Article

Hillmann, Andreas ORCID: 0000-0002-6517-1615, Crane, Martin ORCID: 0000-0001-7598-3126 and Ruskin, Heather J. ORCID: 0000-0001-7101-2242 (2017) HIV models for treatment interruption: adaptation and comparison. Physica A Statistical Mechanics and its Applications, 483 . pp. 44-56. ISSN 0378-4371

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

Kelly, Helena and Downing, Tim (2015) Cross platform standardisation and normalisation experimental pipeline for use in the biodiscovery of dysregulated human circulating miRNAs. PLOS ONE, 10 (9). 0137389-0137389. ISSN 1932-6203

Downing, Tim (2015) Tackling drug resistant infection outbreaks of global pandemic Escherichia coli ST131 using evolutionary and epidemiological genomics. Microorganisms, 2015 (3). pp. 236-267. ISSN 2076-2607

Sîrbu, Alina, Crane, Martin ORCID: 0000-0001-7598-3126 and Ruskin, Heather J. (2015) Data integration for microarrays: enhanced inference for gene regulatory networks. Microarrays, 4 (2). pp. 255-269. ISSN 2076-3905

Loughran, Noeleen B., O'Connell, Mary J., O'Connor, Brendan ORCID: 0000-0002-6857-1614 and Ó Fágáin, Ciarán (2014) Stability properties of an ancient plant peroxidase. Biochimie, 104 . pp. 156-159. ISSN 0300-9084

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

Connell, Sarah, Meade, Kieran G., Allan, Brenda, Lloyd, Andrew T., Downing, Tim, O'Farrelly, Cliona and Bradley, Daniel G. (2013) Genome-wide association analysis of avian resistance to Campylobacter jejuni colonization identifies risk locus spanning the CDH13 gene. G3, 3 (5). pp. 881-890. ISSN 2160-1836

Sîrbu, Alina, Kerr, Gráinne, Crane, Martin ORCID: 0000-0001-7598-3126 and Ruskin, Heather J. ORCID: 0000-0001-7101-2242 (2012) RNA-seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering. PLoS ONE, 7 (12). e50986. ISSN 1932-6203

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

Loughran, Noeleen B., Hinde, Sarah, McCormick-Hill, Sally, Leidal, Kevin, Bloomberg, Sarah, Loughran, Sinéad T., O'Connor, Brendan ORCID: 0000-0002-6857-1614, Ó Fágáin, Ciarán, Nauseef, William and O'Connell, Mary J. (2012) Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase. Molecular Biology and Evolution, 29 (8). pp. 2039-2046. ISSN 1537-1719

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

Decraene, James and McMullin, Barry ORCID: 0000-0002-5789-2068 (2011) The Evolution of complexity in self-maintaining cellular information processing networks. Advances in Complex Systems, 14 (1). pp. 55-75. ISSN 0219-5259

Downing, Tim (2010) Variation in chicken populations may affect the enzymatic activity of lysozyme. Animal Genetics, 41 (2). pp. 213-217. ISSN 1365-2052

Sîrbu, Alina, Ruskin, Heather J. and Crane, Martin ORCID: 0000-0001-7598-3126 (2010) Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinformatics, 11 (59). pp. 1471-2205. ISSN 1471-2105

Downing, Tim, Cormican, Paul, O'Farrelly, Cliona, Bradley, Daniel G. and Lloyd, Andrew T. (2009) Evidence of the adaptive evolution of immune genes in chicken. BMC Research Notes, 2 (254). ISSN 1756-0500

Downing, Tim (2009) Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus. BMC Evolutionary Biology, 9 (136). ISSN 1471-2148

Kerr, Gráinne, Perrin, Dimitri, Ruskin, Heather J. ORCID: 0000-0001-7101-2242 and Crane, Martin ORCID: 0000-0001-7598-3126 (2009) Edge-weighting of gene expression graphs. Advances in Complex Systems, 13 (2). pp. 217-238. ISSN 0219-5259

Barat, Ana, Crane, Martin ORCID: 0000-0001-7598-3126 and Ruskin, Heather J. ORCID: 0000-0001-7101-2242 (2008) Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano- and microspheres. Journal of Pharmaceutical and Biomedical Analysis, 48 (2). pp. 361-368. ISSN 0731-7085

Kerr, Gráinne, Ruskin, Heather J. ORCID: 0000-0001-7101-2242, Crane, Martin ORCID: 0000-0001-7598-3126 and Doolan, Padraig (2008) Techniques for clustering gene expression data. Computers in Biology and Medicine, 38 (3). pp. 283-293. ISSN 0010-4825

Loughran, Noeleen B., O'Connor, Brendan, Ó Fágáin, Ciarán and O'Connell, Mary J. (2008) The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions. BMC Evolutionary Biology, 8 . pp. 101-111. ISSN 1471-2148

Thesis

Gusti, Yusof Shukri Y. (2023) Epigenetic profiling of mouse and human vascular smooth muscle cells, S100β resident vascular stem cells and their lineage-specific progeny in vitro. 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.

Walsh, Darren ORCID: 0000-0002-1239-0267 (2022) Not quite a ‘carbon copy’: investigating the relationship between mitochondrial DNA heteroplasmy and one-carbon metabolism. PhD thesis, Dublin City University.

Kaushik, Prashant (2020) Profiling the dynamic changes in the phosphoproteome of Chinese hamster ovary cells. Master of Laws thesis, Dublin City University.

Motheramgari, Krishna C. ORCID: 0000-0003-2499-2713 (2020) Profiling the landscape of long non- coding RNAs in the Chinese hamster ovary cell transcriptome. 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.

McCartney, Ann (2018) The identification and characterization of RNA-mediated gene fusions across primate genomes. PhD thesis, Dublin City University.

Moran, Ray (2017) Investigating the linear and non-linear mechanisms of protein coding innovation across the animal kingdom. PhD thesis, Dublin City University.

McRae, Kathryn M. (2015) Identification of variation in the sheep genome controlling gastrointestinal nematode resistance. PhD thesis, Dublin City University.

Webb, Andrew Edward (2015) Immunoinformatics: towards an understanding of species-specific protein evolution using phylogenomics and network theory. PhD thesis, Dublin City University.

Hasegawa, Tomonori (2015) On the evolution of genotype-phenotype mapping: exploring viability in the Avida articial life system. PhD thesis, Dublin City University.

Roznovat, Irina-Afrodita (2014) A computational model for colon cancer dynamics. PhD thesis, Dublin City University.

Lynch, Mark (2014) Surface layer proteins as virulence factors in Clostridiun difficile infection. PhD thesis, Dublin City University.

Shakya, Kabita (2013) Content evaluation and tool development for knowledge management system. Master of Science thesis, Dublin City University.

Morgan , Claire C. (2013) The molecular phylogeny of placental mammals and its application to uncovering signatures of molecular adaptation. PhD thesis, Dublin City University.

Raghavan, Karthika (2012) Computational micromodel for epigenetic mechanisms. PhD thesis, Dublin City University.

Porwal, Jyoti (2011) Epigenetic modelling: DNA methylation and working towards model parameterisation. Master of Science thesis, Dublin City University.

Sîrbu, Alina (2011) Gene regulatory network modelling with evolutionary algorithms -an integrative approach. PhD thesis, Dublin City University.

Loughran, Noeleen B. (2010) Evolutionary and Paleobiochemical Analyses of Heme Peroxidases. PhD thesis, Dublin City University.

Mehta, Jai Prakash (2010) Gene expression analysis in breast cancer. PhD thesis, Dublin City University.

Decraene, James (2009) Autocatalytic closure and the evolution of cellular information processing networks. PhD thesis, Dublin City University.

Kerr, Gráinne (2009) Computational analysis of gene expression data. PhD thesis, Dublin City University.

Perrin, Dimitri (2008) Multi-layered model of individual HIV infection progression and mechanisms of phenotypical expression. PhD thesis, Dublin City University.

Barat, Ana (2006) Probabilistic models for drug dissolution. PhD thesis, Dublin City University.

Costello, Sean (2004) Development and evaluation of the virtual pathology slide: a new tool for understanding inter-observer variability in diagnostic microscopy. PhD thesis, Dublin City University.

Conference or Workshop Item

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.

Hu, Feiyan ORCID: 0000-0001-7451-6438 and Smeaton, Alan F. ORCID: 0000-0003-1028-8389 (2016) Periodicity intensity for indicating behaviour shifts from lifelog data. In: The IEEE International Conference on Bioinformatics and Biomedicine 2016 International Workshop on Biomedical and Health Informatics, 15-18 Dec. 2016, Shenzhen, China. ISBN 978-1-5090-1612-9

Sîrbu, Alina, Crane, Martin ORCID: 0000-0001-7598-3126 and Ruskin, Heather J. ORCID: 0000-0001-7101-2242 (2013) EGIA–evolutionary optimisation of gene regulatory networks, an integrative approach. In: 5th Workshop on Complex Networks - CompleNet 2014, 12-14 Mar 2014, Bologna, Italy. ISBN 978-3-319-05400-1

Bezbradica, Marija ORCID: 0000-0001-9366-5113, Barat, Ana, Ruskin, Heather J. and Crane, Martin ORCID: 0000-0001-7598-3126 (2010) Probabilistic models for dissolution of ethylcellulose coated microspheres. In: European Simulation and Modelling Conference 2010, 25-27 Oct 2010, Hasselt, Belgium. ISBN 978-90-77381-57-1

Smeaton, Alan F. ORCID: 0000-0003-1028-8389, Wilkins, Peter, Healy, Graham ORCID: 0000-0001-6429-6339, Ampatzis, Christos, Rusinski, M. and Izzo, Dario (2009) Neurological modeling of what experts vs. non-experts find interesting. In: Neuroscience 2009, 17-21 October 2009, Chicago, USA.

May, Gregory and Warrington, Giles (2009) A comparison of the aerobic energy demands of two commercially available cycle ergometers in trained cyclists. In: ISBS 2009 - 27th International Society of Biomechanics in Sports Conference, 17-21 August 2009, Limerick, Ireland.

O'Connor, Edel, Smeaton, Alan F. ORCID: 0000-0003-1028-8389, O'Connor, Noel E. ORCID: 0000-0002-4033-9135 and Diamond, Dermot ORCID: 0000-0003-2944-4839 (2009) RATB Multi-modal sensor network. In: Environ 2010, 17-19 February 2010, Limerick, Ireland.

McMullin, Barry ORCID: 0000-0002-5789-2068, Kelly, Ciarán and O'Brien, Darragh (2007) Multi-level selectional stalemate in a simple artificial chemistry. In: ECAL 2007 - 9th European Conference on Artificial Life, 10-14 September, 2007, Lisbon, Portugal. ISBN 978-3-540-74912-7

Decraene, James, Mitchell, George G., Kelly, Ciarán and McMullin, Barry ORCID: 0000-0002-5789-2068 (2006) Evolving artificial cell signaling networks. In: European Conference on Complex Systems (ECCS '06), 25-29 Sept 2006, Oxford, UK.

Kelly, Ciarán, McMullin, Barry ORCID: 0000-0002-5789-2068 and O'Brien, Darragh (2006) On Protocell "Computation". In: European Conference on Complex Systems (ECCS '06), 25-29 Sept 2006, Oxford, UK.

Decraene, James, Dittrich, Peter, Hinze, Thomas, Lenser, Thorsten, McMullin, Barry ORCID: 0000-0002-5789-2068 and Mitchell, George G. (2006) A multidisciplinary survey of modeling techniques for biochemical networks. In: IPG 2006: Integrative Post-Genomics conference 2006, 29 Nov-1Dec 2006, Lyon, France.

Perrin, Dimitri ORCID: 0000-0002-4007-5256, Ruskin, Heather J. ORCID: 0000-0001-7101-2242, Burns, John and Crane, Martin ORCID: 0000-0001-7598-3126 (2006) An agent-based approach to immune modelling. In: ICCSA 2006 - Computational Science and Its Applications, 8-11 May, 2006, Glasgow, UK. ISBN 978-3-540-34070-6

McMullin, Barry ORCID: 0000-0002-5789-2068 (2000) Some remarks on autocatalysis and autopoiesis. In: Closure: Emergent Organizations and their Dynamics, 3-5 May 1999, University of Ghent, Belgium.. ISBN 978-1573312493

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.

Bezbradica, Marija ORCID: 0000-0001-9366-5113, Ruskin, Heather J. ORCID: 0000-0001-7101-2242 and Crane, Martin ORCID: 0000-0001-7598-3126 (2011) Modelling drug coatings: A parallel cellular automata model of ethylcellulose-coated microspheres. In: Proceedings of The International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011). IACSIT Press, Singapore, pp. 419-424. ISBN 978-981-08-8718-6