Report of President 2012/2013 - Complex

and Adaptive Systems Laboratory (CASL)

>> Book Chapters

>> Books Edited

>> Peer Reviewed Journals

>> Conference Publications

>> Other Publications

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

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

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

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.

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).

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.

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.

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.

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.

Reviriego et al. (2012) 'Area Efficient Concurrent Error Detection and Correction for

Parallel Filters'. Electronics Letters, 48:1258-1260.

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.

Buchete, NV (2012) 'Unlocking the Atomic-Level Details of Amyloid Fibril Growth

through Advanced Biomolecular Simulations'. Biophysical Journal, 103:1411-1413.

Tofoleanu, F; Buchete, NV (2012) 'Alzheimer's Aβ peptide interactions with lipid

membranes: Fibrils, oligomers and polymorphic amyloid channels'. Prion, 6 (4):339-

345.

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.

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.

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.

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.

N. Friel (2013) 'Estimating the evidence for Gibbs random fields'. Journal of

Computational and Graphical Statistics, 22 (3):518-532.

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.

Vladimir Lobaskin, Maksym Romenskyy (2013) 'Collective dynamics in systems of

active Brownian particles with dissipative interactions'. Physical Review E, 87.

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).

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).

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.

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.

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.

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.

Nolan, Paul, Peter Lynch and Conor Sweeney (2012) 'Simulating the future wind energy

resource of Ireland using the COSMO-CLM model'. Wind Energy.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

I. Alkorta, I. Sanchez-Sanz, J. Elguero (2013) 'Linear free energy relationships in

halogen bonds'. CrystEngComm, 15:3178-3186.

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.

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.

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.

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.

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).

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.

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.

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.

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).

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).

O'Brien, K. T., Haslam, N. J., Shields, D. C. (2013) 'SLiMScape: a protein short linear

motif analysis plugin for Cytoscape'. BMC Bioinformatics, 14.

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.

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.

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.

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.

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.

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.

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.

Haslam, N. J., Shields, D. C. (2012) 'Peptide-binding domains: are limp handshakes

safest?'. Sci Signal, 5 (243).

Dr Niels Warburton

Warburton,N; Barack, L; Sago, N (2013) 'Isofrequency pairing of geodesic orbits in

Kerr geometry'. Phys Rev D.

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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

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

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,

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

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,

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

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

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.

Dr Andrew Parnell

Andrew Parnell (2012) Review of 'Climate Time Series Analysis' by Manfred Mudelsee.

Book Reviews.

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