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Subject: Bioinformatics

Number of items at this level: 51.

Article

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

Shaw, C.D. and Lonchamp, J. and Downing, Tim and Imamura, H. (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterisation. Molecular Microbiology, ? (?). ?-?. 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

Sirbu, Alina and Crane, Martin and Ruskin, Heather (2015) Data integration for microarrays: enhanced inference for gene regulatory networks. Microarrays, 4 (2). pp. 255-269. ISSN 2076-3905

Loughran, Noeleen B and O'Connell, Mary J. and O'Connor, Brendan 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 and Meade, Kieran G. and Allan, Brenda and Lloyd, Andrew T. and Downing, Tim and 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

Sirbu, Alina and Kerr, Grainne and Crane, Martin and Ruskin, Heather J. (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 and Downing, Tim and 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 and 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 and Hinde, Sarah and McCormick-Hill, Sally and Leidal, Kevin and Bloomberg, Sarah and loughran, Sinead and O'Connor, Brendan and Ó'Fágáin, Ciarán and Nauseef, William and O'Connell, Mary (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 (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 and Ruskin, Heather J. and Crane, Martin (2010) Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinformatics, 11 (59). pp. 1471-2205. ISSN 1471-2105

Downing, Tim and Cormican, Paul and O'Farrelly, Cliona and 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, Grainne and Perrin, Dimitri and Ruskin, Heather and Crane, Martin (2009) Edge-weighting of gene expression graphs. Advances in Complex Systems, 13 (2). pp. 217-238. ISSN 0219-5259

Barat, Ana and Crane, Martin and Ruskin, Heather J. (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, Grainne and Ruskin, Heather J. and Crane, Martin 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 and O'Connor, Brendan and Ó'Fágáin, Ciarán and O'Connell, Mary (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

Book Section

Coughlan, Simone and Barreira , Sofia and 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 and Ruskin, Heather and Crane, Martin (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

Conference or Workshop Item

Sirbu, Alina and Crane, Martin and Ruskin, Heather J. (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 and Barat, Ana and Ruskin, Heather and Crane, Martin (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. and Wilkins, Peter and Healy, Graham and Ampatzis, Christos and 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 D. (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 and Smeaton, Alan F. and O'Connor, Noel E. and Diamond, Dermot (2009) RATB Multi-modal sensor network. In: Environ 2010, 17-19 February 2010, Limerick, Ireland.

McMullin, Barry and 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 and Mitchell, George and Kelly, Ciaran and McMullin, Barry (2006) Evolving artificial cell signaling networks. In: European Conference on Complex Systems (ECCS '06), 25-29 Sept 2006, Oxford, UK.

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

Decraene, James and Dittrich, Peter and Hinze, Thomas and Lenser, Thorsten and McMullin, Barry 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 and Ruskin, Heather J. and Burns, John and Crane, Martin (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

Thesis

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.

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

Loughran, Noeleen (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.

This list was generated on Sat Apr 30 01:05:14 2016 IST.