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Digital Organic. Image by Dr. Miguel Nicolau.

Digital Organic. Image by Dr. Miguel Nicolau.

UCD Complex and Adaptive Systems Laboratory

UCD Complex and Adaptive Systems Laboratory - Research Publications 2012/13

Below is the list of research publications for the UCD Complex and Adaptive Systems Laboratory in the academic year 2012/13.




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Book Chapters

Professor Petra Ahrweiler
Schilperoord M, Ahrweiler P (2013) 'Towards a prototype policy laboratory for simulating innovation networks' In: Schilperoord M, Ahrweiler P (eds). Simulating Knowledge Dynamics in Innovation Networks - SKIN. Heidelberg / New York: Springer.  
Dr Claire Gormley
Damien McParland and Isobel Claire Gormley (2013) 'Clustering Ordinal Data via Latent Variable Models' In: Lausen, Berthold; Van den Poel, Dirk; Ultsch, Alfred (Eds.) (eds). Algorithms from and for Nature and Life: Studies in Classification, Data Analysis, and Knowledge Organization. Switzerland: Springer. , pp.127-135 Available Online  
Dr James McDermott
James McDermott and Toby Gifford and Anders Bouwer and Mark Wagy (2013) 'Should Music Interaction Be Easy?' In: Kate Wilkie and Simon Holland and Paul Mulholland and Allan Seago (eds). Music and Human-Computer Interaction. Heidelberg, Germany: Springer. , pp.29-47 Available Online  
James McDermott and Dylan Sherry and Una-May O'Reilly (2013) 'Evolutionary and Generative Music Informs Music HCI---and vice versa' In: Kate Wilkie and Simon Holland and Paul Mulholland and Allan Seago (eds). Music and Human-Computer Interaction. Heidelberg, Germany: Springer. , pp.223-240 Available Online  
Dr Michael O'Neill
Hemberg E., Ho L., O'Neill M., Claussen H. (2013) 'Representing Communication and Learning in Femtocell Pilot Power Control Algorithms' In: Riolo, R. Vladislavleva, E. Ritchie, M.D. Moore, J.H (eds). Genetic Programming Theory and Practice X. Heidelberg: Springer.  
Dr Andrew Parnell
Andrew C. Parnell and W. Roland Gehrels (2013) 'Using chronological models in late holocene sea level reconstructions from salt marsh sediments' In: I. Shennan, B.P. Horton, and A.J. Long (eds). Handbook of Sea Level Research. Chichester: Wiley.  


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Books Edited

Professor Pádraig Cunningham
Padraig Cunningham, Neil J. Hurley, Ido Guy, Sarabjot Singh Anand (Ed.). (2012) 6th ACM Conference on Recommender Systems, RecSys '12. New York: ACM. Available Online  
Dr James McDermott
Machado, Penousal and McDermott, James and Carballal, Adrian (Ed.). (2013) Proceedings of EvoMUSART, the Second International conference on Evolutionary and Biologically Inspired Music, Sound, Art and Design. Heidelberg/Berlin: Springer.  


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Peer Reviewed Journals

Professor Petra Ahrweiler
Ahrweiler P, Schilperoord M, Gilbert N, Pyka A (2013) 'Research policy laboratories. Agent-based modelling for impact assessment and ex-ante evaluation of complex policy instruments'. Research Policy.  
Ahrweiler, P (2012) 'Review of Complex Adaptive Innovation Systems. Relatedness and Transversality in the Evolving Region (Regions and Cities); by Philip Cooke, Routledge: London 2012'. Journal of Artificial Societies and Social Simulation, 15 (4). Available Online  
Professor Christopher Bean
Martini, F. and Lokmer, I. and Jonsdottir, K. and De Barros, L. and Möllhoff, M. and Bean, C. J. and Hauser, F. and Doherty, J. and Ryan, C. and Mongan, J. (2013) 'A passive low-frequency seismic experiment in the Albertine Graben, Uganda'. Geophysical Prospecting, 61:39-61. Available Online  
De Barros, L., Bean, C. J., Zecevic, M., Brenguier, F., Peltier, A. (2013) 'Eruptive fracture location forecasts from high frequency events on Piton de la Fournaise volcano'. Geophysical Research Letters.  
De Barros, L., Lokmer, I., Bean, C.J. (2013) 'Origin of spurious single forces in the course mechanism of volcanic seismicity'. Journal of Volcanology and Geothermal Research, 262:1-6.  
Moni, A., Craig, D., Bean,C.J. (2013) 'Separation and location of microseism sources'. Geophysical Research Letters, 40 (12):3118-3122.  
Murphy, S., O'Brien, G. S., McCloskey, J., Bean, C.J., Nalbant, S. (2013) 'Modelling fluid induced seismicity on a nearby active fault'. Geophysical Journal International, May.  
Zecevic, M.; De Barros, L.; Bean, C.J.; O'Brien, G.S.; Brenguier, F.; (2013) 'Investigating the source characteristics of long-period (LP) seismic events recorded on Piton de la Fournaise volcano, La Réunion'. Journal of Volcanology and Geothermal Research, 258:1-11.  
Eyre, T. S., Bean, C. J., De Barros, L., O'Brien, G. S., Martini, F., Lokmer, I., Mora, M. M., Pacheco J. F., Soto ,G. J., (2013) 'Moment tensor inversion for the source location and mechanism of long period (LP) seismic events from 2009 at Turrialba volcano, Costa Rica'. Journal of Volcanology and Geothermal Research, 258:215-223.  
De Barros, L., F. Martini, C.J. Bean, A. Garcia-Yeguas and J. Ibáñez (2012) 'Imaging magma storage below Teide volcano (Tenerife) using scattered seismic wavefields'. Geophysical Journal International, 191:695-706.  
Dr Chris Bleakley
Reviriego, P.; Bleakley, C.J.; and Maestro, J.A. (2013) 'Diverse Double Modular Redundancy: A New Direction for Soft Error Detection and Correction'. IEEE Design & Test of Computers, 30 (2):87-95. Available Online  
Kamal, A.R.M., Bleakley, C.J., and Dobson, S. (2013) 'Packet-Level Attestation (PLA):A framework for in-network sensor-data reliability'. ACM Transactions on Sensor Networks, 9 (2):19:1-19:28. Available Online  
Razzaque, M.A, Bleakley, C.J. and Dobson, S. (2013) 'Compression in Wireless Sensor Networks: a Survey and Comparative Evaluation'. ACM Transactions on Sensor Networks.  
Lim, J.C and Bleakley, C.J.; (2012) 'Trading Sensing Coverage for an Extended Network Lifetime'. Telecommunication Systems, :1-9. Available Online  
Reviriego et al. (2012) 'Area Efficient Concurrent Error Detection and Correction for Parallel Filters'. Electronics Letters, 48:1258-1260. Available Online  
Professor Anthony Brabazon
Byrne J., Hemberg E., O'Neill M., Brabazon A. (2013) 'A Methodology for User Directed Search in Evolutionary Design'. Genetic Programming and Evolvable Machines, 14.  
Dr Nicolae Buchete
Berezhkovskii, AM; Murphy, RD; Buchete, NV (2013) 'Network random walk model of two-state protein folding: Test of the theory'. The Journal of chemical physics, 138 (3):036101-2. Available Online  
Buchete, NV (2012) 'Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations'. Biophysical Journal, 103:1411-1413. Available Online  
Tofoleanu, F; Buchete, NV (2012) 'Alzheimer's Aβ peptide interactions with lipid membranes: Fibrils, oligomers and polymorphic amyloid channels'. Prion, 6 (4):339-345. Available Online  
Professor Pádraig Cunningham
Redmond, U., Cunningham, P., (2013) 'A temporal network analysis reveals the unprofitability of arbitrage in The Prosper Marketplace'. Expert Systems with Applications, 40 (9):3715-3721.  
Ryan CJ, Krogan NJ., Cunningham P, Cagney, G. (2013) 'All or nothing: protein complexes flip essentiality between distantly related eukaryotes'. Genome Biology and Evolution. Available Online  
Ryan CJ, Krogan NJ, Cunningham P, Cagney G (2013) 'All or Nothing: Protein Complexes Flip Essentiality between Distantly Related Eukaryotes'. Genome Biology and Evolution, 5 (6):1049-1059.  
Dr Kathleen Curran
Puri, T,Frost, ML,Curran, KM,Siddique, M,Moore, AEB,Cook, GJR,Marsden, PK,Fogelman, I,Blake, GM (2013) 'Differences in regional bone metabolism at the spine and hip: a quantitative study using F-18-fluoride positron emission tomography'. Osteoporosis International, 24:633-639.  
Professor Frederic Dias
Elbaz, D,Canaud, B,Ballereau, P,Dias, F (2013) 'Shock propagation in regular wetted arrays of fibers'. Shock Waves, 23:81-89.  
Dutykh, D,Mitsotakis, D,Gardeil, X,Dias, F (2013) 'On the use of the finite fault solution for tsunami generation problems'. Theoretical And Computational Fluid Dynamics, 27:177-199.  
Renzi, E,Dias, F (2013) 'Relations for a periodic array of flap-type wave energy converters'. Applied Ocean Research, 39:31-39.  
O'Brien, L,Dudley, JM,Dias, F (2013) 'Extreme wave events in Ireland: 14 680 BP-2012'. Natural Hazards and Earth System Sciences, 13:625-648.  
Stefanakis, T; Xu, S; Dutykh, D; Dias, F (2013) 'Run-up ampli cation of transient long waves'. Quarterly of Applied Mathematics.  
Viotti, C; Dutykh, D; Dudley, JM; Dias, F (2013) 'Emergence of coherent wave groups in deep-water random sea'. Physical Review E.  
Renzi, E; Dias, F (2013) 'Hydrodynamics of the oscillating wave surge converter in the open ocean'. European Journal of Mechanics - B/Fluids, 41:1-10. Available Online  
Carbone, F; Dutykh, D; Dudley, JM; Dias, F (2013) 'Extreme wave run-up on a vertical cli ff'. Geophysical Research Letters.  
Godin, T; Wetzel, B; Sylvestre, T; Larger, L; Kudlinski, A; Mussot, A; Ben Salem, A; Zghal, M; Genty, G; Dias, F; & Dudley, JM (2013) 'Real time noise and wavelength correlations in octave-spanning supercontinuum generation'. Optics Express.  
Dudley, JM; Sarano, V; Dias, F (2013) 'On Hokusai's Great wave off Kanagawa: localization, linearity and a rogue wave in sub-Antartic waters'. Notes and Records of the Royal Society, 67:159-164.  
Renzi, E; Dias F (2012) 'Relations for a periodic array of flap-type wave energy converters'. Applied Ocean Research, 39:31-39.  
Dr David Edelman
Edelman, D, O'Sullivan P (2013) 'Adaptive Universal Portfolios'. European Journal of Finance, online-ahead-of-print :1-15.  
Professor Nial Friel
A. Caimo, N. Friel (2013) 'Bayesian model selection for exponential random graph models'. Social Networks. Available Online  
McDaid, A., Murphy, T.B., Friel, N., Hurley, N. (2013) 'Improved Bayesian inference for the stochastic block model with application to large networks'. Computational Statistics & Data Analysis, 60:12-31. Available Online  
N. Friel (2013) 'Estimating the evidence for Gibbs random fields'. Journal of Computational and Graphical Statistics, 22 (3):518-532. Available Online  
Dr Marcus Greferath
Byrne, E,Greferath, M,Pernas, J,Zumbragel, J (2013) 'Algebraic decoding of negacyclic codes over Z(4)'. DESIGN CODE CRYPTOGR, 66:3-16.  
Greferath, M,Mc Fadden, C,Zumbragel, J (2013) 'Characteristics of invariant weights related to code equivalence over rings'. DESIGN CODE CRYPTOGR, 66:145-156.  
Dr Therese Holton
I.B. O'Loughlin, B.A. Murray, A. Brodkorb, R.J. FitzGerald, A.A. Robinson, T.A. Holton, P.M. Kelly (2013) 'Whey protein isolate polydispersity affects enzymatic hydrolysis outcomes'. Food Chemistry.  
Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields (2013) 'PeptideLocator: prediction of bioactive peptides in protein sequences'. Bioinformatics.  
Ms Nora Khaldi
Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N (2012) 'EnzymePredictor: A Tool for Predicting and Visualizing Enzymatic Cleavages of Digested Proteins'. Journal of Proteome Research.  
Dr Vladimir Lobaskin
S. R. Maduar, V. Lobaskin, O. I. Vinogradova (2013) 'Electrostatic interaction of heterogeneously charged surfaces with semipermeable membranes'. Faraday discussions. Available Online  
Vladimir Lobaskin, Maksym Romenskyy (2013) 'Collective dynamics in systems of active Brownian particles with dissipative interactions'. Physical Review E, 87. Available Online  
M. Romenskyy, V. Lobaskin (2013) 'Statistical properties of swarms of self-propelled particles with repulsions across the order-disorder transition'. European Physical Journal B (EPJ B), 86 (3). Available Online  
I. Semenov, S. Raafatnia, M. Sega, V. Lobaskin, C. Holm, and F. Kremer (2013) 'Electrophoretic mobility and charge inversion of a colloidal particle studied by single-colloid electrophoresis and molecular dynamics simulations'. Physical Review E, 87 (2). Available Online  
Dr Run Long
Run Long, Ying Dai, Baibiao Huang (2013) 'Fullerene Interfaced with a TiO2(110) Surface May Not Form an Efficient Photovoltaic Heterojunction: First-Principles Investigation of Electronic Structures'. Journal Of Physical Chemistry Letters, 4 (13):2223-2229.  
Run Long (2013) 'Understanding the Electronic Structures of Graphene Quantum Dot Physisorption and Chemisorption onto the TiO2 (110) Surface: A First-Principles Calculation'. Chemphyschem : a European journal of chemical physics and physical chemistry .  
Run Long (2013) 'Electronic Structure of Semiconducting and Metallic Tubes in TiO2/Carbon Nanotube Heterojunctions: Density Functional Theory Calculations'. Journal Of Physical Chemistry Letters, 4 (8):1340-1346. Available Online  
Run Long et al. (2012) 'Photo-Induced Charge Separation across the Graphene-TiO2 Interface Occurs Faster than Energy Losses: a Time-Domain Ab Initio Analysis'. Journal of the American Chemistry Society.  
Professor Peter Lynch
Courtney, Jennifer, Peter Lynch and Conor Sweeney (2013) 'High Resolution Forecasting for Wind Energy Applications using Bayesian Model Averaging'. Tellus, 65. Available Online  
Peter Lynch and Miguel D Bustamante (2013) 'Quaternion Solution for the Rock'n'roller: Box Orbits, Loop Orbits and Recession'. Regular and Chaotic Dynamics, 18 (1-2):166-183. Available Online  
Sweeney, Conor, Peter Lynch and Paul Nolan. (2013) 'Reducing errors of wind speed forecasts by an optimal combination of post-processing methods'. Meteorological Applications, 20 (1):32-40. Available Online  
Nolan, Paul, Peter Lynch and Conor Sweeney (2012) 'Simulating the future wind energy resource of Ireland using the COSMO-CLM model'. Wind Energy. Available Online  
Dr Donal MacKernan
Lucid, Jeremy; Meloni, Simone; MacKernan, Donal; Spohr, Eckhard; Ciccotti, Giovanni (2012) 'Probing the Structures of Hydrated Nafion in Different Morphologies Using Temperature Accelerated Molecular Dynamics simulations'. The journal of physical chemistry. A.  
Professor Joao Marques-Silva
Antonio Morgado, Federico Heras, Mark Liffiton, Jordi Planes, Joao Marques-Silva (2013) 'Iterative and core-guided MaxSAT solving: A survey and assessment'. Constraints, 18 (4):478-534.  
Anton Belov and Ines Lynce and Joao Marques-Silva (2012) 'Towards efficient MUS extraction'. AI Communications, 25 (2):97-116.  
Mikol\'as Janota and Ines Lynce and Vasco M. Manquinho and Joao Marques-Silva (2012) 'PackUp: Tools for Package Upgradability Solving'. JSAT, 8 (1/2):89-94.  
Anton Belov and Joao Marques-Silva (2012) 'MUSer2: An Efficient MUS Extractor'. JSAT, 8 (1/2):123-128.  
Joao Marques-Silva (2012) 'Computing Minimally Unsatisfiable Subformulas: State of the Art and Future Directions'. Journal of Multiple-Valued Logic and Soft Computing, 19 (1-3):163-183.  
Dr James McDermott
David R. White, James McDermott, Mauro Castelli, Luca Manzoni, Brian W. Goldman, Gabriel Kronberger, Wojciech Jaskowski, Una-May O'Reilly, and Sean Luke (2013) 'Better GP Benchmarks: Community Survey Results and Proposals'. Genetic Programming and Evolvable Machines, 14 (1):3-29.  
Edgar Galvan-Lopez and James McDermott and Michael O'Neill and Anthony Brabazon (2012) 'Defining locality as a problem difficulty measure in genetic programming'. Genetic Programming and Evolvable Machines, 12 (4):365-401.  
James McDermott and Jonathan Byrne and John Mark Swafford and Martin Hemberg and Ciaran McNally and Elizabeth Shotton and Erik Hemberg and Michael Fenton and Michael O'Neill (2012) 'A Comparison of Shape Grammars and String-Rewriting Grammars in Evolutionary Architectural Design'. Environment and Planning B: Planning and Design, 39 (4):713-731. Available Online  
McDermott, J; Byrne, J; Mark Swafford, J; Hemberg, M; McNally, C; Shotton, E: Hemberg, E; Fenton, M; O'Neill, M; (2012) 'String-rewriting grammars for evolutionary architectural design'. Environment and Planning B: Planning and Design, 39 (4):713-731. Available Online  
Dr Sean McGarraghy
Carroll, P,Fortz, B,Labbe, M,McGarraghy, S (2013) 'A branch-and-cut algorithm for the ring spur assignment problem'. Networks, 61:89-103.  
Carroll, P,McGarraghy, S (2013) 'A decomposition algorithm for the ring spur assignment problem'. International Transactions in Operational Research, 20 (1):119-139. Available Online  
Professor Gary McGuire
Gologlu, F,McGuire, G,Moloney, R (2013) 'Some congruences of Kloosterman sums and their characteristic polynomials'. Journal of Number Theory, 133:1596-1607.  
Hernando, Fernando; McGuire, Gary (2012) 'Proof of a conjecture of Segre and Bartocci on monomial hyperovals in projective planes'. Designs Codes and Cryptography.  
Professor Thomas Murphy
Gollini, I. and Murphy, T.B. (2013) 'Mixture of Latent Trait Analyzers for Model-Based Clustering of Categorical Data'. Statistics and Computing.  
Galligan, M.C., Saldova, R., Campbell, M.P., Rudd, P.M. and Murphy, T.B. (2013) 'Greedy feature selection for glycan chromatography data using the generalized Dirichlet distribution'. BMC Bioinformatics, 14.  
Collins, E.S., Galligan, M.C., Saldova, R., Adamczyk, B., Abrahams, J.L., Campbell, M.P., Ng, C.T., Veale, D.J., Murphy, T.B., Rudd, P.M., FitzGerald, O. (2013) 'Glycosylation Status of Serum in Inflammatory Arthritis in Response to Anti-TNF Treatment'. Rheumatology, 52 (9):1572-1582.  
McDaid, A., Murphy, T.B., Friel, N., Hurley, N. (2013) 'Improved Bayesian inference for the stochastic block model with application to large networks'. Computational Statistics & Data Analysis, 60:12-31. Available Online  
Salter-Townshend, M. and Murphy, T.B. (2013) 'Variational Bayesian inference for the latent position cluster model for network data'. Computational Statistics & Data Analysis, 57 (1):661-671.  
Dr Michael O'Neill
Hemberg, E,Ho, L,O'Neill, M,Claussen, H (2013) 'A comparison of grammatical genetic programming grammars for controlling femtocell network coverage'. Genetic Programming and Evolvable Machines, 14:65-93.  
Uy, NQ,Hoai, NX,O'Neill, M,McKay, RI,Phong, DN (2013) 'On the roles of semantic locality of crossover in genetic programming'. Information Sciences, 235:195-213.  
Fenton, M, McNally, C, Byrne, J, Hemberg, E & O'Neill, M (2013) 'Automatic innovative truss design using grammatical evolution'. International Research Journal of Automation in Construction.  
McDermott, J, Swafford, JM, Hemberg, M, Byrne, J, Hemberg, E, Fenton, M, McNally, C, Shotton, E, & O'Neill, M; (2012) 'Advantages and limitations of string-rewriting grammars in evolutionary architectural design'. Environment and Planning B: Planning and Design, 39 (4):713-731.  
Professor Adrian Ottewill
Casals, Marc and Dolan, Sam and Ottewill, Adrian C. and Wardell, Barry (2013) 'Self-force and Green function in Schwarzschild spacetime via quasinormal modes and branch cut'. Phys. Rev. D, 88. Available Online  
Casals, Marc and Dolan, Sam R. and Nolan, Brien C. and Ottewill, Adrian C. and Winstanley, Elizabeth (2013) 'Quantization of fermions on Kerr space-time'. Phys. Rev. D, 87. Available Online  
Casals, M,Ottewill, A (2013) 'Analytic investigation of the branch cut of the Green function in Schwarzschild space-time'. Phys Rev D, 87.  
M. Casals and A.C. Ottewill (2012) 'Spectroscopy of the Schwarzschild Black Hole at Arbitrary Frequencies'. Physical Review Letters, 109.  
Dr Andrew Parnell
Andrew C. Parnell, Donald L. Phillips, Stuart Bearhop, Brice X. Semmens, Eric J. Ward, Jonathan W. Moore, Andrew L. Jackson, Richard Inger (2013) 'Bayesian stable isotope mixing models'. Environmetrics.  
Mafalda Viana, Andrew L. Jackson, Norman Graham and Andrew C. Parnell (2012) 'Disentangling spatio-temporal processes in a hierarchical system: a case study in fisheries discards'. Ecography.  
Dr Gianluca Pollastri
A.Lusci, G.Pollastri, P.Baldi (2013) 'Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules'. Journal of Chemical Information and Modeling, 53 (7):1563-1575. Available Online  
C.Mirabello, G.Pollastri (2013) 'Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility'. Bioinformatics, 29 (16):2056-2058. Available Online  
C.Mooney, N.Haslam, T.Holton, G.Pollastri, D.Shields (2013) 'PeptideLocator: Prediction of Bioactive Peptides in Protein Sequences'. Bioinformatics.  
C.Mooney, A.Cessieux, D.Shields, G.Pollastri (2013) 'SCL-Epred: A Generalised De novo Eukaryotic Protein Subcellular Localisation Predictor'. Amino Acids.  
V.Volpato, A.Adelfio, G.Pollastri (2013) 'Accurate prediction of protein enzymatic class by N-to-1 Neural Networks'. BMC Bioinformatics.  
Mr Colm Ryan
Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FC, Johnson JR, Bloom K, Krogan NJ (2013) 'Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation'. Cell reports.  
Ryan CJ, Krogan NJ, Cunningham P, Cagney G (2013) 'All or Nothing: Protein Complexes Flip Essentiality between Distantly Related Eukaryotes'. Genome Biology and Evolution, 5 (6):1049-1059.  
Dr Michael Salter-Townshend
Salter-Townshend, M. and Murphy, T.B. (2013) 'Variational Bayesian inference for the latent position cluster model for network data'. Computational Statistics & Data Analysis, 57 (1):661-671.  
Dr Goar Sanchez
J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz, J. Elguero (2013) 'Phosphorus As a Simultaneous Electron-Pair Acceptor in Intermolecular P...N Pnicogen Bonds and Electron-Pair Donor to Lewis Acids'. The Journal of Physical Chemistry A, 117 (14):3133-3141. Available Online  
R. Aggarwal, V. Kumar, G. Singh, D. Sanz, R. M. Clamunt, I. Alkorta, G. Sanchez-Sanz and J. Elguero (2013) 'An NMR and Computational Study of Azolo[a]pyrimidines with Special Enphasis on Pyrazolo[1,5-a]pyrimidines'. Journal of Heterocyclic Chemistry, 0.  
J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz and J. Elguero (2013) 'Ab Initio Study of Cooperative Effects in Complexes X:HBO:Z with X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO: Structures, Binding Energies, and Spin-Spin Coupling Constants across Intermolecular Bonds'. Zeitschrift fur Physikalische Chemi, 227.  
C. Trujillo, G. Sanchez-Sanz, I. Alkorta, J. Elguero, O. Mo, M. Yanez (2013) 'Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study'. Journal of Molecular Structure, 1048 (0):138-151. Available Online  
D. Sanz, R. M. Claramunt, F. Mathey, I. Alkorta, G. Sanchez-Sanz, J. Elguero (2013) 'Intermolecular spin-spin coupling constants between 31P atoms'. Comptes Rendus Chimie, 16 (10):937-944. Available Online  
I. Alkorta, I. Sanchez-Sanz, J. Elguero (2013) 'Linear free energy relationships in halogen bonds'. CrystEngComm, 15:3178-3186. Available Online  
C. Trujillo, G. Sanchez-Sanz, I. Alkorta, J. Elguero (2013) 'A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model'. Structural Chemistry, 24 (4):1145-1151. Available Online  
I. Rozas, G. Sanchez-Sanz, I. Alkorta, J. Elguero (2013) 'Solvent effects on guanidinium-anion interactions and the problem of guanidinium Y-aromaticity'. Journal of Physical Organic Chemistry, 26 (5):378-385. Available Online  
I. Alkorta, G. Sanchez-Sanz, J. Elguero, J. E. Del Bene (2013) 'Exploring (NH2F)2, H2FP:NFH2, and (PH2F)2 Potential Surfaces: Hydrogen Bonds or Pnicogen Bonds?'. The Journal of Physical Chemistry A, 117 (1):183-191. Available Online  
F. Blanco, B. Kelly, G. Sanchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero, I. Rozas (2013) 'Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases'. The Journal of Physical Chemistry B, 117 (39):11608-11616. Available Online  
A. J. Salkeld M. F. Reid, J.-P. R Wells, G. Sanchez-Sanz, L. Seijo, Z. Barandiaran (2013) 'Effective Hamiltonian parameters for ab-initio energy-level calculations of SrCl2 :Yb2+ and CsCaBr3:Yb2+'. Journal of Physics: Condensed Matter, 25 (41). Available Online  
G. Sanchez-Sanz, C. Trujillo, M. Solimannejad, I. Alkorta, J. Elguero (2013) 'Orthogonal interactions between nitryl derivatives and electron donors: pnictogen bonds'. Phys. Chem. Chem. Phys, 15:14310-14318. Available Online  
G. Sanchez-Sanz, C. Trujillo, I. Rozas, J. Elguero (2013) 'A theoretical study on the aromaticity of benzene and related derivatives incorporating a C-C=C-C fragment'. Tetrahedron, 69 (35):7333-7344. Available Online  
G. Sanchez-Sanz, I. Alkorta, C. Trujillo, J. Elguero (2013) 'Intramolecular Pnicogen Interactions in PHF-(CH2)n-PHF (n=2-6) Systems'. ChemPhysChem, 14 (8):1656-1665. Available Online  
Professor Denis Shields
Khan, W., Duffy, F., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'Predicting binding within disordered protein regions to structurally characterised peptide-binding domains'. PLoS One, 8 (9). Available Online  
Pushker, R., Mooney, C., Davey, N. E., Jacque, J. M., Shields, D. C. (2013) 'Marked variability in the extent of protein disorder within and between viral families'. PLoS One, 8 (4). Available Online  
O'Brien, K. T., Haslam, N. J., Shields, D. C. (2013) 'SLiMScape: a protein short linear motif analysis plugin for Cytoscape'. BMC Bioinformatics, 14. Available Online  
Mooney, C., Cessieux, A., Shields, D. C., Pollastri, G. (2013) 'SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor'. Amino Acids, 45 (2):291-9. Available Online  
den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J., Peal, D. S., Evans, D. M., Nolte, I. M., Segre, A. V., Holm, H., Handsaker, R. E., Westra, H. J., Johnson, T., Isaacs, A., Yang, J., Lundby, A., Zhao, J. H., Kim, Y. J., Go, M. J., Almgren, P., Bochud, M., Boucher, G., Cornelis, M. C., Gudbjartsson, D., Hadley, D., van der Harst, P., Hayward, C., den Heijer, M., Igl, W., Jackson, A. U., Kutalik, Z., Luan, J., Kemp, J. P., Kristiansson, K., Ladenvall, C., Lorentzon, M., Montasser, M. E., Njajou, O. T., O'Reilly, P. F., Padmanabhan, S., St Pourcain, B., Rankinen, T., Salo, P., Tanaka, T., Timpson, N. J., Vitart, V., Waite, L., Wheeler, W., Zhang, W., Draisma, H. H., Feitosa, M. F., Kerr, K. F., Lind, P. A., Mihailov, E., Onland-Moret, N. C., Song, C., Weedon, M. N., Xie, W., Yengo, L. (2013) 'Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders'. Nat Genet, 45 (6):621-31. Available Online  
O'Brien, R. P., Phelan, P. J., Conroy, J., O'Kelly, P., Green, A., Keogan, M., O'Neill, D., Jennings, S., Traynor, C., Casey, J., McCormack, M., Conroy, R., Chubb, A., Ennis, S., Shields, D. C., Cavalleri, G. L., Conlon, P. J. (2013) 'A genome-wide association study of recipient genotype and medium-term kidney allograft function'. Clin Transplant, 27 (3):379-87. Available Online  
Mooney, C., Haslam, N. J., Holton, T. A., Pollastri, G., Shields, D. C. (2013) 'PeptideLocator: prediction of bioactive peptides in protein sequences'. Bioinformatics, 29 (9):1120-6. Available Online  
Vijayakumar, V., Guerrero, A. N., Davey, N., Lebrilla, C. B., Shields, D. C., Khaldi, N. (2012) 'EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins'. J Proteome Res, 11 (12):6056-65. Available Online  
Davey, N. E., Cowan, J. L., Shields, D. C., Gibson, T. J., Coldwell, M. J., Edwards, R. J. (2012) 'SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions'. Nucleic Acids Research, 40 (21):10628-41. Available Online  
Sudol, M., Shields, D. C., Farooq, A. (2012) 'Structures of YAP protein domains reveal promising targets for development of new cancer drugs'. Seminars in Cell and Developmental Biology, 23 (7):827-33. Available Online  
Haslam, N. J., Shields, D. C. (2012) 'Peptide-binding domains: are limp handshakes safest?'. Sci Signal, 5 (243). Available Online  
Dr Niels Warburton
Warburton,N; Barack, L; Sago, N (2013) 'Isofrequency pairing of geodesic orbits in Kerr geometry'. Phys Rev D. Available Online  


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Conference Publications

Dr Chris Bleakley
Kamal, A.R.M., Bleakley, C.J., and Dobson, S. (2012) Congestion Mitigation using In-network Sensor Data Summarization 9th ACM Int. Symp. on Performance Evaluation of Wireless Ad Hoc, Sensor, and Ubiquitous Networks (PE-WASUN), Cyprus,  
Saad, M., et al. (2012) High accuracy Location Estimation of a Mobile Tag using One-way UWB Signalling Ubiquitous Positioning Indoor Navigation and Location Based Service (UPINLBS), Helsinki, Finland,  
Yadav, N., and Bleakley, C.J. (2012) Hybrid Bayesian Fusion of Range-based and Sourceless Location Estimates Under Varying Observability 6th IEEE Int. Conf. on Intelligent Systems (IS), Sofia, Bulgaria, 90 - 95 Available Online  
Professor Anthony Brabazon
Tuite, C., Agapitos, A., O'Neill, M. and Brabazon, A. (2013) Towards a Dynamic Benchmark for Genetic Programming Genetic and Evolutionary Computation Conference (GECCO 2013), Amsterdam,  
Yin, Z., O'Sullivan, C. and Brabazon, A. (2013) Empirical Analysis of Delta Hedging Irish Accounting and Finance Association Annual Conference (IAFA) 2013, Institute of Technology, Tallaght,  
Brabazon, A. and Drechsler, C. (2013) In vino veritas?: Fine wine as an asset class Irish Accounting and Finance Association Annual Conference (IAFA) 2013, Institute of Technology, Tallaght,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2013) Adaptive Distance Metrics for Nearest Neighbour Classification based on Genetic Programming 16th European Conference on Genetic Programming (EuroGP 2013), Vienna,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2012) Controlling Overfitting in Symbolic Regression based on a Bias/Variance Error Decomposition 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taormina, Sicily, Italy, 438 - 447  
Nicolau, M., O'Neill, M. and Brabazon, A. (2012) Applying Genetic Regulatory Networks to Index Trading 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taormina, Sicily, Italy, 428 - 437  
Swafford, J.M., Hemberg, E., O'Neill, M. and Brabazon, A. (2012) Analyzing Module Usage in Grammatical Evolution 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taromina, Sicily, Italy, 347 - 356  
Murphy, E., Nicolau, M., Hemberg, E., O'Neill, M. and Brabazon, A. (2012) Differential Gene Expression with Tree-Adjunct Grammars 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taromina, Sicily, Italy, 377 - 386  
Dr Nicolae Buchete
Tofoleanu, F; Buchete NV (2013) Molecular Interactions of Alzheimer's A beta Peptide Fibrils and Oligomers with Lipid Membranes Biophysical Society 57th Annual Meeting; Biophysical Journal, Philadelphia, PA, 592A - 592A Available Online  
Dr Eimear Byrne
Eimear Byrne (2013) On Nework Coding Bounds International Workshop on Coding and Cryptography,  
Professor Pádraig Cunningham
Greene, D.; Sheridan, G.; Smyth, B.; Cunningham, P. (2012) Aggregating Content and Network Information to Curate Twitter User Lists RSWeb '12 Proceedings of the 4th ACM RecSys workshop on recommender systems and the social web, Dublin, Ireland,  
Greene, D.; O'Callaghan, D.; Cunningham, P. (2012) Identifying Topical Twitter Communities via User List Aggregation 2nd International Workshop on Mining Communities and People Recommenders (COMMPER 2012) at ECML 2012, Bristol, UK,  
Brigadir, I.; Greene, D.; Cunningham, P. (2012) A System for Twitter User List Curation ACM RecSys 2012, Dublin, Ireland,  
O'Callaghan, D; Greene, D.;Conway, M.; Carthy, J.; Cunningham, P. (2012) An Analysis of Interactions Within and Between Extreme Right Communities in Social Media 3rd International Workshop on Mining Ubiquitous and Social Environments (MUSE 2012) at ECML 2012, Bristol, UK,  
Lee C., Cunningham P., (2012) The Geographic Flow of Music International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2012), Istanbul, Turkey, Available Online  
Stabeler M., Lee C., Cunningham P., (2012) An Assessment of Community Finding Algorithms for Community-Based Message Routing in DTNs 10th International Conference on Wired/Wireless Internet Communication, 244 - 256 Available Online  
Professor Frederic Dias
Sarkar, D; Renzi, E; Dias, F (2013) Wave-power extraction by an oscillating wave surge converter in random seas 32nd International Conference on Ocean, Offshore and Arctic Engineering, OMAE13,  
Renzi E; Dias F (2013) Mathematical model of a flap-type wave energy converter 32nd International Conference on Ocean, Offshore and Arctic Engineering, OMAE 2013,  
Renzi, E; Dias, F (2013) Wave-power extraction from a finite array of Oscillating Wave Surge Converters 28th International Workshop on Water Waves and Floating Bodies,  
Dias, F; Renzi, E (2012) Hydrodynamic modelling of the Oscillating Wave Surge Converter 13emes Journees de l'Hydrodynamique,  
Renzi, E; Abdolali, A; Bellotti, G; Dias, F (2012) Mathematical and numerical modelling of a flap-type wave energy converter in a channel 33rd Conference on Hydraulics and Hydraulic Structures, IDRA 2012,  
Renzi, E; Dias, F (2012) Mathematical modelling of an array of flap-type wave energy converters European Fluid Mechanics Conference EFMC9,  
Dr Jos Elkink
Elkink, Johan A. (2013) Spatial, temporal and spatio-temporal clustering of democracy and autocracy Annual Meeting of the American Political Science Association,  
Elkink, Johan A.; Sattler, Thomas (2013) When Knowledge Counts Twice: The role of turnout for EU referendum results 3rd Annual General Conference of the European Political Science Association, Barcelona,  
Elkink, Johan A.; Sattler, Thomas (2012) When Knowledge Counts Twice: The role of turnout for EU referendum results 6th Pan-European Conference of EU Politics, Tampere,  
Professor Nial Friel
N. Friel (2012) Bayesian inference for Gibbs random fields using composite likelihoods Proceedings of the 2012 Winter Simulation Conference, Available Online  
Dr Russell Higgs
Cao, N.; Higgs, R.; O'Hare, G.M.P. (2012) An Intelligent Evaluation Model based on the LEACH Protocol in Wireless Sensor Networks Proceedings of International Conference on Cyber-Enabled Distributed Computing and Knowledge Discovery (CyberC 2012), Sanya, Hainan, China,  
Professor Joao Marques-Silva
Joao Marques-Silva and Federico Heras and Mikolas Janota and Alessandro Previti and Anton Belov (2013) On Computing Minimal Correction Subsets IJCAI,  
Anton Belov and Huan Chen and Alan Mishchenko and Joao Marques-Silva (2013) Core minimization in SAT-based abstraction DATE, 1411 - 1416  
Alessandro Previti and Joao Marques-Silva (2013) Partial MUS Enumeration AAAI,  
Alexey Ignatiev and Mikolas Janota and Joao Marques-Silva (2013) Quantified Maximum Satisfiability: - A Core-Guided Approach SAT, 250 - 266  
William Klieber and Mikolas Janota and Joao Marques-Silva and Edmund M. Clarke (2013) Solving QBF with Free Variables CP, 415 - 431  
Anton Belov and Norbert Manthey and Joao Marques-Silva (2013) Parallel MUS Extraction SAT, 133 - 149  
Anton Belov and Matti Jarvisalo and Joao Marques-Silva (2013) Formula Preprocessing in MUS Extraction TACAS, 108 - 123  
Mikolas Janota and Joao Marques-Silva (2013) On Propositional QBF Expansions and Q-Resolution SAT, 67 - 82  
Joao Marques-Silva and Mikolas Janota and Anton Belov (2013) Minimal Sets over Monotone Predicates in Boolean Formulae CAV, 592 - 607  
Federico Heras and Antonio Morgado and Jordi Planes and Joao Marques-Silva (2012) Iterative SAT Solving for Minimum Satisfiability ICTAI, 922 - 927 Available Online  
Dr James McDermott
James McDermott and Paula Carroll (2013) Program Optimisation with Dependency Injection. In: Krzysztof Krawiec and Alberto Moraglio eds. EuroGP, Vienna, Austria,  
Dr Sean McGarraghy
Seán McGarraghy and Michael Phelan (2013) Generating Supply Chain Ordering Policies using Quantum Inspired Genetic Algorithms and Grammatical Evolution EURO-INFORMS MMXIII: 26TH EUROPEAN CONFERENCE ON OPERATIONAL RESEARCH, Rome, Italy,  
Fagan D., Hemberg E., O'Neill M., McGarraghy S. (2013) Understanding Expansion Order and Phenotypic Connectivity in piGE EuroGP 2013 the 16th European Conference on Genetic Programming,  
Professor Gary McGuire
Gologlu, F; Granger, R; McGuire, G; Zumbragel, J (2013) On the Function Field Sieve and the Impact of Higher Splitting Probabilities Advances in Cryptology--CRYPTO 2013,  
Gologlu, F; Granger, R; McGuire, G; Zumbragel, J (2013) Solving a 6120-bit DLP on a Desktop Computer Selected Areas in Cryptography--SAC 2013,  
Dr Miguel Nicolau
Nicolau, M; O'Neill, M; Brabazon, A (2012) Applying Genetic Regulatory Networks to Index Trading. In: Carlos A. Coello Coello and Vincenzo Cutello and Kalyanmoy Deb and Stephanie Forrest and Giuseppe Nicosia and Mario Pavone eds. Parallel Problem Solving from Nature - PPSN XII, 12th International Conference, Taormina, Italy, 428 - 437 Available Online  
Dr Michael O'Neill
Fenton, M, McNally, C & O'Neill, M (2013) The Interaction between Objectives and Constraints in Evolutionary Structural Engineering Optimisation 12th U.S. National Congress on Computational Mechanics (USNCCM12), Raleigh, North Carolina,  
Tuite, C., Agapitos, A., O'Neill, M. and Brabazon, A. (2013) Towards a Dynamic Benchmark for Genetic Programming Genetic and Evolutionary Computation Conference (GECCO 2013), Amsterdam,  
Fagan D., Hemberg E., O'Neill M., McGarraghy S. (2013) Understanding Expansion Order and Phenotypic Connectivity in piGE EuroGP 2013 the 16th European Conference on Genetic Programming,  
Pham T.A., Nguyen Q.U., Nguyen X.H., O'Neill M. (2013) Examining the Diversity Property of Semantic Similarity based Crossover EuroGP 2013 the 16th European Conference on Genetic Programming,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2013) Adaptive Distance Metrics for Nearest Neighbour Classification based on Genetic Programming 16th European Conference on Genetic Programming (EuroGP 2013), Vienna,  
Shaker N., Yannakakis G.N., Togelius J., Nicolau M., O'Neill M. (2012) Evolving Personalized Content for Super Mario Bros Using Grammatical Evolution Eighth AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment (AIIDE-12),  
Agapitos, A., O'Neill, M. and Brabazon, A. (2012) Controlling Overfitting in Symbolic Regression based on a Bias/Variance Error Decomposition 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taormina, Sicily, Italy, 438 - 447  
Nicolau, M., O'Neill, M. and Brabazon, A. (2012) Applying Genetic Regulatory Networks to Index Trading 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taormina, Sicily, Italy, 428 - 437  
Swafford, J.M., Hemberg, E., O'Neill, M. and Brabazon, A. (2012) Analyzing Module Usage in Grammatical Evolution 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taromina, Sicily, Italy, 347 - 356  
Murphy, E., Nicolau, M., Hemberg, E., O'Neill, M. and Brabazon, A. (2012) Differential Gene Expression with Tree-Adjunct Grammars 12th International Conference on Parallel Problem Solving From Nature (PPSN 2012), Taromina, Sicily, Italy, 377 - 386  
O'Neill M., Brabazon A. (2012) An Analysis of Natural Computing Publication Venues: A focus on Immunocomputing 11th International Conference on Artificial Immune Systems ICARIS 2012,  
O'Neill M., Brabazon A. (2012) A Survey of Immunocomputing in Business Analytics and Finance 11th International Conference on Artificial Immune Systems ICARIS 2012,  
Shaker N., Nicolau M., Yannakakis G.N., Togelius J., O'Neill M. (2012) Evolving Levels for Super Mario Bros Using Grammatical Evolution CIG 2012 IEEE Conference on Computational Intelligence and Games,  
Hemberg E., Ho L., O'Neill M., Claussen H. (2012) Evolving Femtocell Algorithms with Dynamic & Stationary Training Scenarios 12th Int. Conf. on Parallel Problem Solving from Nature - PPSN XII,  


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Other Publications

Dr Claire Gormley
McParland, D. and Gormley, I.C. (2013) Discussion of `How to find an appropriate clustering for mixed-type variables with application to socio-economic stratification' by Hennig, C. and Liao, T.F'. Editorial.  
Professor Thomas Murphy
Russell, N., Cribbin, L. and Murphy, T.B. (2012) upclass: Updated Classification Methods using Unlabelled Data. Software. Available Online  
Dr Andrew Parnell
Andrew Parnell (2012) Review of 'Climate Time Series Analysis' by Manfred Mudelsee. Book Reviews.