Researchers at UCD


Catherine Mooney

School of Computer Science



Prior to joining the School of Computer Science in UCD as Assistant Professor in October 2016 I was a Research Fellow in Prof David Henshall's epilepsy research group in the Royal College of Surgeons in Ireland, working to identify biomarkers of epilepsy and neonatal seizures. Up to 30% of patients are misdiagnosed with epilepsy therefore there is a huge demand for a biomarker which could be used as an adjunct to the diagnosis of epilepsy. This work was funded by an SFI Advance Award in collaboration with the SFI Research Centre INFANT. Through my research to date I have created a distinct niche in the biomarker field tackling important challenges including how to combine cutting-edge computational and biomedical techniques to efficiently integrate multiple data types into a single biomarker.

Prior to RCSI I worked as a Senior Postdoctoral Researcher on a SFI funded TIDA under Dr Aidan Meade, DIT, on cancer biomarkers. In August 2013 I completed a four year postdoctoral research fellowship in clinical bioinformatics with Prof Denis Shields, School of Medicine and Medical Science, UCD, where I developed web servers for short linear motif and peptide property prediction ( The software I developed has been utilised in collaborations with industry, including the Enterprise Ireland-funded industry-academia partnership with the Irish food industry, Food for Health Ireland (FHI), and through data analysis work carried out for a US-based cosmetics company.

I completed my PhD in Protein Structure Prediction using Bidirectional Recurrent Neural Networks (BRNN) under the supervision of Dr Gianluca Pollastri in the School of Computer Science, UCD.




Year 2009 Institution: University College Dublin
Qualification: PhD Subject:



Book Chapters

Barbato, Christian and Ruberti, Francesca and Jimenez-Mateos, Eva M and Engel, Tobias and Mooney, Catherine and Henshall, David C (2016) 'MicroRNAs in Epileptogenesis and Epilepsy' In: CRC Press. , pp.153-182 [Details]
Mooney, C.; Davey, N.; Martin, AJ; Walsh, I.; Shields, D.C.; Pollastri, G. (2011) 'In silico protein motif discovery and structural analysis' In: Yu, Bing; Hinchcliffe, Marcus (eds). In silico tools for gene discovery. Clifton, NJ: Springer. , pp.341-353 Available Online [DOI] [Details]
Mooney, C. and Wang, Y. and Pollastri, G.; (2011) 'De Novo Protein Subcellular Localization Prediction by N-to-1 Neural Networks' In: Rizzo, R. and Lisboa, P (eds). Computational Intelligence Methods for Bioinformatics and Biostatistics. Berlin / Heidelberg: Springer. , pp.31-43 Available Online [DOI] [Details]
Martin, A.J.M. and Mooney, C. and Walsh, I. and Pollastri, G.; (2010) 'Contact Map Prediction by Machine Learning' In: H.Rangwala and G.Karypis (eds). Introduction to Protein Structure Prediction: Methods and Algorithms. Hoboken, NJ, USA: John Wiley & Sons, Inc. , pp.137-163 Available Online [DOI] [Details]

Peer Reviewed Journals

Bau, D; Martin, AJM; Mooney, C; Vullo, A; Walsh, I; Pollastri, G; ; (2006) 'Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins'. BMC Bioinformatics, 7 (NA). [Details]
Pollastri, G; Martin, AJM; Mooney, C; Vullo, A; ; (2007) 'Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information'. BMC Bioinformatics, 8 . Available Online [Details]
Walsh I, Bau D, Martin AJM, Mooney C, Vullo A, Pollastri, G; (2009) 'Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks'. BMC Structural Biology, 9 :5. Available Online [DOI] [Details]
Holton, T. A., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'CPPpred: prediction of cell penetrating peptides'. Bioinformatics, . Available Online [Details]
Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields (2013) 'PeptideLocator: prediction of bioactive peptides in protein sequences'. Bioinformatics, . [Details]
Becker, B A; Glanville, G; Iwashima; McDonnell, C; Goslin, K; Mooney, C (2016) 'Effective compiler error message enhancement for novice programming students'. Computer Science Education, 26 (2-3):148-175. Available Online [DOI] [Details]
Hassan, T; Santi, C; Mooney, C; McElvaney, NG; Greene, CM (2017) 'Alpha-1 antitrypsin augmentation therapy decreases miR-199a-5p, miR-598 and miR-320a expression in monocytes via inhibition of NFκB'. Scientific Reports, 7 (1):13803. [DOI] [Details]
Mooney CM, Jimenez-Mateos EM, Engel T, Mooney C, Diviney M, Venø MT, Kjems J, Farrell MA, O'Brien DF, Delanty N, Henshall DC. (2017) 'RNA sequencing of synaptic and cytoplasmic Upf1-bound transcripts supports contribution of nonsense-mediated decay to epileptogenesis'. Scientific Reports, . [DOI] [Details]
Raoof, R; Jimenez-Mateos, EM; Bauer, S; Tackenberg, B; Rosenow, F; Lang, J; Onugoren, MD; Hamer, H; Huchtemann, T; Körtvélyessy, P; Connolly, NMC; Pfeiffer, S; Prehn, JHM; Farrell, MA; O'Brien, DF; Henshall, DC; Mooney, C (2017) 'Cerebrospinal fluid microRNAs are potential biomarkers of temporal lobe epilepsy and status epilepticus'. Scientific Reports, 7 :3328. [DOI] [Details]
Paul McKiernan, Catherine Mooney, David Henshall, Barry Linnane, Paul McNally, Catherine Greene (2016) 'Serum microRNA levels in paediatric females versus males with cystic fibrosis'. European Respiratory Journal, Supplement, . [DOI] [Details]
Mooney, Catherine and Becker, Brett A and Raoof, Rana and Henshall, David C (2016) 'EpimiRBase: a comprehensive database of microRNA-epilepsy associations'. Bioinformatics, 32 (9):1436-1438. [DOI] [Details]
Hennigan, Kerrie and Conroy, Paul J and Walsh, Marie-Therese and Amin, Mohamed and O'Kennedy, Richard and Ramasamy, Patmapriya and Gleich, Gerald J and Siddiqui, Zeshan and Glynn, Senan and McCabe, Olive and others (2016) 'Eosinophil peroxidase activates cells by HER2 receptor engagement and beta1-integrin clustering with downstream MAPK cell signaling'. Clinical Immunology, 171 :1-11. [DOI] [Details]
Bianchin, Alessandra and Bell, Angus and Chubb, Anthony J and Doolan, Nathalie and Leneghan, Darren and Stavropoulos, Ilias and Shields, Denis C and Mooney, Catherine (2015) 'Design and Evaluation of Antimalarial Peptides Derived from Prediction of Short Linear Motifs in Proteins Related to Erythrocyte Invasion'. PLoS ONE, 10 (6):e0127383. [DOI] [Details]
Mooney, Catherine and Raoof, Rana and El-Naggar, Hany and Sanz-Rodriguez, Amaya and Jimenez-Mateos, Eva M and Henshall, David C (2015) 'High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex-and Sample Timing-Related Variation in Plasma of Healthy Volunteers'. PLoS ONE, 10 (12):e0145316. [DOI] [Details]
Jimenez-Mateos, Eva M and Arribas-Blazquez, Marina and Sanz-Rodriguez, Amaya and Concannon, Caoimhin and Olivos-Ore, Luis A and Reschke, Cristina R and Mooney, Claire M and Mooney, Catherine and Lugara, Eleonora and Morgan, James and others (2015) 'microRNA targeting of the P2X7 purinoceptor opposes a contralateral epileptogenic focus in the hippocampus'. Scientific Reports, 5 :17486. [DOI] [Details]
Sheedy, Caroline and Mooney, Claire and Jimenez-Mateos, Eva and Sanz-Rodriguez, Amaya and Langa, Elena and Mooney, Catherine and Engel, Tobias (2014) 'De-repression of myelin-regulating gene expression after status epilepticus in mice lacking the C/EBP homologous protein CHOP'. International Journal of Physiology, Pathophysiology and Pharmacology, 6 (4):185. [Details]
Kruer, Michael C and Salih, Mustafa A and Mooney, Catherine and Alzahrani, Jawahir and Elmalik, Salah A and Kabiraj, Mohammad M and Khan, Arif O and Paudel, Reema and Houlden, Henry and Azzedine, Hamid and others (2014) 'C19orf12 mutation leads to a pallido-pyramidal syndrome'. Gene, 537 (2):352-356. [DOI] [Details]
Nongonierma, Alice B and Mooney, Catherine and Shields, Denis C and FitzGerald, Richard J (2014) 'In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors'. Peptides, 57 :43-51. [DOI] [Details]
Nongonierma, Alice B and Mooney, Catherine and Shields, Denis C and FitzGerald, Richard J (2013) 'Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides'. Food Chemistry, 141 (1):644-653. [Details]
Mooney, Catherine and Cessieux, Amelie and Shields, Denis C and Pollastri, Gianluca (2013) 'SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor'. Amino Acids, 45 (2):291-299. [Details]
Kruer, Michael C and Jepperson, Tyler and Dutta, Sudeshna and Steiner, Robert D and Cottenie, Ellen and Sanford, Lynn and Merkens, Mark and Russman, Barry S and Blasco, Peter A and Fan, Guang and others (2013) 'Mutations in gamma adducin are associated with inherited cerebral palsy'. Annals of Neurology, 74 (6):805-814. [Details]
Khan, Waqasuddin and Duffy, Fergal and Pollastri, Gianluca and Shields, Denis C and Mooney, Catherine (2013) 'Predicting binding within disordered protein regions to structurally characterised peptide-binding domains'. PloS one, 8 (9):e72838. [Details]
Pushker, Ravindra and Mooney, Catherine and Davey, Norman E and Jacque, Jean-Marc and Shields, Denis C (2013) 'Marked variability in the extent of protein disorder within and between viral families'. PLoS ONE, 8 (4):e60724. [Details]
Norris, Roseanne and Casey, Fergal and FitzGerald, Richard J and Shields, Denis and Mooney, Catherine (2012) 'Predictive modelling of angiotensin converting enzyme inhibitory dipeptides'. Food Chemistry, 133 (4):1349-1354. [Details]
Mooney, Catherine and Haslam, Niall J and Pollastri, Gianluca and Shields, Denis C (2012) 'Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity'. PloS one, 7 (10):e45012. [Details]
Mooney, Catherine and Pollastri, Gianluca and Shields, Denis C and Haslam, Niall J (2012) 'Prediction of short linear protein binding regions'. Journal of Molecular Biology, 415 (1):193-204. [Details]
Mooney, Catherine and Pollastri, Gianluca and others (2011) 'SCLpred: protein subcellular localization prediction by N-to-1 neural networks'. Bioinformatics, 27 (20):2812-2819. [Details]
Walsh, Ian and Martin, Alberto JM and Mooney, Catherine and Rubagotti, Enrico and Vullo, Alessandro and Pollastri, Gianluca (2009) 'Ab initio and homology based prediction of protein domains by recursive neural networks'. BMC Bioinformatics, 10 (1):1. [Details]
Mooney, Catherine and Pollastri, Gianluca (2009) 'Beyond the twilight zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information'. Proteins: Structure, Function, and Bioinformatics, 77 (1):181-190. [Details]
Mooney, Catherine and Vullo, Alessandro and Pollastri, Gianluca (2006) 'Protein structural motif prediction in multidimensional phi-psi space leads to improved secondary structure prediction'. Journal of Computational Biology, 13 (8):1489-1502. [Details]

Other Journals

P Bielefeld, C Mooney, DC Henshall, CP Fitzsimons (2016) 'miRNA-Mediated Regulation of Adult Hippocampal Neurogenesis; Implications for Epilepsy' Brain Plasticity . [DOI] [Details]

Conference Publications

Becker, B; Mooney, C (2016) Categorizing Compiler Error Messages with Principal Component Analysis 12th China-Europe International Symposium on Software Engineering Education Shenyang, China, , 28-MAY-16 - 29-MAY-16 Available Online Link to full text [Details]
Mooney, Catherine and Wang, Yong-Hong and Pollastri, Gianluca (2010) De novo protein subcellular localization prediction by N-to-1 neural networks International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics , pp.31-43 [Details]


Mooney C, Vullo A, Pollastri G; (2006) Protein Backbone Angle Prediction in Multidimensional phi-psi Space UCD CSI Technical Report 2006-1. Reports [Details]


Mooney, C,O'Brien, K,Haslam, NJ,Edwards, RJ,Davey, NE,Duffy, FJ,Golla, K,Stavropoulos, I,Khaldi, N,Chubb, AJ,Lombardi, F,Holton, T,Vijay, V,Devocelle, M,Moran, N,Shields, DC (2012) Computational prediction of bioactive peptides. Abstract [Details]


Research Interests

Machine Learning, Computational Biology, Bioinformatics, Medical-Data Science, Medical Informatics

Research Projects

Sponsor : Enterprise Ireland (EI)
Title : Developing Sensible Sensory Solutions to Support for the Irish Food & Research Sectors. SENSible Solutions
Start Date / End Date : 01-FEB-17 / 31-JAN-19
Sponsor : University College Dublin (UCD)
Title : A clinical decision support system for paediatric epilepsy
Start Date / End Date : 01-APR-17 / 30-SEP-18

Recent Postgraduates




Modules Coordinated

201700   COMP1003J     Computer Science: Introduction to Software (B)
201700   COMP3027J     Computer Science: Data Mining