biology

UCD Biology & Environmental Science

UCD School of Biology & Environmental Science - Research Publications 2015/16

Below is the list of research publications for the UCD School of Biology & Environmental Science in the academic year 2015/16.



Books

Dr Hugh Feeley
Feeley, HB; Baars, J-R, Kelly-Quinn, M. (2016) The Stonefly of Ireland - Distribution, Life Histories & Ecology. Waterford, Ireland: National Biodiversity Data Centre. Available Online  
Assoc Professor Mary Kelly-Quinn
Feeley, HB; Baars, J-R, Kelly-Quinn, M. (2016) The Stonefly of Ireland - Distribution, Life Histories & Ecology. Waterford, Ireland: National Biodiversity Data Centre. Available Online  

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Books Chapter

Dr Benjamin Charlton
Taylor A. M., Charlton B. D. & Reby D. (2016) 'Vocal production by terrestrial mammals: source, filter and function' In: Suthers R, Fitch W. T., Popper A. & Fay D (eds). Vertebrate Sound Production and Acoustic Communication. New York: Springer. , pp.229-259  
Dr Tamara Hochstrasser
Harris, M., T. Hochstrasser, K. Foley, and C. Cave (2016) 'Urban biodiversity management in Ireland. Capturing the experience of practitioners' In: R. A. Francis, J. D. A. Millington, and M. A. Chadwick (eds). Urban landscape ecology: science, policy and practice. London: Routledge.  
Professor Emma C Teeling
Emma C. Teeling, Gareth Jones, and Stephen J. Rossiter (2015) 'Phylogeny, Genes, and Hearing- Implications for the Evolution of Echolocation in Bats' In: Brock Fenton and (eds). Springer Handbook of Auditory Research: Bat Bioacoustics. USA: Springer.  

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Peer Reviewed Journals

Dr Jan-Robert Baars
Mangan, R., Dirilgen, T., Baars, J-R. (2015) 'Responses of adult Hydrellia lagarosiphon to a revised diet: implications for life cycle studies and laboratory culturing techniques'. Entomologia Experimentalis Et Applicata, :1-6.  
Dr Sven Batke
Batke, S; Cascante-Marin, A; Kelly, DL (2016) 'Epiphytes in Honduras: a geographical analysis of the vascular epiphyte flora and its floristic affinities to other Central American countries'. Journal of Tropical Ecology, 58 (3).  
Professor Thomas Bolger
Andriuzzi WS, Schmidt O, Brussaard L, Faber JH, Bolger T (2016) 'Earthworm functional traits and interspecific interactions affect plant nitrogen acquisition and primary production'. Applied Soil Ecology, 104 :148-156. Available Online  
Dirilgen, T. , Arroyo, J. Dimmers, W. J., Faber, J., Stone, D., Martins da Silva, P., Cavalho, F., Schmelz, R., Griffiths, B.S, Francisco, R., Creamer, R.E., Sousa, J.-P. and Bolger,T. (2016) 'Mite community composition across a European transect and its relationships to variation in other components of soil biodiversity'. Applied Soil Ecology, 97 :86-97.  
Andriuzzi, W.S., Ngo, P-T., Geisen, S., Keith, A.M., Dumack, K., Bolger, T., Bonkowski, M., Brussaard, L., Faber, J.H., Chabbi, A., Rumpel, C. and Schmidt, O. (2016) 'Organic matter composition and the protist and nematode communities around anecic earthworm burrows'. Biology and Fertility of Soils, 52 (1):91-100.  
Creamer, R.E., Hannula, S.E., van Leeuwen, J.P., Stone, D., Rutgers, M., Schmelz, R.M., de Ruiter, P.C., Bohse Hendriksen, N., Bolger, T., Bouffaud, M.L.1, Buee, M.1, Carvalho, F.1, Costa, D., Dirilgen, T., Francisco, R., Griffiths, B.S., Griffiths, R., Martin, F., Martins da Silva, P., Mendes, S., Morais, P.V., Pereira, C., Philippot, L., Plassart, P., Redecker, D., Römbke, J., Sousa, J.P., Wouterse, M., and Lemanceau, P. (2016) 'Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe'. Applied Soil Ecology, 97 :112-124.  
Martins da Silva, P., Carvalho, F., Dirilgen, T.,Stone, D., Creamer, R.,Bolger, T and Sousa, J. P. (2016) 'Traits of collembolan life-form indicate land use types and soil properties across an European transect'. Applied Soil Ecology, 97 :69-77.  
Minogue, D., French, P., Bolger, T. and Murphy P.N.C. (2015) 'Characterisation of dairy soiled water in a survey of 60 Irish dairy farms'. Irish Journal of Agricultural and Food Research, 54 (1):1-16.  
Schmelz, R.M., Wisdom, R. and Bolger, T. (2015) 'Phreodrilidae in Irish peatlands: Invasion from down-under or ancient relict?'. Irish Naturalists' Journal, 34 (2):101-103.  
Andriuzzi, W. S., Schmidt, O., Brussaard, L., Faber, J. and Bolger, T (2015) 'Functional diversity in earthworms affects urea- and dung-derived nitrogen in soil, plant nitrogen acquisition and primary production'. Applied Soil Ecology .  
Mr Paul Brooks
Browne M., Brooks, P., Clough, R., Fisher, A. S., Mayer-Pinto, M. and Crowe, T. P. (2016) 'Simulating regimes of chemical disturbance and testing impacts in the ecosystem using a novel programmable dosing-system'. Methods in Ecology and Evolution, 7 (5):609-618.  
Dr Jens Carlsson
Collins PC, Carlsson J, Rowcroft P, Tibbles B (2016) 'Ecosystem status of the deep Black Sea, soft sediment, benthic community'. Marine Policy, 73 :216-223.  
Ferreira DG, Souza-Shibatta L, Shibatta, OA, Sofia SH, Carlsson J, Dias JHP, Makrakis S, Makrakis MC (2016) 'Genetic structure and diversity of migratory freshwater fish in a fragmented Neotropical river system'. Reviews in Fish Biology and Fisheries, 2 :1-23.  
Boschen RE, Collins PCC, Tunnicliffe V, Carlsson J, Gardner JPA, Lowe J, McCrone A, Metaxas A, Sinniger F, Swaddling A (2016) 'A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities'. Ocean and Coastal Management, 122 :37-48.  
Vartia, S; Villanueva-Cañas, JL; Finarelli, JA; Farrell, ED; Collins, PC; Hughes, GM; Carlsson, JEL; Gauthier, DT; McGinnity, P; Cross, TF; FitzGerald, RD; Mirimin, L; Crispie, F; Cotter, PD; Carlsson, J (2016) 'A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding'. Royal Society Open Science, 3 :150565.  
Gustavson MS, Collins PC, Finarelli JA, Egan D, Conchúir RÓ, Wightman GD, King JJ, Gauthier DT, Whelan K, Carlsson JEL & Carlsson J (2015) 'An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water'. Journal of Fish Biology, 87 :1254-1256.  
Dr Benjamin Charlton
Snyder, RJ; Purdue, BM; Zhang, Z; Maple, TL & Charlton, BD (2016) 'Giant panda maternal care: a test of the experience constraint hypothesis'. Scientific Reports, 6 :27509.  
Reby, D; Wyman, MT; Frey, R; Passilongo D; Gilbert, J; Locatelli, Y; Charlton, BD (2016) 'Evidence of biphonation and source-filter interactions in the bugles of male North American elk (Cervus canadensis)'. Journal of Experimental Biology, 219 (8):1224-1236.  
Wyman, MT; Locatelli, Y; Charlton, BD; Reby, D. (2016) 'Female sexual preferences toward conspecific and hybrid male mating calls in two species of polygynous deer, Cervus elaphus and C. nippon'. Journal of Evolutionary Biology, 43 :227-241.  
Charlton, BD (2015) 'The acoustic structure and information content of female koala vocal signals'. PLoS ONE, 10 (10):e0138670.  
Assoc Professor Tasman Crowe
Lyons D.A., Arvanitidis C., Blight A.J., Chatzinikolaou E., Guy-Haim T., Kotta J., Queirós A.M., Rilov G., Somerfield P.J. and Crowe T.P. (2016) 'There are no whole truths in meta-analyses: all their truths are half truths'. Global Change Biology, 22 :968-971.  
Browne M., Brooks, P., Clough, R., Fisher, A. S., Mayer-Pinto, M. and Crowe, T. P. (2016) 'Simulating regimes of chemical disturbance and testing impacts in the ecosystem using a novel programmable dosing-system'. Methods in Ecology and Evolution, 7 (5):609-618.  
Kinsella, C. and Crowe, T. P. (2016) 'Individual and combined effects of copper and freshwater on the biodiversity and functioning of fouling assemblages'. Marine Pollution Bulletin, 107 :136-143.  
Borges, C. D. G., Doncaster, C. P., Crowe, T. P. and Hawkins, S. J. (2016) 'The influence of simulated exploitation on Patella vulgata populations: protandric sex change is density dependent'. Ecology and Evolution, 6 (2):514-531.  
Professor Fiona Doohan
Murphy, BR; Doohan, FM; Hodkinson TR (2016) 'A seed dressing combining fungal endophyte spores and fungicides improves seedling survival and early growth in barley and oat'. Symbiosis, :1-8.  
Ali, SS: Nugent, B; Mullins, E; Doohan FM (2016) 'Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry'. AMB Express, 6 (1):1.  
Perochon A; Jianguang, J; Kahla, A; Arunachalam, C; Scofield, SR; Bowden, S; Wallington, E; Doohan, FM (2015) 'TaFROG encodes a Pooideae orphan protein that interacts with SnRK1 and enhances resistance to the mycotoxigenic fungus Fusarium graminearum'. Plant Physiology, 169 (4):2895-2906.  
Rathore, DS; Lopez-Vernaza, MA; Doohan, F; Connell, DO; Lloyd, A; Mullins, E (2015) 'Profiling antibiotic resistance and electrotransformation potential of Ensifer adhaerens OV14; a non-Agrobacterium species capable of efficient rates of plant transformation'. FEMS Microbiology Letters, 362 (17):fnv126.  
Mr Damian Egan
Gustavson MS, Collins PC, Finarelli JA, Egan D, Conchúir RÓ, Wightman GD, King JJ, Gauthier DT, Whelan K, Carlsson JEL & Carlsson J (2015) 'An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water'. Journal of Fish Biology, 87 :1254-1256.  
Dr Caroline Elliott-Kingston
Elliott-Kingston, C; Haworth, M; Yearsley, JM; Batke, SP; Lawson, T; McElwain, JC. (2016) 'Does size matter? Atmospheric CO2 may be a stronger driver of stomatal closing rate than stomatal size in taxa that diversified under low CO2'. Frontiers in Plant Science, In Review .  
Evans-Fitz.Gerald, C; Porter, AS; Yiotis, C; Elliott-Kingston, C; McElwain JC. (2016) 'Co-ordination in morphological leaf traits of some early diverging angiosperms and one fern after several months exposure to experimental palaeo-atmospheric conditions'. Frontiers in Plant Science, In Review .  
Elliott-Kingston, C; Doyle, OPE; Hunter, A. (2016) 'Benefits of Scenario-based Learning in university education'. Acta Horticulturae .  
Hunter, A; Elliott-Kingston, C. (2016) 'Teaching and assessment strategies for active student learning in university horticultural education'. Acta Horticulturae .  
Hunter, A; Forrest, M; Elliott-Kingston, C; Murphy, L. (2016) 'Introducing landscape design techniques to horticulture students'. Acta Horticulturae .  
Porter, AS; Evans-Fitzgerald, C; McElwain, JC; Yiotis, C; Elliott-Kingston, C. (2015) 'How well do you know your growth chambers? Testing for chamber effect using plant traits'. Plant Methods, 11 (44).  
Dr Hugh Feeley
Feeley, H.B.; Kelly-Quinn, M (2015) 'The nymphal diet of the stonefly Protonemura meyeri (Pictet) (Plecoptera: Nemouridae) in four episodically acidic headwater streams in Ireland'. Irish Naturalists' Journal, 34 (2):104-109.  
Dr John Finarelli
Goswami, A; Finarelli, JA (2016) 'EMMLi: A maximum likelihood approach to the analysis of modularity'. Evolution; international journal of organic evolution, 70 (7):1622-1637.  
Finarelli, JA; Liow, LH (2016) 'Diversification histories for North American and Eurasian carnivorans'. Biological Journal of the Linnean Society, 118 (1):26-38.  
Vartia, S; Villanueva-Cañas, JL; Finarelli, JA; Farrell, ED; Collins, PC; Hughes, GM; Carlsson, JEL; Gauthier, DT; McGinnity, P; Cross, TF; FitzGerald, RD; Mirimin, L; Crispie, F; Cotter, PD; Carlsson, J (2016) 'A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding'. Royal Society Open Science, 3 :150565.  
Gustavson, MS;Collins, PC; Finarelli, JA; Egan, D; Conchúir, RÓ; Wightman, GD; King, JJ; Gauthier, DT; Whelan, K; Carlsson, JE; Carlsson, J (2015) 'An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water'. Journal of Fish Biology .  
Mr Charles Harper
McCaffery F, Hawkins M, Tarleton M, Harper C and Nieuwenhuis M (2015) 'Evaluation of mensuration equipment for upper-stem height and diameter measurements'. Irish Forestry, 72 (1&2):8-20.  
Assoc Professor Mary Kelly-Quinn
Conroy, E, Turner, J.N., Rymszewicz, A, Bruen, M, O'Sullivan, J, Kelly-Quinn, M (2016) 'An Evaluation of Visual and Measurement-Based Methods of Measuring Deposited Fine Sediment'. International Journal of Sediment Research .  
Conroy E., Turner J.N., Rymszewicz A., O'Sullivan J.J., Bruen M., Lawler D., Lally H., M. Kelly-Quinn M. (2016) 'Evaluating the relationship between biotic and sediment metrics using mesocosms and field studies'. Science of the Total Environment .  
Conroy E., Turner J.N., Rymszewicz A., O'Sullivan J.J., Bruen M., Lawler D., Lally H., M. Kelly-Quinn M. (2016) 'The impact of cattle access on ecological water quality in streams: examples from agricultural catchments within Ireland'. Science of the Total Environment, 547 :17-29.  
Feeley, H.B.; Kelly-Quinn, M (2015) 'The nymphal diet of the stonefly Protonemura meyeri (Pictet) (Plecoptera: Nemouridae) in four episodically acidic headwater streams in Ireland'. Irish Naturalists' Journal, 34 (2):104-109.  
O'Callaghan, P., Jocque, M. & Kelly-Quinn, M. (2015) 'Nutrient and sediment-induced macroinvertebrate drift in Honduran cloud forest streams'. Hydrobiologia, 758 :75-86.  
Pedreschi, D., Mariani, S., Coughaln, J., Voigt, C.C., O'Grady, M., Caffrey, J. & Kelly-Quinn, M. (2015) 'Trophic flexibility and opportunism in pike Esox lucius'. Journal of Fish Biology, 87 (4):876-894.  
Dr Ibrahim Khalil
Barrett, M., M.I. Khalil, M.M.R. Jahangir, C. Lee, L.M. Cardenas, G. Collins, K. Richards and V. O¿Flaherty. (2016) '. Carbon amendment and soil depth affects the distribution and abundance of denitrifiers in agricultural soils'. Environmental Science and Pollution Research, 23 (8):7899-7910.  
Professor Jenny McElwain
Elliott-Kingston1, C; Haworth, M; Yearsley, JM; Batke, SP; Lawson, T; McElwain, JC (2016) 'Does size matter? Atmospheric CO2 may be a stronger driver of stomatal closing rate than stomatal size in taxa that diversified under low CO2'. Frontiers in Plant Science . Available Online  
McElwain J.C., Yiotis C. and Lawson T. (2016) 'Using modern plant trait relationships between observed and theoretical maximum stomatal conductance and vein density to examine patterns of plant macroevolution'. New Phytologist, 209 (1):94-103.  
Evans-Fitz.Gerald, C; Porter, AS; Yiotis, C; Elliott-Kingston, C; McElwain JC. (2016) 'Co-ordination in morphological leaf traits of some early diverging angiosperms and one fern after several months exposure to experimental palaeo-atmospheric conditions'. Frontiers in Plant Science, In Review .  
Bacon, KL; Haworth, M; Conroy, E; McElwain, JC. (2015) 'Can atmospheric composition influence plant fossil preservation potential via changes in leaf mass per area? A new hypothesis based on simulated palaeoatmosphere experiments'. Palaeogeography, Palaeoclimatology, Palaeoecology . Available Online  
Steinthorsdottir, M., Porter, A. S., Holohan, A., Kunzmann, L., Collinson, M., and McElwain, J. C. (2015) 'Fossil plant stomata indicate decreasing atmospheric CO2 prior to the Eocene-Oligocene boundary'. Climate of the Past Discussions, 12 (2):439-454. Available Online  
Dr Rainer Melzer
Theißen, G., Melzer, R. (2016) 'Robust views on plasticity and biodiversity'. Annals of Botany, 117 (5):693-697. Available Online  
Melzer, R; Theißen, G. (2016) 'The significance of developmental robustness for species diversity'. Annals of Botany, 117 (5):725-732. Available Online  
Rümpler, F; Gramzow, L., Theißen, G., Melzer, R. (2015) 'Did convergent protein evolution enable phytoplasmas to generate 'zombie plants'?'. Trends in Plant Science, 20 (12):798-806.  
Professor Christoph Mueller
Zhu, T, Zeng, S, Qin, H, Zhou, K, Yang, H, Lan, F, Huang, F, Cao, J, Müller, C (2016) 'Low nitrate retention capacity in calcareous soil under woodland in the karst region of southwestern China'. Soil Biology and Biochemistry, 97 :88-101. Available Online  
Zhang, J, Wang, L, Zhao, W, Hu, H, Feng, X, Müller, C, Cai, Z (2016) 'Soil gross nitrogen transformations along the Northeast China Transect (NECT) and their response to simulated rainfall events'. Scientific Reports, 6 :22830. Available Online  
Zhang, J, Tian, P, Tang, J, Yuan, L, Ke, Y, Cai, Z, Zhu, B, Müller, C (2016) 'The characteristics of soil N transformations regulate the composition of hydrologic N export from terrestrial ecosystem'. Journal of Geophysical Research, 121 .  
Wilson, D, Farrell, C A, Fallon, D, Moser, G, Müller, C, Renou-Wilson, F (2016) 'Multi-year greenhouse gas balances at a rewetted temperate peatland'. Global Change Biology, 10.1111/gcb.13325 .  
Wang, J, Cheng, Y, Zhang, J, Müller, C, Cai, Z (2016) 'Soil gross nitrogen transformations along a secondary succession transect in the north subtropical forest ecosystem of southwest China'. Geoderma, 280 :88-95.  
Shi, X-Z, Hu, H-W, Müller, C, He, J-Z, Chen, D, Suter, H (2016) 'Effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and nitrifiers in two contrasting agricultural soils'. Applied and Environmental Microbiology, 62 (17):5236-5248. Available Online  
Renou-Wilson, F, Müller, C, Moser, G, WIlson, D (2016) 'To graze or not to graze? Four years greenhouse gas balances and vegetation composition from a rained and a rewetted organic soil under grassland'. Agriculture, Ecosystems & Enviroment, 222 :156-170.  
McGeough, K L, Watson, C J, Müller, C, Laughlin, R J, Chadwick, D R (2016) 'Evidence that the efficacy of the nitrification inhibitor dicyandiamide (DCD) is affected by soil properties in UK soils'. Soil Biology and Biochemistry, 94 :222-232.  
Masse, J, Prescott, C E, Müller, C, Grayston, S J (2016) 'Gross nitrogen transformation rates differ in reconstructed oil-sands soils from natural boreal-forest soils as revealed using a 15N tracing method'. Geoderma, 282 :37-48.  
Jansen-Willems, A B, Lanigan, G J, Clough, T J, Andresen, L C, Müller, C (2016) 'Long-term elevation of temperature affects organic N turnover and associated N2O emissions in a permanent grassland soil'. Biogeosciences Discussions, 10.5194/soil-2016-38 . Available Online  
Jansen-Willems, A, Lanigan, G, Grünhage, L, Müller, C (2016) 'Carbon cycling in temperate grassland under elevated temperature'. Ecology and Evolution, in press, IDECE-2015-12-00896 .  
Jahangir, M N R, Fenton, O, Gill, L, Müller, C, Johnston, P, Richards, K G (2016) 'Carbon and nitrogen dynamics and greenhouse gases emissions in constructed wetlands: A review'. Hydrology and Earth System Sciences, 20 :1-15.  
Haworth, M, Moser, G, Raschi, A, Kammann, C, Grünhage, L, Müller, C (2016) 'Carbon dioxide fertilisation and supressed respiration induce enhanced spring biomass roduction in a mixed species temperate meadow exposed to moderate carbon dioxide enrichment'. Functional Plant Biology, 43 :26-39.  
Haider, G, Steffens, D, Müller, C, Kammann, C I (2016) 'Standard extraction methods may underestimate nitrate stocks captured by field aged biochar'. Journal of Environmental Quality, 45 (4):1196-1204.  
Gao, W-L, Kou, L, Zhang, J, Müller, C, Wang, H, Yang, H, Shenggong, L (2016) 'Enhanced deposition of nitrate alters microbial cycling of N in a subtropical forest soil'. Biology and Fertility of Soils, 10.1007/s00374-016-1134-4 .  
Gao, W-L, Kou, L, Yang, H, Zhang, J, Müller, C, Li, S (2016) 'Ammonium fertilization causes a decoupling of ammonium cycling in a boreal forest'. Soil Biology and Biochemistry, 101 :114-123.  
Gao, W-L, Kou, L, Yang, H, Zhang, J, Müller, C, Li, S (2016) 'Are nitrate production and retention processes in subtropical acidic forest soils responsive to ammonium deposition?'. Soil Biology and Biochemistry, 100 :102-109.  
De Menezes, A B, Müller, C, Clipson, N, Doyle, E M (2016) 'The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment'. Microbiology - Society for General Microbiology, 10.1099/mic.0.000341 .  
Chen, Z, Zhang, J, Xiong, Z, Pan, G, Müller, C (2016) 'Enhanced gross nitrogen transformation rates and nitrogen supply in paddy field under elevated atmospheric carbon dioxide and temperature'. Soil Biology and Biochemistry, 94 :80-87.  
Chen, Z, DIng, W, Xu, Y, Müller, C, Yu, H, Fan, J (2016) 'Increased N2O emissions during soil drying after waterlogging and spring thaw in a record wet year'. Soil Biology and Biochemistry, 101 :152-164.  
Barry, C D, Renou-Wilson, F, WIlson, D, Müller, C, Foy, R H (2016) 'Magnitude, form and bioavailability of fluvial carbon exports from Irish organic soils under pasture'. Aquatic Sciences, 78 :541-560.  
Aydogan, E L, Busse, H-J, Moser, G, Müller, C, Kämpfer, P, Glaeser, S P (2016) 'Aureimonas galii sp. nov. and Aureimonas pseudogalii sp. nov. isolated from the phyllosphere of Galium album'. Journal of Systematics and Evolution, 10.1099/ijsem.0.001200 . Available Online  
Andresen, L C, Müller, C, de Dato, G, Dukes, J S, Emmett, B A, Estiarte, M, Jentsch, A, Kröel-Dulay, G, Lüscher, A, Niu, S, Peñuelas, J, Reich, P, Reinsch, S, Ogava, R, Schmidt, I K, Schneider, M K, Sternberg, M, Tietema, A, Zhu, K, Bilton, M C (2016) 'Shifting impacts of climate change: long-term patterns of plant response to elevated CO2, drought and warming across ecosystems'. Advances in Ecological Sciences, 10.1016/bs.aecr.2016.07.001 .  
Zhao, W, Zhang, J, Müller, C, Cai, Z (2016) 'Mechanisms behind the stimulation of nitrification by N input in subtropical acid forest soil'. Journal of Soils and Sediments, 10.1007/s11368-016-1461-y .  
Zhang, J, Wang, J, Müller, C, Cai, Z (2016) 'Ecological and practical significances of crop species referential N uptake matching with soil N dynamics'. Soil Biology and Biochemistry, 103 :63-70.  
Lenhart, K, Kammann, C, Boeckx, P, Six, J, Müller, C (2016) 'Quantification of ecosystem C cynamics in a long-term FACE study on permanent grassland'. Rapid communications in mass spectrometry : RCM, 30 :963-972.  
Rex, D., S. Schimmelpfennig, A. Willems, G. Moser, C. Kammann, and C. Müller (2015) 'Microbial community shifts 2.6 years after top dressing of Miscanthus biochar, hydrochar and feedstock on a temperate grassland site'. Plant and Soil .  
Dr Alexandre Perochon
Perochon A; Jianguang, J; Kahla, A; Arunachalam, C; Scofield, SR; Bowden, S; Wallington, E; Doohan, FM (2015) 'TaFROG encodes a Pooideae orphan protein that interacts with SnRK1 and enhances resistance to the mycotoxigenic fungus Fusarium graminearum'. Plant Physiology, 169 (4):2895-2906.  
Dr Florence Renou-Wilson
David Wilson, Catherine Farrell, David Fallon, Gerald Moser, Christoph Müller and Florence Renou-Wilson (2016) 'Multi-year greenhouse gas balances at a rewetted temperate peatland'. Global Change Biology .  
D. Wilson, D. Blain, J. Couwenberg, C.D. Evans, D. Murdiyarso, S.E. Page, F. Renou-Wilson, J.O. Rieley, A. Sirin, M. Strack and E.-S. Tuittila (2016) 'Greenhouse gas emission factors associated with rewetting of organic soils'. Mires and Peatlands, 17 (04):1-28. Available Online  
Renou-Wilson, F., Müller, C., Moser, G. and Wilson, D. (2016) 'To graze or not to graze: comparing 4 years GHG balances and vegetation from a temperate drained and a rewetted organic soil under grassland'. Agriculture, Ecosystems and Environment, 222 (156-170).  
C. D. Barry, F. Renou-Wilson, D. Wilson, C. Mueller, R. H. Foy (2016) 'Magnitude, form and bioavailability of fluvial carbon exports from Irish organic soils under pasture'. Aquatic Sciences . Available Online  
Evans, C.D., Renou-Wilson, F. and Strack, M. (2015) 'The role of waterborne carbon in the greenhouse gas balance of drained and re-wetted peatlands'. Aquatic Sciences .  
Dr Emmanuel Reynaud
Gutierrez-Heredia L., Murphy E.; Benzoni F. and Reynaud E.G. (2016) 'End to end digitisation and analysis of three-dimensional coral models, from communities to corallites'. PLoS ONE .  
Doyle H., Callaghan E. and Reynaud E.G. (2016) 'Glass Invertebrate Blaschka models in Ireland Institutions'. Journal of the History of Collections .  
Choi S.Y., Habimana O., Flood P., Reynaud E.G., Rodriguez B.J., Zhang N., Casey E., and Gilchrist M.D. (2016) 'Adhesive response of Pseudomonas fluorescens bacterial cells and MDCK mammalian cells to injection molded polymer surfaces of varying roughness'. Colloids and Surfaces B: Biointerfaces, 145 :46-54.  
Flood P., Alvarez L., and Reynaud E.G. (2016) 'Free-floating epithelial micro-tissue arrays: A low cost and versatile technique'. Biofabrication .  
Professor Jeremy Simpson
Panarella A, Bexiga MG, Galea G, O' Neill ED, Salvati A, Dawson KA, Simpson JC (2016) 'A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells'. Scientific Reports, 6 :28865.  
Grossi M, Morgunova M, Cheung S, Scholz D, Conroy E, Terrile M, Panarella A, Simpson JC, Gallagher WM, O'Shea DF (2016) 'Lysosome triggered near-infrared fluorescence imaging of cellular trafficking processes in real time'. Nature Communications, 7 :10855.  
Murphy CM, Paré S, Galea G, Simpson JC, Smith SG (2016) 'Accurate and semi-automated analysis of bacterial association with mammalian cells'. Journal of Microbiology Methods, 122 :8-12.  
Singan VR, Simpson JC (2016) 'Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images'. Source Code for Biology and Medicine, 11 :2.  
Galea G, Simpson JC (2015) 'High-content analysis of Rab protein function at the ER-Golgi interface'. Bioarchitecture, 5 (3-4):44-53.  
Dr Gavin Stewart
Zhong, C., Kang, J., Stewart, G., Zhou, J., Huang, X., Mi, J., Liu, J., Yang, C., Zhang, Y., and Long, R. (2016) 'Comparison of aquaporin-1 expression between yak (Bos grunniens) and indigenous cattle (Bos taurus) in Qinghai-Tibetan Plateau'. Animal Production Science .  
Coyle J., McDaid S., Walpole C and Stewart G.S. (2016) 'UT-B urea transporter localization in the bovine gastrointestinal tract'. Journal of Membrane Biology, 249 :77-85.  
Dr Jonathan Yearsley
Elliott-Kingston1, C; Haworth, M; Yearsley, JM; Batke, SP; Lawson, T; McElwain, JC (2016) 'Does size matter? Atmospheric CO2 may be a stronger driver of stomatal closing rate than stomatal size in taxa that diversified under low CO2'. Frontiers in Plant Science . Available Online  
Dussex, N; Broquet, T; Yearsley, JM (2016) 'Contrasting dispersal inference methods for the greater white-toothed shrew'. Journal of Wildlife Management, 80 (5):812-823. Available Online  
Prat-Guitart, N; Rein, G; Hadden, RM; Belcher, CM; Yearsley, JM; (2016) 'Effects of spatial heterogeneity in moisture content on the horizontal spread of peat fires'. Science of the Total Environment . Available Online  
Prat-Guitart, N; Rein, G; Hadden, RM; Belcher, CM; Yearsley, JM; (2016) 'Spread rate of self-sustained smouldering fires under controlled moisture content and bulk density conditions'. International Journal of Wildland Fire, 25 (4):456-465. Available Online  
Gargan, LM; Cornette, RI; Yearsley, JM; Montgomery, WI; Pauper, J; Alves, PC; Butler, F; . Pascal, M; Tresset, A; Herrel, A; Lusby, J; Tosh, DG; Searle, JB; McDevitt, AD; (2016) 'Molecular and morphological insights into the origin of the invasive greater white-toothed shrew (Crocidura russula) in Ireland'. Biological Invasions, 18 (3):857-871. Available Online  
Dr Charilaos Yiotis
McElwain J.C., Yiotis C. and Lawson T. (2016) 'Using modern plant trait relationships between observed and theoretical maximum stomatal conductance and vein density to examine patterns of plant macroevolution'. New Phytologist, 209 (1):94-103.  

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Other Journals

Dr Caroline Elliott-Kingston
A.S.Porter, C.Evans.FitzGerald, J.C.McElwain, C.Yiotis, C.Elliott-Kingston (2015) 'How well do you know your growth chambers? Testing for chamber effect using plant traits' Plant Methods .  

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Conference Publications

Dr Jan-Robert Baars
Mangan, Rosie, Baars, Jan-Robert (2015) Weed biological control in Ireland ENTO'15, Trinity College, Dublin, Ireland,  
Professor Fiona Doohan
Benbow, HR; Zhou, B; Christodoulou, T; Brennan, C; Mullins, E; Doohan, FM (2016) Identifying genetic resistance to Septoria tritici blotch in wheat using next-generation RNA sequencing 9th international symposium on Septoria Diseases of Cereals, Paris, France, 113  
Benbow, HR; Zhou, B; Christodoulou, T; Brennan, C; Mullins, E; Doohan, FM (2016) Identifying genetic resistance to Septoria tritici blotch in wheat using next-generation RNA sequencing Irish Plant Scientists Association Meeting, Dublin, Ireland, 45  
Christodoulou, T; Brennan, C; Mullins, E; Uauy, C; Doohan, FM (2016) Screening a wheat tilling population for altered susceptibility to Septoria Tritici Blotch disease 9th International Symposium on Septoria Diseases of Cereals, Paris, France,  
Benbow, HR; Zhou, B; Christodoulou, T; Brennan, C; Mullins, E; Doohan, FM (2016) Identifying genetic resistance to Septoria tritici blotch in wheat using next-generation RNA sequencing Monogram, Cambridge, UK, 33  
Doohan, FM (2016) Wheat resistance to FHB and STB disease Monogram, Cambridge, UK, 34  
Christodoulou, T; Brennan, C; Mullins, E; Uauy, C; Doohan, FM (2016) Screening a wheat tilling population for altered susceptibility to Septoria Tritici Blotch disease Irish Plant Scientists Association Meeting, Dublin, Ireland,  
Kehoe, S; Ward, P; Doohan, F (2016) Investigating the potential of Auranta Harvest to increase the productivity of major crop plant species Irish Plant Scientists Association Meeting, Dublin, Ireland, 58  
Zhou, B; Christodoulou, T; Brennan, C; Feechan, A; Doohan, F (2016) Identification of wheat proteins involved in the host response to Zymoseptoria tritici 9th International Symposium on Septoria diseases of Cereals, Paris, France,  
Alcalde, E; Corrigan, A; Doohan, FM (2016) Elucidating the beneficial effects of two biostimulants in crop performance and stress resistance in cereals Irish Plant Scientists Association Meeting, Dublin, Ireland,  
Brennan, CJ; O'Driscoll, A; Benbow, H; Mullins, E; Doohan, FM (2016) Mining for orphan genes of wheat during infection by the pathogenic fungus Zymoseptoria tritici 13th European Conference of Fungal Genetics, Paris, France,  
Vary, S; Mullins, E; Doohan, FM (2015) The effect of elevated CO2 on disease resistance of wheat Annual Meeting of the Controlled Environment Users' Group, Dublin, Ireland, 30  
Dr Hugh Feeley
Hallouin,T., Bruen, M., Kelly-Quinn, M., Christie, M., Bullock, C., Kelly, F., Feeley, H.B. (2016) Multi-Criteria Decision Analysis and Ecosystem Services: knowledge gaps and challenges for policy and decision-making 8th International Congress on Environmental Modelling and Software, July 10-14, Toulouse, FRANCE,  
Dr John Finarelli
Goswami, A; Finarelli, JA (2016) A maximum likelihood approach to assessing modularity with 3-D morphometric data 11th Interntaional Congress of Vertebrate Morphology,  
Dr Margherita Gioria
Gioria M, Pysek, P (2015) The legacy of plant invasions: changes in the soil seed bank of invaded plant communities International Conference on the Ecology and Management of Alien Plant Invasions 2015,  

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Published Reports

Dr Hugh Feeley
Kelly-Quinn, M.; Bruen, M.; Harrison, S.; Healy, M.; Clarke, J.; Drinan, T.; Feeley, H.B.; Finnegan, J.; Graham, C.; Regan, J.; Blacklocke, S. (2016) Assessment of the impacts of forest operations on the ecological quality of water (HYDROFOR). Report No.169. Environmental Protection Agency, Johnstown Castle, Co. Wexford. Available Online  
Assoc Professor Mary Kelly-Quinn
Kelly-Quinn, M.; Bruen, M.; Harrison, S.; Healy, M.; Clarke, J.; Drinan, T.; Feeley, H.B.; Finnegan, J.; Graham, C.; Regan, J.; Blacklocke, S. (2016) Assessment of the impacts of forest operations on the ecological quality of water (HYDROFOR). Report No.169. Environmental Protection Agency, Johnstown Castle, Co. Wexford. Available Online  
Hannigan, E. & Kelly-Quinn, M. (2016) Characterisation of Reference Conditions for Rare River Types: A Literature Review (2013-W-FS-15) report No. 166. Environmental Protection Agency, Wexford, Ireland. Available Online  

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Other Publications

Dr John Finarelli
Goswami, A; Lucas, T; Sivasubramaniam, P; Finarelli, JA (2016) EMMLi: A Maximum Likelihood Approach to the Analysis of Modularity (R Package) Version 0.1. Electronic Publication.  
Cheronet, O; Finarelli, JA (2016) WaverR: An R package for data estimation using weighted averages of multiple regressions. (R package) Version 1.0. Electronic Publication.  
Dr Andrew Jackson
Jackson, ALR (2016) A conversation with Andrew Jackson on the use of satellite and aerial imagery in environmental disputes. Interview. Available Online  
Dr Emmanuel Reynaud
Gutierrez-Heredia L., Keogh C., Keaveney S. and E.G.Reynaud, (2016) 3D printing solutions for coral studies, education and monitoring. Reviews.  
Röttinger E., Amiel A.R., Le Bescot N., Gutierrez-Heredia L., Flood P. and E.G. Reynaud. (2016) Dreaming of a digital ocean. England: Invited papers.  
Lowenstein W., Reynaud E.G., Nefau T., Couteron J.-P. and Duplessy C. (2016) Le volume mort des seringues n¿est pas l¿ennemi du filtre de vie !. Invited papers. Available Online  
Flood P., Page H and E.G.Reynaud (2016) Using hydrogels in microscopy: a tutorial. Reviews.  

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