Publications

Journals
  1. Sleator RD. Under the microscope: from pathogens to probiotics and back. Bioengineered 2015; 6(5):275-282.
  2. Sleator RD. Designer Probiotics: Development and Applications in Gastrointestinal Health. World J Gastrointest Pathophysiol. 2015; 6(3):73-8.
  3. Feeney A, Sleator RD. Functional Screening of the Cronobacter sakazakii Genome reveals a role for ProP (ESA_02131) in carnitine uptake. Bioengineered. 2015; 6(3):161-5.
  4. Walsh P, Bekaert M, Carroll J, Manning T, Kelly B, O’Driscoll A, Lu X, Smith C, Dickinson P, Templeton K, Ghazal P, Sleator RD. Draft Genome sequence of six different Staphylococcus epidermidis clones, isolated individually from preterm neonates presenting with sepsis at Edinburgh’s Royal Infirmary. Genome Announc. 2015; 3(3). pii: e00471-15.
  5. Lynch KM, Lucid A, Arendt EK, Sleator RD, Lucey B, Coffey A. Genomics of the Weissella cibaria species with an examination of its metabolic traits. Microbiology. 2015; 161(Pt 4):914-30.
  6. O'Driscoll A, Belogrudov V, Carroll J, Kropp K, Walsh P, Ghazal P, Sleator RD. HBLAST: Parallelised sequence similarity - A Hadoop MapReducable basic local alignment search tool. J Biomed Inform. 2015; 54:58-64.
  7. Feeney A, Kropp KA, O'Connor R, Sleator RD. Cronobacter sakazakii: stress survival and virulence potential in an opportunistic foodborne pathogen. Gut microbes 2014; 5:711-8.
  8. Feeney A, Johnston CD, Lucid A, O'Mahony J, Coffey A, Lucey B, Sleator RD. The role of the Cronobacter sakazakii ProP C-terminal coiled coil domain in osmotolerance. Gut pathogens 2014; 6:46.
  9. Sleator RD. The genetic code. Rewritten, revised, repurposed. Artificial DNA, PNA & XNA 2014; 2014;5(2):e29408.
  10. Johnston CD, Bannantine JP, Govender R, Endersen L, Pletzer D, Weingart H, Coffey A, O'Mahony J, Sleator RD. Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis
  11. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, Ghazal P, Sleator RD. Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom. Genome Announc. 2014; 2(5). pii: e00908-14.
  12. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, Ghazal P, Sleator RD. Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient. Genome Announc. 2014; 2(5). pii: e00907-14.
  13. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Templeton K, Smith C, Dickinson P, O'Driscoll A, Ghazal P, Sleator RD. Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of a Preterm Neonatal Blood Sepsis Patient. Genome Announc. 2014; 2(5). pii: e00906-14.
  14. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Templeton K, Smith C, Dickinson P, O'Driscoll A, Ghazal P, Sleator RD. Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient. Genome Announc. 2014; 2(5). pii: e00904-14.
  15. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, Ghazal P, Sleator RD. Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland. Genome Announc. 2014; 2(5). pii: e00877-14.
  16. Kropp KA, Lucid A, Carroll J, Belgrudov V, Walsh P, Kelly B, Smith C, Dickinson P, O'Driscoll A, Templeton K, Ghazal P, Sleator RD. Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland. Genome Announc. 2014; 2(5). pii: e00875-14.
  17. Feeney A, Johnston CD, Govender R, O'Mahony J, Coffey A, Sleator RD. Analysis of the role of the Cronobacter sakazakii ProP homologues in osmotolerance. Gut pathogens 2014; 6:15.
  18. Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family beta-carotene 15,15'-monooxygenase. PloS one 2014; 9:e103318.
  19. Koziel M, O'Doherty P, Vandamme P, Corcoran GD, Sleator RD, Lucey B. Campylobacter corcagiensis sp. nov., isolated from faeces of captive lion-tailed macaques (Macaca silenus). International journal of systematic and evolutionary microbiology 2014; 64:2878-83.
  20. Sleator RD. Genetics just got SEXY: Sequences encoding XY. Bioengineered 2014; 5:214-5.
  21. Culligan EP, Marchesi JR, Hill C, Sleator RD. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Frontiers in microbiology 2014; 5:189.
  22. Koziel M, Lucid A, Bullman S, Corcoran GD, Lucey B, Sleator RD. Draft Genome Sequence of Campylobacter corcagiensis Strain CIT045T, a Representative of a Novel Campylobacter Species Isolated from Lion-Tailed Macaques (Macaca silenus). Genome Announc. 2014; 2(2). pii: e00248-14.
  23. Koziel M, Corcoran GD, Sleator RD, Lucey B. Detection and molecular analysis of Campylobacter ureolyticus in domestic animals. Gut pathogens 2014; 6:9.
  24. Lucid A, Bullman S, Koziel M, Corcoran GD, Cotter PD, Sleator RD, Lucey B. Draft Genome Sequence of Campylobacter ureolyticus Strain CIT007, the First Whole-Genome Sequence of a Clinical Isolate. Genome Announc. 2014; 2(2). pii: e00262-14.
  25. O'Donovan D, Corcoran GD, Lucey B, Sleator RD. Campylobacter ureolyticus: a portrait of the pathogen. Virulence 2014; 5:498-506.
  26. O'Doherty A, Koziel M, De Barra L, Corcoran D, Bullman S, Lucey B, Sleator RD. Development of nalidixic acid amphotericin B vancomycin (NAV) medium for the isolation of Campylobacter ureolyticus from the stools of patients presenting with acute gastroenteritis. British journal of biomedical science 2014; 71:6-12.
  27. Sleator RD. The synthetic biology future. Bioengineered 2014; 5:69-72.
  28. Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PloS one 2013; 8:e82985.
  29. Manning T, Sleator RD, Walsh P. Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics. Bioengineered 2014; 5:80-95.
  30. Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014; 5:399-412.
  31. Walsh P, Carroll J, Sleator RD. Accelerating in silico research with workflows: a lesson in Simplicity. Computers in biology and medicine 2013; 43:2028-35.
  32. Bullman S, Lucid A, Corcoran D, Sleator RD, Lucey B. Genomic investigation into strain heterogeneity and pathogenic potential of the emerging gastrointestinal pathogen Campylobacter ureolyticus. PloS one 2013; 8:e71515.
  33. Sleator RD, O'Driscoll A. Digitizing humanity. Artificial DNA, PNA & XNA 2013; 4:37-8.
  34. O'Driscoll A, Daugelaite J, Sleator RD. 'Big data', Hadoop and cloud computing in genomics. Journal of biomedical informatics 2013; 46:774-81.
  35. Koziel M, Kiely R, Blake L, O'Callaghan I, Corcoran GD, Lucey B, Sleator RD. Improved detection of bacterial pathogens in patients presenting with gastroenteritis by use of the EntericBio real-time Gastro Panel I assay. Journal of clinical microbiology 2013; 51:2679-85.
  36. Sleator RD. A beginner's guide to phylogenetics. Microbial ecology 2013; 66:1-4.
  37. Johnston C, Douarre PE, Soulimane T, Pletzer D, Weingart H, MacSharry J, Coffey A, Sleator RD, O'Mahony J. Codon optimisation to improve expression of a Mycobacterium avium ssp. paratuberculosis-specific membrane-associated antigen by Lactobacillus salivarius. Pathogens and disease 2013; 68:27-38.
  38. O' Driscoll A, Sleator RD. Synthetic DNA: the next generation of big data storage. Bioengineered 2013; 4:123-5.
  39. Hoffmann RF, McLernon S, Feeney A, Hill C, Sleator RD. A single point mutation in the listerial betL sigma(A)-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity. Bioengineered 2013; 4:401-7.
  40. Sleator RD. Synthetic ribosomes: making molecules that make molecules. Bioengineered 2013; 4:63-4.
  41. Talip BA, Sleator RD, Lowery CJ, Dooley JS, Snelling WJ. An Update on Global Tuberculosis (TB). Infectious diseases 2013; 6:39-50.
  42. Manning T, Sleator RD, Walsh P. Naturally selecting solutions: the use of genetic algorithms in bioinformatics. Bioengineered 2013; 4:266-78.
  43. Smith, Claire L., et al. "Identification of a human neonatal immune-metabolic network associated with bacterial infection." Nature communications 5 (2014).
  44. Paul Walsh, Brian Kelly, Michael Bekaert, Roy Sleator, John Carroll, Xiangwu Lu  Enhancing Reproducibility in Bioinformatics for Microbiology , SMBE 2015, Hofburg Vienna, Austria.
  45. Lawlor B, Walsh P. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software . Bioengineered. 2015;6(4):193-203. doi:10.1080/21655979.2015.1050162.
  46. Paul Walsh, Micheál Mac Aogáin, Brendan Lawlor, FindR-TB: A cloud–based tool for antibiotic resistance prediction in Mycobacterium tuberculosis, Proceeding of CERC 2016 Collaborative European Research Conference Cork Institute of Technology – Cork, Ireland 23 - 24 September 2016 www.cerc–conference.eu ISSN 2220 – 4164
  47. Towards a host-pathogen integrated molecular diagnostic for bacterial infection in newborn babies, Forster, Dantoft, Kropp, Dickinson, Smith, Mullins, Kelly, Sleator, Lawlor, Konstantinidiou, Walsh, Ghazal, Proceeding of CERC 2016 Collaborative European Research Conference Cork Institute of Technology – Cork, Ireland 23 - 24 September 2016 www.cerc–conference.eu ISSN 2220 – 4164
  48. Metamorphosis: Changing the shape of genomic data using Kafka, B Lawlor, P Walsh, Proceeding of CERC 2016 Collaborative European Research Conference Cork Institute of Technology – Cork, Ireland 23 - 24 September 2016 www.cerc–conference.eu ISSN 2220 – 4164.
  49. Measuring the Matches: Genome Alignment and Benchmarking, Xiangwu Lu, Audrey M. Michel  , Pavel V. Baranov  and Paul Walsh, Proceeding of CERC 2016 Collaborative European Research Conference Cork Institute of Technology – Cork, Ireland 23 - 24 September 2016 www.cerc–conference.eu ISSN 2220 – 4164.
  50. Development of a Bioinformatics Pipeline to Identify Antibiotic Resistance Biomarkers of Bacterial Pathogens, D. Mullins, N. Konstantinidou, R.D. Sleator, B. Kelly  1 , T. Forster, W. A. Dantoft, P. Ghazal, P. Walsh, Proceeding of CERC 2016 Collaborative European Research Conference Cork Institute of Technology – Cork, Ireland 23 - 24 September 2016 www.cerc–conference.eu ISSN 2220 – 4164.

Conferences
  1. ‘Following my gut feelings: from pathogens to probiotics and back’ International conference on Biomedical engineering and biotechnology (ICBEB2016). August 2016, Hangzhou, China.
  2. ‘New lecturer research award lecture’ Society for Applied Microbiology Summer Conference. July 2016, Edinburgh, Scotland.
  3. ‘Staphylococcus epidermidis clones isolated from preterm neonates presenting with sepsis’ Microbiology Annual Conference 2016. March 2016, Liverpool, UK.
  4.  ‘PanView: A user friendly pipeline for genome assembly and analysis’ 3rd International ‘Omics Synthesis Conference – IEOS2015, July 2015, St Andrews, Fife, Scotland.
  5. ‘Following my Gut Feelings…’ ‘European Congress of Clinical Microbiology and Infectious Diseases – ESCMID 2015, April 2015, Copenhagen, Denmark.
  6. CERC Collaborative  European Research Conference 2014, http://cerc-conference.eu/
  7. CERC Collaborative  European Research Conference 2016, http://cerc-conference.eu/
 
 
 

This project is partly funded by the European Commission