Article

Manikandan, N. Arul, McCann, Ronán ORCID: 0000-0002-2071-0785, Dimitrios, Kakavas, Rochfort, Keith D. ORCID: 0000-0003-1198-5952, Sreenilayam, Sithara ORCID: 0000-0002-5282-3645, Alkan, Godze, Stornetta, Tom, McGivern, Allan Robert, Grintzalis, Konstantinos ORCID: 0000-0002-6276-495X, Friedrich, Bernd ORCID: 0000-0002-2934-2034, Foley, Greg ORCID: 0000-0002-2284-4218, Brabazon, Dermot ORCID: 0000-0003-3214-6381 and Freeland, Brian ORCID: 0000-0003-3705-5745 (2023) Production of silver nano-inks and surface coatings for anti-microbial food packaging and Its ecological impact. International Journal of Molecular Sciences, 24 . ISSN 1422-0067

Sørensen, Helena Mylise, Rochfort, Keith D. ORCID: 0000-0003-1198-5952, Maye, Susan, MacLeod, George, Brabazon, Dermot ORCID: 0000-0003-3214-6381, Loscher, Christine ORCID: 0000-0002-5276-7321 and Freeland, Brian ORCID: 0000-0003-3705-5745 (2022) Exopolysaccharides of lactic acid bacteria: production, purification and health benefits towards functional food. Nutrients, 14 . ISSN 2072-6643

Fitzgerald, Shane ORCID: 0000-0002-6570-4485, Furlong, Ciara ORCID: 0000-0002-2949-8688, Holland, Linda ORCID: 0000-0002-0103-0151 and Morrin, Aoife ORCID: 0000-0002-3031-4794 (2022) Multi-strain and -species investigation of volatile metabolites emitted from planktonic and biofilm Candida cultures. Metabolites, 12 (5). ISSN 2218-1989

Donnelly, Dan ORCID: 0000-0002-8150-7019, Blanchard, Lucien, Dabros, Michal ORCID: 0000-0002-0176-0015, O'Hara, Seamus, Foley, Greg ORCID: 0000-0002-2284-4218, Freeland, Brian ORCID: 0000-0003-3705-5745 and Brabazon, Dermot ORCID: 0000-0003-3214-6381 (2021) Fed-batch system for propagation of brewer’s yeast. Journal of the American Society of Brewing Chemists, 80 (2). pp. 190-200. ISSN 0361-0470

Kottelat, Jérémy ORCID: 0000-0002-9535-3612, Freeland, Brian ORCID: 0000-0003-3705-5745 and Dabros, Michal ORCID: 0000-0002-0176-0015 (2021) Novel strategy for the calorimetry-based control of fed-batch cultivations of saccharomyces cerevisiae. Processes, 9 (4). ISSN 2227-9717

Fitzgerald, Shane ORCID: 0000-0002-6570-4485, Duffy, Emer ORCID: 0000-0003-4557-6487, Holland, Linda ORCID: 0000-0002-0103-0151 and Morrin, Aoife ORCID: 0000-0003-1061-8528 (2020) Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria. Scientific Reports, 10 . ISSN 2045-2322

Downing, Tim (2016) Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife, 2016 (5). p. 12613. ISSN 2050-084X

Shaw, C.D., Lonchamp, J., Downing, Tim and Imamura, Hideo (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterisation. Molecular Microbiology, 99 (6). pp. 1134-1148. ISSN 1365-2958

Rogers, Matthew B. and Downing, Tim (2014) Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. Plos genetics, 10 (1). p. 1004092. ISSN 1553-7404

Mannaert, An, Downing, Tim, Imamura, Hideo and Dujardin, Jean-Claude (2012) Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania. Trends in Parasitology, 28 (9). pp. 370-376. ISSN 1471-4922

Van Aerschot, Manu, Decuypere, Saskia and Downing, Tim (2012) Genetic markers for SSG-resistance in Leishmania donovani and SSG-treatment failure of visceral leishmaniasis patients in the Indian subcontinent. Journal of Infectious Diseases, 206 (5). pp. 752-755. ISSN 1537-6613

Downing, Tim (2012) The battle of the SNPs. Nature Reviews Microbiology, 10 (6). ISSN 1740-1534

Downing, Tim and Imamura, Hideo (2011) Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Research, 2011 (21). pp. 2143-2156. ISSN 1549-5469

Jain, Anand, Gazzola, Giulio, Panzera, Aurora, Zanoni, Michele and Marsili, Enrico (2011) Visible spectroelectrochemical characterization of geobacter sulfurreducens biofilms on optically transparent indium tin oxide electrode. Electrochimica Acta, 56 (28). pp. 10776-10785. ISSN 0013-4686

Aldrovandi, Aba, Marsili, Enrico, Stante, Loredana, Paganin, Patrizia, Tabacchioni, Silvia and Giondano, Andrea (2009) Sustainable Power Production in a Membrane-less and Mediator-less Wastewater Microbial Fuel Cell. Bioresource Technology, 100 (13). pp. 3252-3260. ISSN 0960-8524

Marsili, Enrico, Baron, Daniel B., Shikare, Indraneel D., Coursolle, Dan, Gralnick, Jeffrey A. and Bond, Daniel R. (2008) Shewanella secretes flavins that mediate extracellular electron transfer. Proceedings of the National Academy of Sciences of the United States of America (PNAS) ISSN 1091-6490, 105 (10). pp. 3969-3973. ISSN 1091-6490

Daly, Stephen J., Dillon, Paul P., Manning, Bernadette M., Dunne, Lynsey, Killard, Anthony J. and O'Kennedy, Richard (2002) Fv antibodies to aflatoxin B1 derived from a pre-immunized antibody phage display library system. Food and Agricultural Immunology, 14 (4). pp. 255-274. ISSN 1465-3443

Thesis

Furlong, Ciara ORCID: 0000-0002-2949-8688 (2024) Investigating the inhibitory effect of Candida parapsilosis on Staphylococcus aureus biofilm formation. PhD thesis, Dublin City University.

Delgado Ollero, Adrian ORCID: 0000-0003-0791-0720 (2024) Development and testing of a novel approach to measuring biofouling on sensors and tidal energy materials. PhD thesis, Dublin City University.

Larkin, Ciara (2023) Examining the TRPV3 cation channel in a culture model of human epidermis. PhD thesis, Dublin City University.

Pulleyblank, Coren (2021) Analysis of oxygenated polycyclic aromatic hydrocarbons in contaminated soil and water systems to Inform remediation strategy and risk assessment. PhD thesis, Dublin City University.

Grey, Anthony (2020) Blue carbon and edaphic influences on microbial metabolism: Bull Island’s sediments and polyhydroxyalkanoates (PHAs) distribution. PhD thesis, Dublin City University.

Decano, Arun Gonzales ORCID: 0000-0002-6058-6483 (2019) A population phylogenomic analysis of the origin and spread of Escherichia coli sequence type 131 (ST131). PhD thesis, Dublin City University.

Marques Passos, Thayse (2018) An investigation of photodynamic inactivation of gram-positive and gram-negative bacteria for water disinfection using a cationic porphyrin. PhD thesis, Dublin City University.

McGlade, Declan (2017) The development of a graphene-copper composite for use in drinking water treatment. PhD thesis, Dublin City University.

McLoughlin, Alisha (2016) Staphylococcus aureus mediated disruption of blood-brain barrier phenotype in human brain microvascular endothelial cells. PhD thesis, Dublin City University.

Cooke, Colm (2014) Siderophore mediated iron acquisation by Sinorhizobium meliloti. PhD thesis, Dublin City University.

Binti Wan Mohd Noor, Wan Syaidatul Aqma (2013) An investigation of the phenotypic and genotypic changes in Pseudomonas putida CP1 following substrate-dependent autoaggregation. PhD thesis, Dublin City University.

Connolly, James (2013) On the uses of atmospheric and laser plasmas for biomedical applications. PhD thesis, Dublin City University.

O'Reilly, Shane S. (2013) Organic carbon cycling in marine sediments and seabed seepage features in Irish waters. PhD thesis, Dublin City University.

Cassidy, Norah (2013) The investigation of Cry toxins from bacillus thuringiensis and the potential use as novel carbohydrate binding proteins. PhD thesis, Dublin City University.

Almeida, Ana (2013) The response of planktonic and aggregated bacterial cells in aqueous media to photodisinfection techniques. PhD thesis, Dublin City University.

Schuler, Moira Monika (2012) Real-time monitoring and control of the specific growth rate in yeast fed-batch cultures based on process analytical technology tools such as biocalorimetry or spectroscopy. PhD thesis, Dublin City University.

Fox, Mary (2011) Protein glycosylation in the gram-negative gamma proteobacterium photorhabdus luminescens. PhD thesis, Dublin City University.

Creavin, Aileen (2010) PA-IIL as a model lectin for the structural and functional characterisation of related lectins. PhD thesis, Dublin City University.

McMahon, Kenneth (2009) Structural and functional characterisation of lectins from the PA-IL superfamily. PhD thesis, Dublin City University.

Murphy, James T. (2008) Autonomous agent-based modelling of resistance frequencies in pathogenic bacteria. PhD thesis, Dublin City University.

Gilhawley, Fergal (2008) Factors governing nitrification in an activated sludge system treating a pharmaceutical wastewater. PhD thesis, Dublin City University.

Ferguson, Damien (2008) A study of clinical strains of Pseudomonas Aeruginosa and the investigation of antibiotic resistance mechanisms in the multidrug resistant strain PA13. PhD thesis, Dublin City University.

Hearty, Stephen (2005) Production and application of monoclonal antibodies suitable for the specific detection of listeria monocytogenes. PhD thesis, Dublin City University.

Fathei Shaeikh, Amani (2004) Biofouling of high purity water systems. Master of Engineering thesis, Dublin City University.

Conference or Workshop Item

Delgado Ollero, Adrián ORCID: 0000-0003-0791-0720, Richards, Chloe, Williams, Molly, Power, Sean, Free, Louis, Bruciu Burgina, Ciprian Constantin ORCID: 0000-0001-8682-9116, Gómez Álvarez, Elena and Regan, Fiona ORCID: 0000-0002-8273-9970 (2021) Biofouling studies on marine rated materials and coatings. In: Environ 2021 - 31st Annual Irish Environmental Researchers Colloquium, 16 - 18 June 2021, Cork/Online.

Richards, Chloe, Barrett, Alan, Maguire, Ivan, Kwiatkowska, Sandra and Regan, Fiona ORCID: 0000-0002-8273-9970 (2019) Marine inspired textured materials for reduction of biofouling on surfaces. In: OCEANS 2019, 17 - 20 June 2019, Marseilles, France.

Mary Rose, Sweeney and Burke, Teresa ORCID: 0000-0001-8093-9912 (2018) Proceedings of the school of nursing and human sciences research expo 2019. In: School of Nursing and Human Sciences Research Expo 2019, 5 Dec 2018, School of Nursing and Human Sciences.

Richards, Chloe, Briciu Burghina, Ciprian Constantin ORCID: 0000-0001-8682-9116 and Regan, Fiona ORCID: 0000-0002-8273-9970 (2018) Assessment of biofilm formation on novel transparent coatings for application to a low cost optical sensor deployed in an estuarine environment. In: Europtrode 2018, 25 - 28 Mar 2018, Naples, Italy.

Coleman, Simon and Diamond, Dermot ORCID: 0000-0003-2944-4839 (2014) Bridging worlds: from macro and micro scale to prototype and product. In: th International Symposium On Macro- and Supramolecular Architectures and Materials (MAM 14), 23-27 Nov 2014, Johannesburg, South Africa.

O'Reilly, Shane S., Szpak, Michal, Monteys, Xavier, Flanagan, Paul, Allen, Christopher and Kelleher, Brian (2014) Hydrographic controls on marine organic matter fate and microbial diversity in the western Irish Sea. In: European Geosciences Union Meeting, 27 Apr - 2 May, Vienna, Austria.

O'Reilly, Shane S., Flanagan, Paul, Frau, Allessandra, Pentlavalli, Prasanna, Monteys, Xavier, Allen, Christopher and Kelleher, Brian (2013) Ireland’s unseen majority – microbial diversity of the seabed. In: Atlantic Ireland 2013 Conference, 11 Nov 2013, Dublin, Ireland.

Cassidy, Norah, Thompson, Roisin, Clarke, Paul A., Keogh, Damien, O'Connell, Michael and O'Connor, Brendan ORCID: 0000-0002-8999-5184 (2012) Regions of the Cry1Ac toxin predicted to be under positive selection are shown to be the carbohydrate binding sites and can be altered in their glycoprotein target specificity. In: Glycosciences Ireland, 14 Jun 2012, NUIG, Galway, Ireland.

Cassidy, Norah, Thompson, Roisin, Clarke, Paul A., Keogh, Damien, O'Connor, Brendan ORCID: 0000-0002-8999-5184 and O'Connell, Michael (2011) The investigation of a recombinant GalNAc binding protein from bacillus thuringiensis as a tool for glycan analysis and detection. In: The EMBO meeting, 10-13 Sept 2011, Vienna, Austria.

Cooke, Colm, Keogh, Damien, Thompson, Roisin, Clarke, Paul A., O'Connor, Brendan ORCID: 0000-0002-8999-5184 and O'Connell, Michael (2011) Exploitation of siderophores for the speciation of iron. In: Research Review Day 2011, 15 Jun 2011, DCU, Dublin, Ireland.

Larragy, Ruth, Thompson, Roisin, Clarke, Paul A., O'Connell, Michael and O'Connor, Brendan ORCID: 0000-0002-8999-5184 (2011) Exploiting prokaryotic chitin-binding proteins for glycan recognition. In: Research Review Day 2011, 15 Jun 2011, DCU, Dublin, Ireland.

Shakalisava, Yuliya (2010) Survey of microbiological water quality in Dublin area. In: Environ 2010, 17-19 February 2010, Limerick, Ireland.

Shakalisava, Yuliya and Diamond, Dermot ORCID: 0000-0003-2944-4839 (2009) Early warning of microbiological contamination of water. In: Biodetection Technologies 2009, 25-26 June 2009, Baltimore, MD, USA.

Thompson, Roisin, Clarke, Paul A., Goel, Alok, O'Connell, Michael and O'Connor, Brendan ORCID: 0000-0002-6857-1614 (2008) Lectin based glycoprotein analysis. In: Glycosciences Ireland, 12 Dec 2008, NUIG, Galway, Ireland.

Szczepaniak, Jakub and O'Connor, Brendan ORCID: 0000-0002-6857-1614 (2007) Cloning of hemagglutinin (HA) protein of influenza A virus - Potential for sialic acid linkage discrimination. In: Centre for BioAnalytical Sciences meeting 2007, 6 Oct 2007, DCU, Dublin, Ireland.

Creavin, Aileen and O'Connor, Brendan ORCID: 0000-0002-6857-1614 (2007) Affinity tagging & purification of the fucose binding LecB protein. In: Centre for BioAnalytical Sciences meeting 2007, 10 Jun 2007, DCU, Dublin, Ireland.

Book Section

Coughlan, Simone, Barreira, Sofia, Seoighe, Cathal and Downing, Tim (2014) Genome-wide variant discovery using sequence assembly, mapping and population-wide analysis. In: Bioinformatics and data analysis in microbiology. Caister Academic Press.