journal of contaminant hydrology, 170, 53-67.
130. Villamor, G. B., Le, Q. B., Djanibekov, U., van Noordwijk, M., & Vlek, P. L. (2014). Biodiversity in rubber agroforests, carbon emissions, and rural livelihoods: An agent-based model of land-use dynamics in lowland Sumatra. Environmental Modelling & Software, 61, 151-165.
131. Vu, Q. M., Le, Q. B., & Vlek, P. L. (2014). Hotspots of human-induced biomass productivity decline and their social–ecological types toward supporting national policy and local studies on combating land degradation. Global and Planetary Change, 121, 64-77.
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135. Wellmer, F., Graciet, E., & Riechmann, J. L. (2014). Specification of floral organs in Arabidopsis. Journal of experimental botany, 65(1), 1-9.
136. Wnetrzak, R., Leahy, J. J., Chojnacka, K. W., Saeid, A., Novotny, E., Jensen, L. S., & Kwapinski, W. (2014). Influence of pig manure biochar mineral content on Cr (III) sorption capacity. Journal of Chemical Technology and Biotechnology, 89(4), 569-578.
137. Wolter, A., Hager, A. S., Zannini, E., Czerny, M., & Arendt, E. K. (2014). Impact of sourdough fermented with Lactobacillus plantarum FST 1.7 on baking and sensory properties of gluten-free breads. European Food Research and Technology, 1-12.
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2013

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6. Carney, K. N., Rodgers, M., Lawlor, P. G., & Zhan, X. (2013). Treatment of separated piggery anaerobic digestate liquid using woodchip biofilters. Environmental Technology, 34(5), 663-670.
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12. Ding, S., Wang, Y., Xu, D., Zhu, C., & Zhang, C. (2013). Gel-Based Coloration Technique for the Submillimeter-Scale Imaging of Labile Phosphorus in Sediments and Soils with Diffusive Gradients in Thin Films. Environmental science & technology, 47(14), 7821-7829.
13. Donoghue MTA, Fort A, Clifton R, Xhang X, McKeown PC, Borevitz JO and Spillane C (2013). CmCGG-methylation independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants. DNA Research Nov 7.
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36. Lynch, D., Henihan, A. M., Bowen, B., Lynch, D., McDonnell, K., Kwapinski, W., & Leahy, J. J. (2013). Utilisation of poultry litter as an energy feedstock. Biomass and Bioenergy, 49, 197-204.
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38. McArdle, S., Leahy, J. J., Curtin, T., & Tanner, D. (2013). Hydrogenation of sunflower oil over Pt–Ni bimetallic supported catalysts: Preparation, characterization and catalytic activity. Applied Catalysis A: General.
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45. Murray, H., Meunier, G., van den Berg, C., Cave, R., & Stengel, D. (2013). Voltammetric characterization of macroalgae-exuded organic ligands (L) in response to Cu and Zn: a source and stimuli for L. Environmental Chemistry.
46. Nardozza, S., Boldingh, H.L., Osorio, S., Hohne, M., Wohlers, M., Gleave, A.P., Macrae, E.A., Richardson, A.C., Atkinson, R.G., Sulpice, R., Fernie, A.R., and Clearwater, M.J. (2013). Metabolic analysis of kiwifruit (Actinidia deliciosa) berries from extreme genotypes reveals hallmarks for fruit starch metabolism. Journal of Experimental Botany
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50. O’Flynn, C. J., Healy, M. G., Wilson, P., Hoekstra, N. J., Troy, S. M., & Fenton, O. (2013). Chemical amendment of pig slurry: control of runoff related risks due to episodic rainfall events up to 48 h after application. Environmental Science and Pollution Research, 1-9.
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52. Perdereau, A. C., Douglas, G. C., Hodkinson, T. R., & Kelleher, C. T. (2013). High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources. Biotechnology for biofuels, 6(1), 114.
53. Rahte, S., Evans, R., Eugster, P. J., Marcourt, L., Wolfender, J. L., Kortenkamp, A., & Tasdemir, D. (2013). Salvia officinalis for Hot Flushes: Towards Determination of Mechanism of Activity and Active Principles. Planta medica, (EFirst).
54. Rawson, A., Brunton, N. P., Rai, D. K., McLoughlin, P., Tiwari, B. K., & Tuohy, M. G. (2013). Stability of falcarinol type polyacetylenes during processing of Apiaceae vegetables. Trends in Food Science & Technology.
55. Rawson, A., Hossain, M. B., Patras, A., Tuohy, M., & Brunton, N. (2013). Effect of boiling and roasting on the polyacetylene and polyphenol content of fennel (Foeniculum vulgare) bulb. Food Research International, 50(2), 513-518.
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