share this page

Recent SIGMA Publications

awards

 

  • Best Video Award BIOMED 2015 - Evolve
  • Best paper award, Irish Human Computer Interaction (IHCI) conference 2013, “Mobile distractions that affect usability but not performance, and vice versa”, Robin Deegan
  • IICE Best Paper Award - Prof. Paul Walsh, S-Cube Project
  • Outstanding Paper Award - Internet Research 2008, "Approaches for personalised knowledge retrival.", Prof. Paul Walsh  et al.

2016

  • Smith, Claire L., Walsh et al. "Identification of a human neonatal immune-metabolic network associated with bacterial infection." Nature communications 5 (2014).
  • Paul Walsh, Brian Kelly, Michael Bekaert, Roy Sleator, John Carroll, Xiangwu Lu  Enhancing Reproducibility in Bioinformatics for Microbiology , SMBE 2015, Hofburg Vienna, Austria.
  • 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.
  • 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
  • Paul Walsh, Rapidly Visualizing NGS Cancer Data Sets with Cloud Computing, Road Mapping Infrastructures for Advanced Visual Interfaces Supporting Big Data Applications in Virtual Research Environments, AVI 2016 WORKSHOP – BARI, ITALY, JUNE 7, 2016.
  • Paul Walsh, Microbiological Sequence Analysis, Invited Speaker, Gulf Congress of Clinical Microbiology and Infectious Diseases (GCCMID2016), Dubai.
  • Manning, Timmy, and Paul Walsh. "The importance of physicochemical characteristics and nonlinear classifiers in determining HIV-1 protease specificity." Bioengineered 7.2 (2016): 65-78.
  • Felix Engel, Paul Walsh, Towards an Open Archival Information System compliant exchange format to ensure reproducibility of assays in cancer care, MEDICON 2016, XIV Mediterranean Conference On Medical And Biological Engineering And Computing March 31st - April 2nd 2016, Paphos, Cyprus.
  • K. Kennedy, P.Walsh, T. Mastaglio, T. Scully. Genetic Optimisation for a Stochastic Model for Opportunistic Maintenance Planning of Offshore Wind Farms. International Conference on Multidisciplinary Engineering Design Optimization MEDO 2016, http://medo2016.northumbria.ac.uk/
  • 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.
  • 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
  • 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
  • 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.
  • 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.
  • Concordance in the Cloud- A Multidisciplinary Software Tool for Breast Core Biopsy Correlation, Michael W Bennett, Tim Manning, Brian Kelly, Noel Murphy, Paul Walsh, Tara Jane Browne, Fionnuala O'Connell, LABORATORY INVESTIGATION. Vol. 96. 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA: NATURE PUBLISHING GROUP, 2016 https://goo.gl/f9zsQQ.
  • Pathology-Driven Cloud-Based Mutidisciplinary Team Meeting Software, Fionnuala O'Connell, Tim Manning, Brian Kelly, Noel Murphy, Paul Walsh, Tara Jane Browne, Michael W Bennett. LABORATORY INVESTIGATION. Vol. 96. 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA: NATURE PUBLISHING GROUP, 2016 https://goo.gl/f9zsQQ.

2015

  • Bernhard G. Humm, Paul Walsh: "Flexible yet Efficient Management of Electronic Health Records". In: Hamid R. Arabnia, Leonidas Deligiannidis, Quoc-Nam Tran (Eds): Proceedings of the 2015 International Conference on Computational Science and Computational Intelligence. Las Vegas, Nevada, USA, 7-9 Decemeber 2015. IEEE Conference Publishing Services 2015. ISBN 978-1-4673-9795-7/15, DOI 10.1109/CSCI.2015.85.
  • Ulrich Beez, Bernhard G. Humm, Paul Walsh: "Semantic AutoSuggest for Electronic Health Records". In: Hamid R. Arabnia, Leonidas Deligiannidis, Quoc-Nam Tran (Eds): Proceedings of the 2015 International Conference on Computational Science and Computational Intelligence. Las Vegas, Nevada, USA, 7-9 Decemeber 2015. IEEE Conference Publishing Services 2015. ISBN 978-1-4673-9795-7/15, DOI 10.1109/CSCI.2015.85
  • Enhancing Reproducibility in Bioinformatics for Microbiology Paul Walsh, B. Kelly, M. Bekaert, R. Sleator, J. Carroll, X. Lu, Society for Molecular Biology and Evolution, SMBE 2015, Vienna.
  • Keary, Alphonsus, and Paul Walsh et al., Using Online Role-Playing Games For Entrepreneurship Training, Game-Based Learning and the Power of Play: exploring evidence, challenges and future directions. In Press Cambridge Scholars Publishing 2016.
  • Walsh, P., et al. "Draft genome sequences of six different Staphylococcus epidermidis clones, isolated individually from p Roy I and i.e. got the CB you didn’t look at the did you reterm neonates presenting with sepsis at Edinburgh’s Royal Infirmary." Genome announcements 3.3 (2015): e00471-15.
  • Lawlor, B., Walsh P., Engineering Bioinformatics: Building Reliability, Performance and Productivity into Bioinformatics Software, Bioengineered, Bioengineered (2015), In Press.
  • O’Driscoll, A., Belogrudov, V., Carroll, J., Kropp, K., Walsh, P., Ghazal, P., & Sleator, R. D. (2015). HBLAST: Parallelised sequence similarity–A Hadoop MapReducable basic local alignment search tool. Journal of biomedical informatics, 54, 58-64.

2014

  • Walsh, Paul, and John Carroll. "Simplicity—Enabling a rapid route to publication." Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on. IEEE, 2014.
  • Keary, Alphonsus, and Paul Walsh. "How affective computing could complement and advance the quantified self." In Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on, pp. 24-31. IEEE, 2014.
  • Keary, Alfie, Sam Redfern, and Paul Walsh. "Current Trends and Developments, Future Requirements, and Predictions for Computer Mediated Communications and E-Collaboration.", IGI Global, 2014.
  • Tristan Cabela, Gabriel Hautreuxa, Eric Boyera, Simon Wongb, Nicolas Mignereyc, Xiangwu Lud, Paul Walsh, Novel HPC Technologies for Rapid Analysis in Bioinformatics, Partnership for Advanced Computing in Europe White Paper, http://www.prace-ri.eu/shape-pilot-projects/
  • K A Kropp, A Lucid, J Carroll, V Belgrudov, P Walsh, B Kelly, C Smith, P Dickinson, A O'Driscoll, K Templeton, P Ghazal, R D Sleator, Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient. Genome Announcements 09/2014; 2(5). DOI: 10.1128/genomeA.00907-14
  • Kropp, K. A., A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, C. Smith et al. "Draft genome sequence of a Streptococcus agalactiae strain isolated from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland." Genome announcements 2, no. 5 (2014): e00875-14.
  • Kropp, K. A., A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, K. Templeton et al. "Draft genome sequence of a Pantoea sp. isolated from a preterm neonatal blood sepsis patient." Genome announcements 2, no. 5 (2014): e00904-14.
  • Kropp, K. A., A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, C. Smith et al. "Draft genome sequence of a Staphylococcus warneri strain isolated from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland." Genome announcements 2, no. 5 (2014): e00877-14.
  • Kropp, K. A., et al. "Draft genome sequence of a Staphylococcus aureus isolate taken from the blood of a preterm neonatal blood sepsis patient."Genome announcements 2.5 (2014): e00906-14.
  • K A Kropp, A Lucid, J Carroll, V Belgrudov, P Walsh, B Kelly, C Smith, P Dickinson, A O'Driscoll, K Templeton, P Ghazal, R D Sleator., 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 Announcements 09/2014; 2(5). DOI: 10.1128/genomeA.00908-14
  • Asperges, R., Dell’Aquila, E., Di Ferdinando, A., Friedrich, R., Keary, A., Lean, Moizer, J., Walsh, P. (2014). S-Cube Project (S3 ): Training Soft Skills In Social Enterprises Using Virtual Environments for Role Play. (D. O'Byrne, & J. Lean, Eds.) Plymouth [e-book]: University of Plymouth Press.
  • Deegan, Robin (2014), COMPLEX MOBILE LEARNING THAT ADAPTS TO LEARNERS COGNITIVE LOAD. International Journal of Mobile and Blended Learning (IJMBL), (In press)
  • Deegan, Robin (2014), Mobile HCI: Issues surrounding cognition, distraction, usability and performance.. International Journal of Mobile HCI, (IJMHCI) (In press)
  • 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.

2013

  • Keary, Alfie, Sam Redfern, and Paul Walsh. "Current Trends and Developments, Future Requirements, and Predictions for Computer Mediated Communications and E-Collaboration.",  Book Chapter in Knowledge Discovery, Transfer, and Management in the Information Age (2013): 212. Jennex, Murray E., IGI Global, 2013.
  • Walsh, Paul, John Carroll, and Roy D. Sleator. "Accelerating in silico research with workflows: a lesson in simplicity." Computers in biology and medicine43.12 (2013): 2028-2035.
  • Aisling O’ Driscoll, Udo Bleimann, Patrick Bours, Bernhard Humm, Ingo Stengel, Paul Walsh (Co-Chairs): Proceedings of the 4th Collaborative European Research Conference (CERC 2013), Cork, Ireland, 2013. ISSN: 2220-4164
  • An Analysis of Next Generation Sequence Clipping Tools, Paul Walsh, Xiangwu Lu and John Carroll, CERC 2013 ISSN 2220-4164.
  • Manning, Timmy, Roy D. Sleator, and Paul Walsh. "Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics." Bioengineered 5.2 (2014): 80-95.
  • Manning, Timmy, Roy D. Sleator, and Paul Walsh. "Naturally selecting solutions: the use of genetic algorithms in bioinformatics." Bioengineered 4.5 (2013): 266-278.
  • Paul Walsh, John Carroll, Roy D. Sleator: Accelerating in silico research with workflows: A lesson in Simplicity. Comp. in Bio. and Med. 43(12): 2028-2035 (2013)
  • Timmy Manning, Paul Walsh: Improving the Performance of CGPANN for Breast Cancer Diagnosis Using Crossover and Radial Basis Functions. EvoBIO 2013: 165-176
  • Manning, Timothy P; Sleator, Roy D; Walsh, Paul (2013) Naturally selecting solutions: The use of genetic algorithms in bioinformatics. Bioengineered 4 (5), 266–278. doi: 10.4161/bioe.23041
  • Manning, Timothy P; Sleator, Roy D; and Walsh, Paul (2013) Biologically inspired intelligent decision making: A commentary on the use of Artificial Neural Networks in bioinformatics, Bioengineered 5 (2). doi: 10.4161/bioe.26997
  • Deegan, R. (2013) Managing distractions in complex settings In proceedings of MobileChi, 2013, August, Berlin, Germany
  • Deegan, R. (2013) Measuring simultaneous sources of Cognitive Load within a mobile learner. In proceedings of International Cognitive Load Theory Conference, 2013, June, Toulouse, France
  • Deegan, R. (2013) Mobile distractions that affect usability but not performance, and vice versa. In Proceedings of Irish Human Computer Interaction Conference, 2013, June, Dublin, Ireland.
  • Deegan, R. (2013) MOBILE LEARNING APPLICATION INTERFACES: FIRST STEPS TO A COGNITIVE LOAD AWARE SYSTEM. In Proceedings of IADIS Mobile Learning Conference, 2013, March 14-16th, Lisbon, Portugal.
  • Keary, A., Walsh, P., O’Byrne, D., Moizer, J., Lean, J., Di Ferdinando, A., Simona, L. S. (2013) ‘Using Online-Role-Play-Games for Entrepreneurship Training’ Ireland Game Based Learning Symposium, Ireland, June 2013.
  • An Analysis of Next Generation Sequence Clipping Tools, Paul Walsh, Xiangwu Lu and John Carroll, CERC 2013 ISSN 2220-4164.
    Manning, Timmy, Roy D. Sleator, and Paul Walsh. "Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics." Bioengineered 5.2 (2014): 80-95.

2012

  • Keary, A., & Redfern, S. (2012). Future Directions of the Conferencing and Collaboration Field. International Journal of e-Collaboration (IJeC), 8(2), 47-70. doi:10.4018/jec.2012040104
  • Manning T, Walsh P. , Automatic Task Decomposition for the NeuroEvolution of Augmenting Topologies (NEAT) Algorithm, 10th European Conference on Evolutionary Machine Learning and Data Mining in Computational Biology (EvoBIO 2012), (67-76)Springer Verlag Lecture Notes in Computer Science.
  • T. Neef, S. Morana, B. G. Humm: A Criteria-Driven Method for Architecting Domain-Specific IE Applications. In P. Bours, B. Humm, R. Loew, I. Stengel, P. Walsh (Eds): Proceedings of the 3rd Collaborative European Research Conference (CERC 2012), pp. 21-28, Darmstadt, Germany, 2012.

 

2011

  • Paul Walsh, Prasad Gade: The use of an aesthetic measure for the evolution of fractal landscapes. IEEE Congress on Evolutionary Computation 2011: 1613-1619
  • Deegan, R., and Rothwell, P., (2011) Usability in Mobile Learning: Results from a study of learning under varying levels of extraneous cognitive load. In Proceedings of Irish Human Computer Interaction Conference, 2011, September 8 to 9, 2011, Cork Institute of Technology, Ireland.
  • CERC2011 Collaborative European Research Conference, 14. - 15. January 2011 Cork, Ireland, editor Paul Walsh et al., ISSN:  2220-416
  • Requirements Gathering For A Bioinformatics Workflow Tool, J. Carroll, P. Walsh, P. Rothwell, R. D. Sleator, Collaborative European Research Conference,  14. - 15. January 2011, Cork, Ireland, editor Paul Walsh et al., ISSN:  2220-416

 

2010

  • Paul Walsh, Prasad Gade: Terrain generation using an Interactive Genetic Algorithm. IEEE Congress on Evolutionary Computation 2010: 1-7
  • Manning, Timothy P (2010), Automated de novo sequencing of the tandem mass spectra of peptides. This MSc thesis was submitted to Cork Institute of Technology (CIT) October 2010
  • Deegan R and Rothwell, P. (2010). A classification of M-Learning applications from a Usability Perspective. Journal of the Research Center for Educational Technology Vol 6, No 1 (2010)
  • Deegan. R. and Rothwell, P. (2010) The application of Cognitive Load Theory to the Usability of m-learning applications: First steps. In Proceedings of Irish Human Computer Interaction Conference. 2010, 69-72
  • A Video Game for Science Education, Paul Walsh, Conference Proceedings of the 5th Plymouth-Learning Conference, ed. Steve Wheeler, Plymouth, 2010.
  • Normen Haas, Bernhard Humm, Ingo Stengl, Paul Walsh: Commoditisation as a Criterion for Semantic Service Provisioning. In Udo G. Bleimann, Paul S. Dowland, Steven M. Furnell, Oliver Schneider (Eds): Proceedings of the 8th International Network Conference (INC 2010), pp 335-344. Heidelberg, Germany, July, 2010.
  • Vorhersage der Teamleistung von virtuellen Software-Entwicklungs-Teams in Bezug auf die zu erwartende Projektkomplexität (Expected Performance of Virtual Software Development Teams based on Project Complexity), Friedrich, Ralf und Udo Bleimann, Thomas Martens, Ingo Stengel, Paul Walsh, in: Querschnitt (Beiträge aus Forschung und Entwicklung der Hochschule Darmstadt), Nr. 24, Feb. 2010, 98-101.
© 2017 CIT | web development by Granite Digital