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'Speak of the devil...'. Image by Emiliano Renzi.

'Speak of the devil...'. Image by Emiliano Renzi.

UCD Complex and Adaptive Systems Laboratory

UCD Complex and Adaptive Systems Laboratory - Research Publications 2013/14

Below is the list of research publications for the UCD Complex and Adaptive Systems Laboratory in the academic year 2013/14.




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Book Chapters

Dr Chris Bleakley
Gonzalez, J.R, Saad, M., and Bleakley, C.J. (2013) 'Wideband Ultrasonic Transmitter and Sensor Array for In-Air Applications' In: Iniewski, K (eds). Smart Sensors for Industrial Applications. USA: CRC Press, pp.411-432 Available Online  
Gonzalez, J.R., Saad, M., and Bleakley, C.J. (2013) 'Wideband Ultrasonic Transmitter and Sensor Array for In-Air Applications' In: Choudhary, V., and Iniewski, K (eds). MEMS: Fundamental Technology and Applications. USA: CRC Press, pp.227-248 Available Online  
Dr Claire Gormley
Gormley, I.C. and Murphy, T.B. (2014) 'Mixed membership models for rank data: Investigating structure in Irish voting data' In: Airoldi, E., Blei, D. Erosheva, E., Fienberg, S (eds). Handbook of Mixed Membership Models. Boca Raton, FL: CRC Press, pp.297-320  
Professor Mohand Kechadi
Chabo, Y, Bertaux, A, Nicolle, C, Kechadi, M-T (2014) 'Event reconstruction: A state of the art' In: M M Cruz-Cunha, I M Portela (eds). Handbook of Research on Digital Crime, Cyberspace Security, and Information Assurance. New York, USA: IGI Global.  
Savvas I.K., Sofianidou, G.N., Kechadi, M-T. (2013) 'Applying the K-Means Algorithm in Big Raw Data Sets with Hadoop and MapReduce' In: W. Hu, and N. Kaabouch (eds). Big Data Management, Technologies, and Applications. NY: Hershey, PA, pp.23-46  
Professor Thomas Murphy
Gormley, I.C. and Murphy, T.B. (2014) 'Mixed membership models for rank data: Investigating structure in Irish voting data' In: Airoldi, E., Blei, D. Erosheva, E., Fienberg, S (eds). Handbook of Mixed Membership Models. Boca Raton, FL: CRC Press, pp.297-320  
Salter-Townshend, M. and Murphy, T.B. (2013) 'Sentiment Analysis of Online Media' In: Lausen, B., van del Poel, D. and Ultsch, A (eds). Algorithms from and for Nature and Life. Heidelberg: Springer, pp.137-146  
Dr Andrew Parnell
L. Staunton, T. Clancy, C. Tonry, S. Ademowo, M. Dharsee,C B. Hernández, K. Evans, R.W. Watson, A.C. Parnell And S.R. Pennington (2013) 'Protein Quantification by MRM for Biomarker Validation' In: Claire Eyers and Simon Gaskell (eds). Quantitative Proteomics. London: Royal Society of Chemistry.  
Dr Diane Payne
Pablo Lucas and Diane Payne (2014) 'Usefulness of Agent-based Simulation in Testing Collective Decision-Making models' In: Francisca Adamatti, Gra?iz Pereira Dimuro and Helder Coelho (eds). Interdisciplinary Applications of Agent-Based Social Simulation and Modeling. Hershey, PA: IGI Global, pp.1-314  
Dr Michael Salter-Townshend
Salter-Townshend, M. and Murphy, T.B. (2013) 'Sentiment Analysis of Online Media' In: Lausen, B., van del Poel, D. and Ultsch, A (eds). Algorithms from and for Nature and Life. Heidelberg: Springer, pp.137-146  


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Books Edited

Dr James McDermott
Romero, Juan, McDermott, James, Correia, Jo (Ed.). (2014) Evolutionary and Biologically Inspired Music, Sound, Art and Design: Proceedings of EvoMUSART 2014. Heidelberg: Springer. Available Online  
Dr Miguel Nicolau
Miguel Nicolau and Krzysztof Krawiec and Malcolm I. Heywood and Mauro Castelli and Pablo Garcia-Sanchez and Juan J. Merelo and Victor M. Rivas Santos and Kevin Sim (Ed.). (2014) Genetic Programming, 17th European Conference, EuroGP 2014, Granada, Spain, April 23-25, 2014, Proceedings. Berlin: Springer. Available Online  


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Peer Reviewed Journals

Professor Christopher Bean
Inzaa, L.A., Métaxian, J.P., Mars, J.I., Bean, C.J., O'Brien, G.S., Macedo, O. and Zandomeneghi, D. (2014) 'Analysis of dynamics of vulcanian activity of Ubinas volcano, using multicomponent seismic antennas'. Journal of Volcanology and Geothermal Research, 270:35-52.  
Bean, C.J., de Barros, L., Lokmer, I., Métaxian, J.P., O'Brien, G.S. and Murphy, S. (2014) 'Long-period seismicity in the shallow volcanic edifice formed from slow-rupture earthquakes'. Nature Geoscience, 7 (1):71-75.  
De Barros, L., Bean, C.J., Zecevic, M., Brenguier, F. and Peltier, A. (2013) 'Eruptive fracture location forecasts from high frequency events on Piton de la Fournaise volcano'. Geophysical Research Letters, 40:4599-4603.  
Zuccarello, L., Burton, M.R., Saccorotti, G., Bean, C.J. and Patanè, D.. (2013) 'The coupling between very long period seismic events, volcanic tremor, and degassing rates at Mount Etna volcano'. Journal of Geophysical Research-Solid Earth, 118 (9):4910-4921.  
Dr Chris Bleakley
Bober, W., and Bleakley, C.J. (2014) 'BailighPulse: A Low Duty Cycle Data Gathering Protocol For Mostly-Off Wireless Sensor Networks'. Elsevier Computer Networks, 69:51-65. Available Online  
Ballal, T. and Bleakley, C.J. (2014) 'GNSS Instantaneous Ambiguity Resolution and Attitude Determination Exploiting the Receiver Antenna Configuration'. IEEE Transactions on Aerospace and Electronic Systems (TAES), 50 (3):2061-2069. Available Online  
Kamal, A.R.M.; Bleakley, C.J. and Dobson, S. (2014) 'Failure Detection in Wireless Sensor Networks: A Sequence-based Dynamic Approach'. ACM Transactions on Sensor Networks, 10 (2):35:1-35:29. 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, 10 (1):5:1-5:44. Available Online  
Pontarelli, S. et al. (2013) 'Low Complexity Concurrent Error Detection for Complex Multiplication'. IEEE Transactions on Computers, 62 (9):1899-1903. Available Online  
Professor Anthony Brabazon
Brabazon, A., Cui, W. and O'Neill, M. (2013) 'Examining the Role of Perception, Social and Private Information in Honey Bee Foraging Algorithms'. International Journal of Innovative Computing and Applications, 5 (4):240-261.  
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 (3):287-314.  
Dr Nicolae Buchete
Jambrina, PG; Bohuszewicz, O; Buchete, NV; Kolch, W; Rosta, E (2014) 'Molecular mechanisms of asymmetric RAF dimer activation'. Biochemical Society Transactions, 42 (4):784-790. Available Online  
Professor Pádraig Cunningham
Cunningham, P., Harrigan, M., Wu, G., O'Callaghan, D., (2013) 'Characterizing ego-networks using motifs'. network science, 1 (2):170-190. Available Online  
Lee, C., Cunningham, P., (2013) 'Community detection: effective evaluation on large social networks'. Journal of Complex Networks. Available Online  
Professor Frederic Dias
Renzi, E; Dias, F (2014) 'Motion-resonant modes of large articulated damped oscillators in waves'. Journal of Fluids and Structures, 49:705-715. Available Online  
Sarkar, D; Renzi, E; Dias, F (2014) 'Wave farm modelling of oscillating wave surge converters'. Proceedings Of The Royal Society A-Mathematical Physical And Engineering Sciences, 470 (20140118). Available Online  
Renzi, E; Abdolali, A; Bellotti, G; Dias, F (2014) 'Wave-power absorption from a finite array of oscillating wave surge converters'. Renewable Energy, 63:55-68. Available Online  
Henry, A; Rafiee, A; Schmitt, P; Dias, F; Whittakerm T (2014) 'The characteristics of wave impacts on an oscillating wave surge converter'. Journal of Ocean and Wind Energy, 1:101-110.  
Sarkar, D; Renzi, E; Dias, F (2014) 'Interactions Between an Oscillating Wave Surge Converter and a Heaving Wave Energy Converter'. Journal of Ocean and Wind Energy, 1:135-142.  
Banner M; Barthelemy X; Fedele F; Allis M; Benetazzo A; Dias F; Peirson W (2014) 'Linking reduced breaking crest speeds to unsteady nonlinear water wave group behavior'. Physical Review Letters, 112.  
Gallagher S; Tiron R; Dias F (2014) 'A long-term nearshore wave hindcast for Ireland: Atlantic and Irish Sea coasts (1979 -2012)'. Ocean Dynamics, 64:1163-1180.  
Viotti C; Carbone F; Dias F (2014) 'Conditions for extreme wave run-up on a vertical barrier by nonlinear dispersion'. Journal of Fluid Mechanics, 748:768-788.  
Viotti C; Dias F (2014) 'Extreme waves induced by strong depth transitions: Fully nonlinear results'. Physics of Fluids, 26.  
Tiron R; Mallon F; Dias F; Reynaud E (2014) 'The challenging life of wave energy devices at sea. A few points to consider '. Renewable and Sustainable Energy Reviews.  
Stefanakis T; Dias F; Synolakis C (2014) 'Tsunami generation above a sill'. Pure and Applied Geophysics.  
Stefanakis T; Contal E; Vayatis N; Dias F; Synolakis C (2014) 'Can small islands protect nearby coasts from tsunamis ? An active experimental design'. Proceedings Of The Royal Society A-Mathematical Physical And Engineering Sciences.  
Dias, F (2014) 'Ship waves and Kelvin'. Journal of Fluid Mechanics, 746:1-4.  
Stefanakis, T., Xu, S., Dutykh, D., Dias, F. (2013) 'Run-up amplification of transient long waves'. Quarterly of Applied Mathematics.  
Dr Jos Elkink
Baturo, Alexander; Elkink, Johan A. (2014) 'Office or Officeholder? Regime Deinstitutionalisation and Sources of Individual Political Influence'. Journal of Politics, 76 (3):859-872. Available Online  
Professor Nial Friel
Friel, N., Hurn, M. and Wyse, J. (2014) 'Improving power posterior estimation of statistical evidence'. Statistics and Computing, 24:709-723. Available Online  
Silvia Pandolfi, Francesco Bartloucci, Nial Friel (2014) 'A generalized multiple-try version of the reversible jump algorithm'. Computational Statistics & Data Analysis, 72:298-314.  
N. Friel (2013) 'Estimating the evidence for Gibbs random fields'. Journal of Computational and Graphical Statistics, 22 (3):518-532. Available Online  
Dr Claire Gormley
McParland, D., Gormley, I.C., McCormick, T.H., Clark, S.J., Kabudula, C.W. and Collinson, M.A. (2014) 'Clustering South African households based on their asset status using latent variable models'. Annals of Applied Statistics, 8 (2):747-776. Available Online  
Nyamundanda, G., Gormley, I.C. and Brennan, L. (2013) 'A dynamic probabilistic principal components model for the analysis of longitudinal metabolomics data'. Journal of the Royal Statistical Society: Series C (Applied Statistics).  
Nyamundanda, G., Gormley, I.C., Fan,Y., Gallagher, W.M. and Brennan, L. (2013) 'MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach'. BMC Bioinformatics.  
Dr Russell Higgs
Higgs, R. (2013) 'Revisiting the linear information flow algorithm'. International Journal of Information and Coding Theory, 2:96-104.  
Dr Therese Holton
Khaldi, N., Holton, T.A., Shields, D.C. (2014) 'Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences'. Journal of Dairy Science.  
Holton, T.A., Wilkinson, M, Pisani, D. (2014) 'The shape of modern tree reconstruction methods'. Systematic Biology.  
Thérèse A. Holton, Vaishnavi Vijayakumar, Nora Khaldi (2013) 'Bioinformatics: Current perspectives and future directions for food and nutritional research facilitated by a Food-Wiki database'. Trends in Food Science & Technology.  
Holton, T. A., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'CPPpred: prediction of cell penetrating peptides'. Bioinformatics. Available Online  
Dr Neil Hurley
Archambault, Daniel and Hurley, Neil (2014) 'Visualization of trends in subscriber attributes of communities on mobile telecommunications networks'. Social Network Analysis and Mining, 4 (1).  
Professor Mohand Kechadi
Tselios, D, Savvas, I, Kechadi, M-T (2014) 'MPM Job Shop Scheduling Problem: a bi-objective approach'. International Journal of Simulation Systems, Science and Technology, 14:45-54.  
Chabot, Y, Bertaux, A, Nicolle, C, Kechadi, MT (2014) 'A complete formalized knowledge representation model for advanced digital forensics timeline analysis'. Digital Investigation, 11:95-105.  
Faheem, M., Le-Khac, N.A., Kechdadi, M-T. (2014) 'Smartphone Forensic Analysis: A Case Study for Obtaining Root Access of an Android Samsung S3 Device and Analyse the Image without an Expensive Commercial Tool'. Eurasip Journal on Information Security, 5 (1):83-90.  
De Marco, L, Ferrucci, F, Kechadi, M-T (2014) 'Reference Architecture for a Cloud Forensic Readiness System'. ICST Transactions: Security and Safety, 1 (1).  
Bo, Wu, Chen, CC, Kechadi, M-T, Sun L, (2013) 'A Comparative Evaluation of Filter-based Feature Selection Methods for Hyper-Spectral Band Selection'. International Journal of Remote Sensing, 34 (22):7974-7990.  
Dr Run Long
Run Long et al. (2014) 'Minimizing Electron-Hole Recombination on TiO2 Sensitized with PbSe Quantum Dots: Time-Domain Ab Initio Analysis'. Journal Of Physical Chemistry Letters, 5:2941-2946.  
Alexey Akimov, Run Long et al. (2014) 'Coherence penalty functional: A simple method for adding decoherence in Ehrenfest dynamics'. The Journal of chemical physics, 140.  
Run Long et al. (2014) 'Charge separation across P3HT/Carbon Nanotube Interface: First-Principles Calculations of Electronic Structures'. Chemical Physics Letters, 597:45-50.  
Run Long et al. (2014) 'Asymmetry in Electron and Hole Transfer at a Polymer-Carbon Nanotube Heterojunction'. Nano Letters, 14:3335-3341.  
De Nyago Tafen, Run Long et al. (2014) 'TiO2 dimensionality determines the mechanism of photoinduced electron injection from a CdSe nanoparticle'. Nano Letters, 14:1970-1976.  
Run Long et al. (2014) 'Instantaneous Generation of Charge-Separated State on TiO2 Surface Sensitized with Plasmonic Nanoparticles'. Journal of the American Chemistry Society, 136:4343-4354.  
Run Long et al. (2013) 'Defects Are Needed for Fast Photo-Induced Electron Transfer from a Nanocrystal to a Molecule: Time-Domain Ab Initio Analysis'. Journal of the American Chemistry Society, 135:18892-18900.  
Dr Hender Lopez Silva
Galvagno, M; Tseluiko, D; Lopez, H; Thiele, U (2014) 'Continuous and Discontinuous Dynamic Unbinding Transitions in Drawn Film Flow'. Physical Review Letters, 112.  
Dr Donal MacKernan
Y. Wang, D. MacKernan, D. Cubero, D. F. Coker, and N. Quirke (2014) 'Single electron states in polyethylene'. The Journal of chemical physics, 140.  
Professor Joao Marques-Silva
Anton Belov and Mikoláš Janota and Inês Lynce and Joao Marques-Silva (2014) 'Algorithms for computing minimal equivalent subformulas'. Artif. Intell, 216:309-326. Available Online  
Dr James McDermott
Jonathan Byrne, Michael Fenton, Erik Hemberg, James McDermott, Michael O'Neill (2014) 'Optimising Complex Pylon Structures with Grammatical Evolution'. Information Sciences.  
James McDermott (2013) 'Graph Grammars for Evolutionary 3D Design'. Genetic Programming and Evolvable Machines, 14 (3):369-393.  
Professor Gary McGuire
Faruk Gologlu, Gary McGuire (2014) 'On theorems of Carlitz and Payne on permutation polynomials over finite fields with an application to x−1+L(x)'. Finite Fields and Their Applications.  
Fernando Hernando, Gary McGuire, Francisco Monserrat (2014) 'On the classification of Exceptional Planar Functions over Fp'. Geometriae Dedicata.  
Cem Guneri, Gary McGuire (2014) 'Supersingular curves over finite fields and weight divisibility of codes'. Journal of Computational Mathematics.  
Professor Thomas Murphy
Gollini, I. and Murphy, T.B. (2014) 'Mixture of Latent Trait Analyzers for Model-Based Clustering of Categorical Data'. Statistics and Computing, 24 (4):569-588.  
Salter-Townshend, M. and Murphy, T.B. (2014) 'Role analysis in networks using a mixture of exponential random graph models'. Journal of Computational and Graphical Statistics.  
Salter-Townshend, M. and Murphy, T.B. (2014) 'Mixtures of Biased Sentiment Analysers'. Advances in Data Analysis and Classification, 8 (1):85-103.  
Caron, F., Teh, Y.W. and Murphy, T.B. (2014) 'Bayesian nonparametric Plackett-Luce models for the analysis of preferences for college degree programmes'. Annals of Applied Statistics, 8 (2):1145-1181. Available Online  
Boyce, S., Fan, Y., Watson, R.W. and Murphy, T.B. (2013) 'Evaluation of prediction models for the staging of prostate cancer'. BMC Medical Informatics and Decision Making, 13.  
Professor Michael O'Neill
Fenton M., McNally C., Byrne J., Hemberg E., JMcDermott J., O'Neill M. (2014) 'Automatic innovative truss design using grammatical evolution'. Automation in Construction.  
Brabazon, A., Cui, W. and O'Neill, M. (2013) 'Examining the Role of Perception, Social and Private Information in Honey Bee Foraging Algorithms'. International Journal of Innovative Computing and Applications, 5 (4):240-261.  
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 (3):287-314.  
Professor Adrian Ottewill
Hodgkinson, Lee and Louko, Jorma and Ottewill, Adrian C. (2014) 'Static detectors and circular-geodesic detectors on the Schwarzschild black hole'. Phys. Rev. D, 89. Available Online  
Barry Wardell, Chad R. Galley, Anil Zenginoglu, Marc Casals, Sam R. Dolan, Adrian C. Ottewill (2014) 'Self-force via Green functions and worldline integration'. Physical Review D.  
Anna Heffernan, Adrian Ottewill and Barry Wardell (2014) 'High-order expansions of the Detweiler-Whiting singular ?eld in Kerr spacetime'. Physical Review D, 89:024030-1-024030-20.  
Dr Andrew Parnell
Donald L Phillips, Richard Inger, Stuart Bearhop, Andrew L Jackson, Jonathan W Moore, Andrew C Parnell, Brice X Semmens, Eric J Ward (2014) 'Best practices for use of stable isotope mixing models in food web studies'. Canadian Journal of Zoology. Available Online  
Andrew C Kemp, Christopher E Bernhardt, Benjamin P Horton, Robert E Kopp, Christopher H Vane, W Richard Peltier, Andrea D Hawkes, Jeffrey P Donnelly, Andrew C Parnell, Niamh Cahill (2014) 'Late Holocene sea-and land-level change on the US southeastern Atlantic coast'. MARINE GEOLOGY, 357 (1):90-100.  
Andrew C Parnell, James Sweeney, Thinh K Doan, Michael Salter?Townshend, Judy RM Allen, Brian Huntley, John Haslett (2014) 'Bayesian inference for palaeoclimate with time uncertainty and stochastic volatility'. Journal of the Royal Statistical Society: Series C (Applied Statistics).  
D De Vleeschouwer, AC Parnell (2014) 'Reducing time-scale uncertainty for the Devonian by integrating astrochronology and Bayesian statistics'. Geology, 42 (6):491-494.  
B Hernández, A Parnell, SR Pennington (2014) 'Why have so few proteomic biomarkers "survived" validation? (Sample size and independent validation considerations)'. Proteomics, 14 (13-14):1587-1592.  
Andrew C Kemp, Benjamin P Horton, Christopher H Vane, Christopher E Bernhardt, D Reide Corbett, Simon E Engelhart, Shimon C Anisfeld, Andrew C Parnell, Niamh Cahill (2013) 'Sea-level change during the last 2500 years in New Jersey, USA'. Quaternary Science Reviews, 81:90-104.  
Valentina Franco-Trecu, Massimiliano Drago, Federico G Riet-Sapriza, Andrew Parnell, Rosina Frau, Pablo Inchausti (2013) 'Bias in Diet Determination: Incorporating Traditional Methods in Bayesian Mixing Models'. PLoS ONE, 8 (11).  
Dr Diane Payne
O'Loughlin, Eamonn; Payne, Diane; (2014) 'Building Rich Social Network Data: A schema to assist in designing, collecting and evaluating social network data'. Social Network Analysis and Mining. Available Online  
Dr Gianluca Pollastri
C.Mirabello, A.Adelfio, G.Pollastri (2014) 'Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction'. Biomolecules, 4 (1):160-180. Available Online  
P.Kukic, C.Mirabello, G.Tradigo, I.Walsh, P.Veltri, G.Pollastri (2014) 'Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks'. BMC Bioinformatics, 15 (6). Available Online  
A.Adelfio, V.Volpato, G.Pollastri (2013) 'SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks'. SpringerPlus, 2. Available Online  
W.Khan, F.Duffy, G.Pollastri, D.C.Shields, C.Mooney (2013) 'Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains'. PLoS ONE, 8 (9). Available Online  
T.A.Holton, G.Pollastri, D.C.Shields, C.Mooney (2013) 'CPPpred: Prediction of Cell Penetrating Peptides'. Bioinformatics, 29 (23):3094-3096. Available Online  
Dr Colm Ryan
Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM (2013) 'Chemical Genetics of Rapamycin-Insensitive TORC2 in S. cerevisiae'. Cell reports, 5 (6):1725-1736.  
Ryan CJ, Cimerman?i?, P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ (2013) 'High-resolution network biology: connecting sequence with function'. Nature reviews. Genetics, 14 (12):865-879.  
Dr Goar Sanchez
Cristina Trujillo, Goar Sánchez-Sanz , Ieva Karpavi?ien?, Ullrich Jahn, Inga ?ikotien?, and LubomírRulíšek, (2014) 'Divergent Pathways and Competitive Mechanisms of Metathesis Reactions Between 3-Arylprop-2-inyl esters and Aldehydes: An Experimental and Theoretical Study'. Chemistry-A European Journal, 20.  
C. Trujillo, G. Sánchez-Sanz, I. Alkorta, J. Elguero (2014) 'A computational study of 3-azonia-, 3-phosphonia- and 3-arsonia- spiro[2.2]pentanes and related three-membered heterocycles'. ChemPhysChem, 15.  
Goar Sanchez-Sanz and Cristina Trujillo and Ibon Alkorta and Jose Elguero (2014) 'Theoretical study of cyanophosphines: Pnicogen vs. dipole-dipole interactions'. Computational and Theoretical Chemistry, (0). Available Online  
R. Aggarwal, V. Kumar, G. Singh, D. Sanz, R. M. Claramunt, I. Alkorta, G. Sanchez-Sanz, J. Elguero (2014) 'An NMR and Computational Study of Azolo[a]pyrimidines with Special Emphasis on Pyrazolo[1,5-a]pyrimidines'. Journal of Heterocyclic Chemistry. Available Online  
Marin-Luna M, Sanchez-Sanz G, O'Sullivan P, Rozas I. (2014) 'Guanidine complexes of Platinum: a theoretical study'. Journal of Physical Chemistry A, 118.  
G. Sánchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero (2014) 'Intramolecular pnicogen interactions in phosphorus and arsenic analogues of proton sponges'. Physical Chemistry Chemical Physics, 16.  
I. Alkorta, G. Sánchez-Sanz, J. Elguero J.E. Del Bene (2014) 'Pnicogen Bonds between X=PH3 (X = O, S, NH, CH2) and Phosphorus and Nitrogen Bases'. Journal of Physical Chemistry A, 118.  
Professor Denis Shields
Nongonierma AB, Mooney C, Shields DC, FitzGerald RJ (2014) 'In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors'. Peptides, 57:43-51.  
Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB (2014) 'Predicting the important enzymes in human breast milk digestion'. FOOD CHEM, 62 (29):7225-7232.  
Stavropoulos I, Golla K, Moran N, Martin F, Shields DC (2014) 'Cadherin juxtamembrane region derived peptides inhibit TGFβ1 induced gene expression'. Bioarchitecture, 4 (3):103-110.  
Ruhanen H, Hurley D, Ghosh A, O'Brien KT, Johnston CR, Shields DC (2014) 'Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey'. Frontiers in microbiology, 5.  
Khaldi, N., Holton, T.A., Shields, D.C. (2014) 'Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences'. Journal of Dairy Science.  
Nongonierma, A. B., Mooney, C., Shields, D. C., Fitzgerald, R. J. (2013) 'Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides'. Food Chem, 141 (1):644-53. Available Online  
Yadav, S., Cotlarciuc, I., Munroe, P. B., Khan, M. S., Nalls, M. A., Bevan, S., Cheng, Y. C., Chen, W. M., Malik, R., McCarthy, N. S., Holliday, E. G., Speed, D., Hasan, N., Pucek, M., Rinne, P. E., Sever, P., Stanton, A., Shields, D. C., Maguire, J. M., McEvoy, M., Scott, R. J., Ferrucci, L., Macleod, M. J., Attia, J., Markus, H. S., Sale, M. M., Worrall, B. B., Mitchell, B. D., Dichgans, M., Sudlow, C., Meschia, J. F., Rothwell, P. M., Caulfield, M., Sharma, P. (2013) 'Genome-wide analysis of blood pressure variability and ischemic stroke'. Stroke, 44 (10):2703-9. Available Online  
Holton, T. A., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'CPPpred: prediction of cell penetrating peptides'. Bioinformatics. Available Online  
Dr Niels Warburton
Akcay, S; Warburton, N; Barack, L (2013) 'Frequency-domain algorithm for the Lorenz-gauge gravitational self-force'. Phys Rev D.  


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Other Journals

Dr James McDermott
James McDermott (2014) 'Visualizing Evolutionary Search Spaces' SIGEvolution Newsletter, 7 (1):2-10.Available Online  
Professor Thomas Murphy
Breen, K.J., Boyce, S., Boyd Lyons, A., Lundon, D., Fitzpatrick, J.M., Murphy, T.B and Watson, R.W. (2014) 'External validation of the 2007 and 2013 updated Partin tables in a cohort of Irish men' BJU International, 114 (Supplement 2):21-21.  
Boyce S., Murphy L., Fitzpatrick J.M., Murphy T.B., Watson R.W.G. (2013) 'Validation of a panel of serum biomarkers to inform surgical intervention for prostate cancer' Journal of Clinical Urology, 6 (5):339-339.  
Dr Niels Warburton
Warburton, N; Wardell, B (2013) 'Applying the effective-source approach to frequency-domain self-force calculations' arXiv.Available Online  


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Conference Publications

Professor Christopher Bean
Craig, D., Bean, C.J., Moni, A., Lokmer, I. and Donne, S. (2014) Location of Multiple Coincident Noise Sources in the N.E. Atlantic, offshore Ireland EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-13146  
Thun, J., Bean, C.J. and Lokmer, I. (2014) Analysis of volcanic long-period events with quasi-static displacements from high-density seismological networks EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12910  
Bean, C.J., Lokmer, I., DeBarros, L. and Amitrano, D. (2014) Controls on upper edifice rheology and consequences for seismicity-deformation relationship on volcanoes EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-15399  
Thun, J., Bean, C.J. and Lokmer, I. (2014) Detection of quasi-static displacement components of LP seismic sources near the volcanic summit EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12723  
Volk, M.F., Bean, C.J., Lokmer, I. and Craig, D. (2014) Apparent changes in seismic wave velocity related to microseism noise source variations EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-13045  
Donne, S., Nicolau, M., Bean, C.J., Lokmer, I., Craig, D., Creamer, C. and Lambkin, K. (2014) Ocean Wave Height Estimation in the Northeast Atlantic, Offshore Ireland, Using Terrestrial Microseism Data: A Comparison and Analysis of two Evolutionary Approaches EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12432  
Möllhoff, M. and Bean, C.J. (2014) Microseism Noice Levels in Ireland EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-3620  
Volk, M., Bean, C., Lokmer, I. and Craig, D. (2013) Investigation of apparent seismic velocity changes caused by microseism noise source variability American Geophysical Union, Fall Meeting, San Francisco, USA, S43B-2527  
Bean, C.J., Lokmer, I., de Barros, L., Eyre, T.S. and Metaxian, J. (2013) Shallow Long Period (LP) seismicity as signatures of shallow edifice deformation at volcano American Geophysical Union, Fall Meeting, San Francisco, USA, V43D-06  
Bean, C.J., Volk, M., Donne, S., Craig, D., Ying, Y., Möllhoff, M., Braiden, A. and Lokmer, I. (2013) Ocean wave generated microseisms in the NE Atlantic: An emerging passive seismic imagery tool Atlantic Ireland 2013, Abstracts Volume, Dublin, Ireland, P. 87-88 Available Online  
Volk, M., Bean, C.J. and Lokmer, I. (2013) Using ambient seismic noise for subsurface imaging UCD Earth Gathering, Dublin, Ireland, Abstracts  
Dr Chris Bleakley
Taylor, K. et al (2014) Lower Body Reaction Testing Using Ultrasonic Motion Capture IEEE Engineering in Medicine and Biology Conf. (EMBC), 36th Annual Int, Chicago, USA,  
Siddig, A., Makki, A., and Bleakley, C.J. (2013) Lighthouse: Precise 802.11-based Localization 4th Int. Conf. on Indoor Positioning and Indoor Navigation (IPIN), Montbeliard-Belfort, France, Available Online  
Professor Anthony Brabazon
Tuite, C., O'Neill, M., Brabazon, A. (2014) The Relationship between Semantic Distance and Performance in Dynamic Symbolic Regression Problems 20th International Conference on Soft Computing (Mendel 2014), Brno, Czech Republic,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2014) Ensemble Bayesian Model Averaging in Genetic Programming IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Beijing, 2451 - 2458  
Byrne, J., Nicolau, M., Brabazon, A. and O'Neill, M. (2014) An Examination of Synchronisation in Artificial Gene Regulatory Networks IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China, 2764 - 2769  
Agapitos, A., McDermott, J., O'Neill, M. and Brabazon, A. (2014) Higher Order Functions for Kernel Regression 17th European Conference on Genetic Programming (EuroGP 2014), Granada, Spain, 1 - 12  
Nicolau, M., O'Neill, M. and Brabazon, A. (2014) Dynamic Index Trading using a Gene Regulatory Network Model 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
McDermott, J., Agapitos, A., Brabazon, A. and O'Neill, M. (2014) Geometric Semantic Genetic Programming for Financial Data 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Lipinski, P. and Brabazon, A. (2014) Pattern Mining in Ultra-High Frequency Order Books 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Byrne,J., Cardiff, P., Brabazon, A. O'Neill, M. (2014) Evolving an Aircraft Using a Parametric Design System 16th European Conference on the Applications of Evolutionary Computation (EvoMusArt 2014), 119 - 130  
Wilinski, M., Cui, W. and Brabazon, A. (2014) An Analysis of the Price Impact Function of Invididual Trades on the London Stock Exchange IEEE Conference on Computational Intelligence for Financial Engineering and Economics 2014, London,  
Dr Nicolae Buchete
Kaskova-Gheorghescu, A; Buchete, NV; Thompson, J (2014) Fractal analysis of the chick extra-embryonic angiogenesis following cadmium exposure Irish Journal of Medicinal Science, S25 - S25  
Kelly, CM; Buchete, NV (2014) Conformational and Dynamic Properties of Extracellular Domains of Cell Adhesion Molecules Biophysical Society 58th Annual Meeting; Biophysical Journal, 51a - 52a Available Online  
Professor Pádraig Cunningham
Qin, X., Salter-Townshend, M., Cunningham, P. (2014) Exploring the Relationship between Membership Turnover and Productivity in Online Communities Eighth International Conference on Weblogs and Social Media (ICWSM 2014),  
Professor Frederic Dias
Sarkar, D; Renzi, E; Dias, F (2014) Oscillating wave surge converters: interactions in a wave farm 33rd International Conference on Ocean, Offshore and Arctic Eng., OMAE14,  
Renzi, E; Dias, F (2014) Time-Domain Hydroacoustic Green Function for Surface Pressure Disturbance. In: M. Kashiwagi eds. 29th International Workshop on Water Waves and Floating Bodies,  
Dias, F., Dutykh, D., O'Brien, L., Renzi, E., Stefanakis, T. (2013) On the modelling of tsunami generation and tsunami inundation Procedia IUTAM: MS02: Mechanics of natural disasters,  
Tiron, R; Gallagher, S; Dias, F (2013) The Influence of Coastal Morphology on the Wave Climate and Wave Energy Resource of the West Irish Coast 10th European Wave and Tidal Energy Conference, EWTEC 2013, Aalborg, Denmark,  
Sarkar, D; Renzi, E; Dias, F (2013) Wave Power Absorption from a Flap-type Wave Energy Converter Near a Straight Coast 10th European Wave and Tidal Energy Conference, EWTEC 2013, Aalborg, Denmark,  
Dr Russell Higgs
Cao, N; Higgs, R; O'Hare, G. (2014) Intelligent evaluation models based on the Single-hop protocol in wireless sensor networks 28th International Conference on Advanced Information Networking and Applications Workshops (WAINA), 239 - 244  
Dr Neil Hurley
McDaid, A., Hurley, N. and Murphy, T.B. (2014) Overlapping Stochastic Community Finding. In: Xindong Wu, Martin Ester, Guandong Xu eds. 2014 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM'14), Beijing, China,  
Hurley, Neil (2013) Personalised Ranking with Diversity ACM 7th Conference on Recommender Systems, Hong Kong, China, Available Online  
Professor Mohand Kechadi
B. Busstra, M. Tahar Kechadi and N-A. Le-Khac (2014) Android and Wireless data-extraction using Wi-Fi 4th IEEE international conference on Innovative Computing Technology (INTECH 2014),  
Christos Sgaras, M. Tahar Kechadi and N-A. Le-Khac (2014) Forensics Acquisition and Analysis of instant messaging and VoIP applications th IAPR International Workshop on Computational Forensics (IWCF 2014), Springer Verlag LNCS,  
N-A. Le-Khac and M. Tahar Kechadi (2014) Toward a new cloud-based approach to preserve the privacy for detecting suspicious cases of money laundering Global Premier International Conference on Cryptography and Security 2014 (ICCS 2014),  
LeKhac, N.A., Kechadi, M-T. (2014) Forensics Acquisition of Tango VoIP International Conference on Challenges in IT, Engineering and Technology (ICCIET 2014), Phuket, Thailand,  
Houari, R., Bounceur, A., Kechadi, M-T., (2014) Handling Missing Data Problems with Sampling Methods (INDS 2014), Bejaia, Algeria,  
Farina, J., Scanlon, M. and Kechadi, M-T. (2014) BitTorrent Sync: First Impressions and Digital Forensic Implications Digital Forensics Research Workshop (DFRWS EU 2014), Amsterdam, Netherlands,  
Scanlon, M. and Kechadi, M-T (2014) The Case for a Collaborative Universal Peer-to-Peer Botnet Investigation Framework 9th International Conference on Cyber Warfare and Security (ICCWS-2014), CERIAS, Purdue University, Indiana, USA,  
Bounceur, A., and Kechadi, M-T., (2014) CupCarbon: A Multi-Agent and Discrete Event Wireless Sensor Network Design and Simulation Tool Based-on the Open Street Map Framework 7th International ICST Conference on Simulation Tools and Techniques, Lisbon, Portugal,  
Tobin, Patrick, Kechadi, M-T., (2014) Virtual Machine Forensics by means of Introspection and Kernel Code Injection 9th International Conference on Cyber Warfare and Security (ICCWS 2014) West Lafayette, Indiana, USA,  
Mark Roeloffs, M. Tahar Kechadi and N-A. Le-Khac (2014) Forensic Investigation of TomTom Application on Android Mobile devices The 10th Annual IFIP WG 11.9 International Conference on Digital Forensics (IFIP WG11.9 2014), Springer Verlag,  
Houari, R., Bounceur, A., Kechadi, M-T. (2013) Data Reduction in Huge Datasets through Removing Redundant Combinations of Dimensions International Conference in Digital Information Processing and Communications(ICDIPC 2013), Hammamet, Tunisia,  
Scanlon, M. and Kechadi, M-T. (2013) Universal Peer-to-Peer Network Investigation Framework. In: IEEE eds. International Workshop on Emerging Cyberthreats and Countermeasures (ECTCM 2013), part of the Eight International Conference on Availability, Reliability and Security (ARES2013), Regensburg, Germany, Available Online  
Scanlon, M. and Kechadi, M-T. (2013) Digital Evidence Bag Selection for P2P Network Investigation The 7th International Symposium on Digital Forensics and Information Security (DFIS-2013); Future Information Technology, Application, and Service, Gwangju, Korea, Available Online  
Professor Joao Marques-Silva
Yuri Malitsky and Barry O'Sullivan and Alessandro Previti and Joao Marques-Silva (2014) Timeout-Sensitive Portfolio Approach to Enumerating Minimal Correction Subsets for Satisfiability Problems ECAI, 1065 - 1066 Available Online  
Joao Marques-Silva and Alexey Ignatiev and Antonio Morgado and Vasco M. Manquinho and Ines Lynce (2014) Efficient Autarkies ECAI, 603 - 608 Available Online  
Alexey Ignatiev and Antonio Morgado and Vasco M. Manquinho and Ines Lynce and Joao Marques-Silva (2014) Progression in Maximum Satisfiability ECAI, 453 - 458 Available Online  
Anton Belov and Marijn Heule and Joao Marques-Silva (2014) MUS Extraction Using Clausal Proofs SAT, 48 - 57 Available Online  
Joao Marques-Silva and Alessandro Previti (2014) On Computing Preferred MUSes and MCSes SAT, 58 - 74 Available Online  
Alexey Ignatiev and Antonio Morgado and Joao Marques-Silva (2014) On Reducing Maximum Independent Set to Minimum Satisfiability SAT, 103 - 120 Available Online  
Alexey Ignatiev and Mikolas Janota and Joao Marques-Silva (2014) Towards efficient optimization in package management systems ICSE, 745 - 755 Available Online  
Yuri Malitsky and Barry O'Sullivan and Alessandro Previti and Joao Marques-Silva (2014) A Portfolio Approach to Enumerating Minimal Correction Subsets for Satisfiability Problems CPAIOR, 368 - 376 Available Online  
Arie Gurfinkel and Anton Belov and Joao Marques-Silva (2014) Synthesizing Safe Bit-Precise Invariants TACAS, 93 - 108 Available Online  
Alexey Ignatiev and Antonio Morgado and Jordi Planes and Joao Marques-Silva (2013) Maximal Falsifiability - Definitions, Algorithms, and Applications LPAR, 439 - 456 Available Online  
Mikol'as Janota and Radu Grigore and Joao Marques-Silva (2013) On QBF Proofs and Preprocessing LPAR, 473 - 489 Available Online  
Anton Belov and Antonio Morgado and Joao Marques-Silva (2013) SAT-Based Preprocessing for MaxSAT LPAR, 96 - 111 Available Online  
Antonio Morgado and Federico Heras and Joao Marques-Silva (2013) Model-Guided Approaches for MaxSAT Solving ICTAI, Washington DC, USA,  
William Klieber and Mikolas Janota and Joao Marques-Silva and Edmund M. Clarke (2013) Solving QBF with Free Variables CP, 415 - 431 Available Online  
Dr James McDermott
James McDermott, Alexandros Agapitos, Anthony Brabazon and Michael ONeill (2014) Geometric Semantic Genetic Programming for Financial Data. In: Anna I Esparcia-Alc?r, Andrea Tettamanzi, Alexandros Agapitos eds. evoapplications: European Conference on the Applications of Evolutionary Computation: evoFIN Evolutionary computation in finance and economics, Granada, Spain,  
Professor Thomas Murphy
McDaid, A., Hurley, N. and Murphy, T.B. (2014) Overlapping Stochastic Community Finding. In: Xindong Wu, Martin Ester, Guandong Xu eds. 2014 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM'14), Beijing, China,  
Professor Michael O'Neill
Tuite, C., O'Neill, M., Brabazon, A. (2014) The Relationship between Semantic Distance and Performance in Dynamic Symbolic Regression Problems 20th International Conference on Soft Computing (Mendel 2014), Brno, Czech Republic,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2014) Ensemble Bayesian Model Averaging in Genetic Programming IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Beijing, 2451 - 2458  
Brabazon, A., Cui, W. and O'Neill, M. (2014) A Framework for Bat Foraging Algorithm Design IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China,  
Byrne, J., Nicolau, M., Brabazon, A. and O'Neill, M. (2014) An Examination of Synchronisation in Artificial Gene Regulatory Networks IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China, 2764 - 2769  
O'Neill M., Nicolau M., Agapitos A. (2014) Experiments in Program Synthesis with Grammatical Evolution: a focus on Integer Sorting IEEE Congress on Evolutionary Computation,  
Donne S., Nicolau M., Bean C., O'Neill M. (2014) Wave Height Quantification using Land Based Seismic Data with Grammatical Evolution IEEE Congress on Evolutionary Computation,  
Agapitos, A., McDermott, J., O'Neill, M. and Brabazon, A. (2014) Higher Order Functions for Kernel Regression 17th European Conference on Genetic Programming (EuroGP 2014), Granada, Spain, 1 - 12  
Nicolau, M., O'Neill, M. and Brabazon, A. (2014) Dynamic Index Trading using a Gene Regulatory Network Model 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
McDermott, J., Agapitos, A., Brabazon, A. and O'Neill, M. (2014) Geometric Semantic Genetic Programming for Financial Data 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Byrne,J., Cardiff, P., Brabazon, A. O'Neill, M. (2014) Evolving an Aircraft Using a Parametric Design System 16th European Conference on the Applications of Evolutionary Computation (EvoMusArt 2014), 119 - 130  


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Other Publications

Dr Claire Gormley
Nyamundanda, G., Gormley, I.C., Fan, Y., Gallagher, W and Brennan, L. (2013) MetSizeR: a statistical tool for estimating sample sizes for metabolomic experiments. Software.  
Dr Andrew Parnell
Andrew Parnell, Thinh Doan and James Sweeney (2014) Bclim: Bayesian Palaeoclimate Reconstruction from Pollen. Software. Available Online  


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Andrew C Parnell, James Sweeney, Thinh K Doan, Michael Salter?Townshend, Judy RM Allen, Brian Huntley, John Haslett (2014) 'Bayesian inference for palaeoclimate with time uncertainty and stochastic volatility'. Journal of the Royal Statistical Society: Series C (Applied Statistics).  
D De Vleeschouwer, AC Parnell (2014) 'Reducing time-scale uncertainty for the Devonian by integrating astrochronology and Bayesian statistics'. Geology, 42 (6):491-494.  
B Hernández, A Parnell, SR Pennington (2014) 'Why have so few proteomic biomarkers survived validation?(Sample size and independent validation considerations)'. Proteomics, 14 (13-14):1587-1592.  
Andrew C Kemp, Benjamin P Horton, Christopher H Vane, Christopher E Bernhardt, D Reide Corbett, Simon E Engelhart, Shimon C Anisfeld, Andrew C Parnell, Niamh Cahill (2013) 'Sea-level change during the last 2500 years in New Jersey, USA'. Quaternary Science Reviews, 81:90-104.  
Valentina Franco-Trecu, Massimiliano Drago, Federico G Riet-Sapriza, Andrew Parnell, Rosina Frau, Pablo Inchausti (2013) 'Bias in Diet Determination: Incorporating Traditional Methods in Bayesian Mixing Models'. PLoS ONE, 8 (11).  
Dr Diane Payne
O'Loughlin, Eamonn; Payne, Diane; (2014) 'Building Rich Social Network Data: A schema to assist in designing, collecting and evaluating social network data'. Social Network Analysis and Mining. Available Online  
Dr Gianluca Pollastri
C.Mirabello, A.Adelfio, G.Pollastri (2014) 'Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction'. Biomolecules, 4 (1):160-180. Available Online  
P.Kukic, C.Mirabello, G.Tradigo, I.Walsh, P.Veltri, G.Pollastri (2014) 'Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks'. BMC Bioinformatics, 15 (6). Available Online  
A.Adelfio, V.Volpato, G.Pollastri (2013) 'SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks'. SpringerPlus, 2. Available Online  
W.Khan, F.Duffy, G.Pollastri, D.C.Shields, C.Mooney (2013) 'Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains'. PLoS ONE, 8 (9). Available Online  
T.A.Holton, G.Pollastri, D.C.Shields, C.Mooney (2013) 'CPPpred: Prediction of Cell Penetrating Peptides'. Bioinformatics, 29 (23):3094-3096. Available Online  
Dr Colm Ryan
Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM (2013) 'Chemical Genetics of Rapamycin-Insensitive TORC2 in S. cerevisiae'. Cell reports, 5 (6):1725-1736.  
Ryan CJ, Cimerman?i? P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ (2013) 'High-resolution network biology: connecting sequence with function'. Nature reviews. Genetics, 14 (12):865-879.  
Dr Goar Sanchez
Cristina Trujillo, Goar Sánchez-Sanz , Ieva Karpavi?ien?, Ullrich Jahn, Inga ?ikotien?, and LubomírRulíšek, (2014) 'Divergent Pathways and Competitive Mechanisms of Metathesis Reactions Between 3-Arylprop-2-inyl esters and Aldehydes: An Experimental and Theoretical Study'. Chemistry-A European Journal, 20.  
C. Trujillo, G. Sánchez-Sanz, I. Alkorta, J. Elguero (2014) 'A computational study of 3-azonia-, 3-phosphonia- and 3-arsonia- spiro[2.2]pentanes and related three-membered heterocycles'. ChemPhysChem, 15.  
Goar Sanchez-Sanz and Cristina Trujillo and Ibon Alkorta and Jose Elguero (2014) 'Theoretical study of cyanophosphines: Pnicogen vs. dipole-dipole interactions'. Computational and Theoretical Chemistry, (0). Available Online  
R. Aggarwal, V. Kumar, G. Singh, D. Sanz, R. M. Claramunt, I. Alkorta, G. Sanchez-Sanz, J. Elguero (2014) 'An NMR and Computational Study of Azolo[a]pyrimidines with Special Emphasis on Pyrazolo[1,5-a]pyrimidines'. Journal of Heterocyclic Chemistry. Available Online  
Marin-Luna M, Sanchez-Sanz G, O'Sullivan P, Rozas I. (2014) 'Guanidine complexes of Platinum: a theoretical study'. Journal of Physical Chemistry A, 118.  
G. Sánchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero (2014) 'Intramolecular pnicogen interactions in phosphorus and arsenic analogues of proton sponges'. Physical Chemistry Chemical Physics, 16.  
I. Alkorta, G. Sánchez-Sanz, J. Elguero J.E. Del Bene (2014) 'Pnicogen Bonds between X=PH3 (X = O, S, NH, CH2) and Phosphorus and Nitrogen Bases'. Journal of Physical Chemistry A, 118.  
Professor Denis Shields
Nongonierma AB, Mooney C, Shields DC, FitzGerald RJ (2014) 'In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors'. Peptides, 57:43-51.  
Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB (2014) 'Predicting the important enzymes in human breast milk digestion'. FOOD CHEM, 62 (29):7225-7232.  
Stavropoulos I, Golla K, Moran N, Martin F, Shields DC (journal name Bioarchitecture) (2014) 'Cadherin juxtamembrane region derived peptides inhibit TGFβ1 induced gene expression'. Architecture, 4 (3):103-110.  
Ruhanen H, Hurley D, Ghosh A, O'Brien KT, Johnston CR, Shields DC (2014) 'Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey'. Frontiers in microbiology, 5.  
Khaldi, N., Holton, T.A., Shields, D.C. (2014) 'Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences'. Journal of Dairy Science.  
Nongonierma, A. B., Mooney, C., Shields, D. C., Fitzgerald, R. J. (2013) 'Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides'. Food Chem, 141 (1):644-53. Available Online  
Yadav, S., Cotlarciuc, I., Munroe, P. B., Khan, M. S., Nalls, M. A., Bevan, S., Cheng, Y. C., Chen, W. M., Malik, R., McCarthy, N. S., Holliday, E. G., Speed, D., Hasan, N., Pucek, M., Rinne, P. E., Sever, P., Stanton, A., Shields, D. C., Maguire, J. M., McEvoy, M., Scott, R. J., Ferrucci, L., Macleod, M. J., Attia, J., Markus, H. S., Sale, M. M., Worrall, B. B., Mitchell, B. D., Dichgans, M., Sudlow, C., Meschia, J. F., Rothwell, P. M., Caulfield, M., Sharma, P. (2013) 'Genome-wide analysis of blood pressure variability and ischemic stroke'. Stroke, 44 (10):2703-9. Available Online  
Holton, T. A., Pollastri, G., Shields, D. C., Mooney, C. (2013) 'CPPpred: prediction of cell penetrating peptides'. Bioinformatics. Available Online  
Dr Niels Warburton
Akcay, S; Warburton, N; Barack, L (2013) 'Frequency-domain algorithm for the Lorenz-gauge gravitational self-force'. Phys Rev D.  


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Other Journals

Dr James McDermott
James McDermott (2014) 'Visualizing Evolutionary Search Spaces' SIGEvolution Newsletter, 7 (1):2-10.Available Online  
Professor Thomas Murphy
Breen, K.J., Boyce, S., Boyd Lyons, A., Lundon, D., Fitzpatrick, J.M., Murphy, T.B and Watson, R.W. (2014) 'External validation of the 2007 and 2013 updated Partin tables in a cohort of Irish men' BJU International, 114 (Supplement 2):21-21.  
Boyce S., Murphy L., Fitzpatrick J.M., Murphy T.B., Watson R.W.G. (2013) 'Validation of a panel of serum biomarkers to inform surgical intervention for prostate cancer' Journal of Clinical Urology, 6 (5):339-339.  
Dr Niels Warburton
Warburton, N; Wardell, B (2013) 'Applying the effective-source approach to frequency-domain self-force calculations' arXiv.Available Online  


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Conference Publications

Professor Christopher Bean
Craig, D., Bean, C.J., Moni, A., Lokmer, I. and Donne, S. (2014) Location of Multiple Coincident Noise Sources in the N.E. Atlantic, offshore Ireland EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-13146  
Thun, J., Bean, C.J. and Lokmer, I. (2014) Analysis of volcanic long-period events with quasi-static displacements from high-density seismological networks EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12910  
Bean, C.J., Lokmer, I., DeBarros, L. and Amitrano, D. (2014) Controls on upper edifice rheology and consequences for seismicity-deformation relationship on volcanoes EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-15399  
Thun, J., Bean, C.J. and Lokmer, I. (2014) Detection of quasi-static displacement components of LP seismic sources near the volcanic summit EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12723  
Volk, M.F., Bean, C.J., Lokmer, I. and Craig, D. (2014) Apparent changes in seismic wave velocity related to microseism noise source variations EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-13045  
Donne, S., Nicolau, M., Bean, C.J., Lokmer, I., Craig, D., Creamer, C. and Lambkin, K. (2014) Ocean Wave Height Estimation in the Northeast Atlantic, Offshore Ireland, Using Terrestrial Microseism Data: A Comparison and Analysis of two Evolutionary Approaches EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-12432  
Möllhoff, M. and Bean, C.J. (2014) Microseism Noice Levels in Ireland EGU General Assembly 2014 - Geophysical Research Abstracts Volume 16, Vienna, Austria, EGU2014-3620  
Volk, M., Bean, C., Lokmer, I. and Craig, D. (2013) Investigation of apparent seismic velocity changes caused by microseism noise source variability American Geophysical Union, Fall Meeting, San Francisco, USA, S43B-2527  
Bean, C.J., Lokmer, I., de Barros, L., Eyre, T.S. and Metaxian, J. (2013) Shallow Long Period (LP) seismicity as signatures of shallow edifice deformation at volcano American Geophysical Union, Fall Meeting, San Francisco, USA, V43D-06  
Bean, C.J., Volk, M., Donne, S., Craig, D., Ying, Y., Möllhoff, M., Braiden, A. and Lokmer, I. (2013) Ocean wave generated microseisms in the NE Atlantic: An emerging passive seismic imagery tool Atlantic Ireland 2013, Abstracts Volume, Dublin, Ireland, P. 87-88 Available Online  
Volk, M., Bean, C.J. and Lokmer, I. (2013) Using ambient seismic noise for subsurface imaging UCD Earth Gathering, Dublin, Ireland, Abstracts  
Dr Chris Bleakley
Taylor, K. et al (2014) Lower Body Reaction Testing Using Ultrasonic Motion Capture IEEE Engineering in Medicine and Biology Conf. (EMBC), 36th Annual Int, Chicago, USA,  
Siddig, A., Makki, A., and Bleakley, C.J. (2013) Lighthouse: Precise 802.11-based Localization 4th Int. Conf. on Indoor Positioning and Indoor Navigation (IPIN), Montbeliard-Belfort, France, Available Online  
Professor Anthony Brabazon
Tuite, C., O'Neill, M., Brabazon, A. (2014) The Relationship between Semantic Distance and Performance in Dynamic Symbolic Regression Problems 20th International Conference on Soft Computing (Mendel 2014), Brno, Czech Republic,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2014) Ensemble Bayesian Model Averaging in Genetic Programming IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Beijing, 2451 - 2458  
Byrne, J., Nicolau, M., Brabazon, A. and O'Neill, M. (2014) An Examination of Synchronisation in Artificial Gene Regulatory Networks IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China, 2764 - 2769  
Agapitos, A., McDermott, J., O'Neill, M. and Brabazon, A. (2014) Higher Order Functions for Kernel Regression 17th European Conference on Genetic Programming (EuroGP 2014), Granada, Spain, 1 - 12  
Nicolau, M., O'Neill, M. and Brabazon, A. (2014) Dynamic Index Trading using a Gene Regulatory Network Model 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
McDermott, J., Agapitos, A., Brabazon, A. and O'Neill, M. (2014) Geometric Semantic Genetic Programming for Financial Data 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Lipinski, P. and Brabazon, A. (2014) Pattern Mining in Ultra-High Frequency Order Books 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Byrne,J., Cardiff, P., Brabazon, A. O'Neill, M. (2014) Evolving an Aircraft Using a Parametric Design System 16th European Conference on the Applications of Evolutionary Computation (EvoMusArt 2014), 119 - 130  
Wilinski, M., Cui, W. and Brabazon, A. (2014) An Analysis of the Price Impact Function of Invididual Trades on the London Stock Exchange IEEE Conference on Computational Intelligence for Financial Engineering and Economics 2014, London,  
Dr Nicolae Buchete
Kaskova-Gheorghescu, A; Buchete, NV; Thompson, J (2014) Fractal analysis of the chick extra-embryonic angiogenesis following cadmium exposure Irish Journal of Medicinal Science, S25 - S25  
Kelly, CM; Buchete, NV (2014) Conformational and Dynamic Properties of Extracellular Domains of Cell Adhesion Molecules Biophysical Society 58th Annual Meeting; Biophysical Journal, 51a - 52a Available Online  
Professor Pádraig Cunningham
Qin, X., Salter-Townshend, M., Cunningham, P. (2014) Exploring the Relationship between Membership Turnover and Productivity in Online Communities Eighth International Conference on Weblogs and Social Media (ICWSM 2014),  
Professor Frederic Dias
Sarkar, D; Renzi, E; Dias, F (2014) Oscillating wave surge converters: interactions in a wave farm 33rd International Conference on Ocean, Offshore and Arctic Eng., OMAE14,  
Renzi, E; Dias, F (2014) Time-Domain Hydroacoustic Green Function for Surface Pressure Disturbance. In: M. Kashiwagi eds. 29th International Workshop on Water Waves and Floating Bodies,  
Dias, F., Dutykh, D., O'Brien, L., Renzi, E., Stefanakis, T. (2013) On the modelling of tsunami generation and tsunami inundation Procedia IUTAM: MS02: Mechanics of natural disasters,  
Tiron, R; Gallagher, S; Dias, F (2013) The Influence of Coastal Morphology on the Wave Climate and Wave Energy Resource of the West Irish Coast 10th European Wave and Tidal Energy Conference, EWTEC 2013, Aalborg, Denmark,  
Sarkar, D; Renzi, E; Dias, F (2013) Wave Power Absorption from a Flap-type Wave Energy Converter Near a Straight Coast 10th European Wave and Tidal Energy Conference, EWTEC 2013, Aalborg, Denmark,  
Dr Russell Higgs
Cao, N; Higgs, R; O'Hare, G. (2014) Intelligent evaluation models based on the Single-hop protocol in wireless sensor networks 28th International Conference on Advanced Information Networking and Applications Workshops (WAINA), 239 - 244  
Dr Neil Hurley
McDaid, A., Hurley, N. and Murphy, T.B. (2014) Overlapping Stochastic Community Finding. In: Xindong Wu, Martin Ester, Guandong Xu eds. 2014 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM'14), Beijing, China,  
Hurley, Neil (2013) Personalised Ranking with Diversity ACM 7th Conference on Recommender Systems, Hong Kong, China, Available Online  
Professor Mohand Kechadi
B. Busstra, M. Tahar Kechadi and N-A. Le-Khac (2014) Android and Wireless data-extraction using Wi-Fi 4th IEEE international conference on Innovative Computing Technology (INTECH 2014),  
Christos Sgaras, M. Tahar Kechadi and N-A. Le-Khac (2014) Forensics Acquisition and Analysis of instant messaging and VoIP applications th IAPR International Workshop on Computational Forensics (IWCF 2014), Springer Verlag LNCS,  
N-A. Le-Khac and M. Tahar Kechadi (2014) Toward a new cloud-based approach to preserve the privacy for detecting suspicious cases of money laundering Global Premier International Conference on Cryptography and Security 2014 (ICCS 2014),  
LeKhac, N.A., Kechadi, M-T. (2014) Forensics Acquisition of Tango VoIP International Conference on Challenges in IT, Engineering and Technology (ICCIET 2014), Phuket, Thailand,  
Houari, R., Bounceur, A., Kechadi, M-T., (2014) Handling Missing Data Problems with Sampling Methods (INDS 2014), Bejaia, Algeria,  
Farina, J., Scanlon, M. and Kechadi, M-T. (2014) BitTorrent Sync: First Impressions and Digital Forensic Implications Digital Forensics Research Workshop (DFRWS EU 2014), Amsterdam, Netherlands,  
Scanlon, M. and Kechadi, M-T (2014) The Case for a Collaborative Universal Peer-to-Peer Botnet Investigation Framework 9th International Conference on Cyber Warfare and Security (ICCWS-2014), CERIAS, Purdue University, Indiana, USA,  
Bounceur, A., and Kechadi, M-T., (2014) CupCarbon: A Multi-Agent and Discrete Event Wireless Sensor Network Design and Simulation Tool Based-on the Open Street Map Framework 7th International ICST Conference on Simulation Tools and Techniques, Lisbon, Portugal,  
Tobin, Patrick, Kechadi, M-T., (2014) Virtual Machine Forensics by means of Introspection and Kernel Code Injection 9th International Conference on Cyber Warfare and Security (ICCWS 2014) West Lafayette, Indiana, USA,  
Mark Roeloffs, M. Tahar Kechadi and N-A. Le-Khac (2014) Forensic Investigation of TomTom Application on Android Mobile devices The 10th Annual IFIP WG 11.9 International Conference on Digital Forensics (IFIP WG11.9 2014), Springer Verlag,  
Houari, R., Bounceur, A., Kechadi, M-T. (2013) Data Reduction in Huge Datasets through Removing Redundant Combinations of Dimensions International Conference in Digital Information Processing and Communications(ICDIPC 2013), Hammamet, Tunisia,  
Scanlon, M. and Kechadi, M-T. (2013) Universal Peer-to-Peer Network Investigation Framework. In: IEEE eds. International Workshop on Emerging Cyberthreats and Countermeasures (ECTCM 2013), part of the Eight International Conference on Availability, Reliability and Security (ARES2013), Regensburg, Germany, Available Online  
Scanlon, M. and Kechadi, M-T. (2013) Digital Evidence Bag Selection for P2P Network Investigation The 7th International Symposium on Digital Forensics and Information Security (DFIS-2013); Future Information Technology, Application, and Service, Gwangju, Korea, Available Online  
Professor Joao Marques-Silva
Yuri Malitsky and Barry O'Sullivan and Alessandro Previti and Joao Marques-Silva (2014) Timeout-Sensitive Portfolio Approach to Enumerating Minimal Correction Subsets for Satisfiability Problems ECAI, 1065 - 1066 Available Online  
Joao Marques-Silva and Alexey Ignatiev and Antonio Morgado and Vasco M. Manquinho and Ines Lynce (2014) Efficient Autarkies ECAI, 603 - 608 Available Online  
Alexey Ignatiev and Antonio Morgado and Vasco M. Manquinho and Ines Lynce and Joao Marques-Silva (2014) Progression in Maximum Satisfiability ECAI, 453 - 458 Available Online  
Anton Belov and Marijn Heule and Joao Marques-Silva (2014) MUS Extraction Using Clausal Proofs SAT, 48 - 57 Available Online  
Joao Marques-Silva and Alessandro Previti (2014) On Computing Preferred MUSes and MCSes SAT, 58 - 74 Available Online  
Alexey Ignatiev and Antonio Morgado and Joao Marques-Silva (2014) On Reducing Maximum Independent Set to Minimum Satisfiability SAT, 103 - 120 Available Online  
Alexey Ignatiev and Mikolas Janota and Joao Marques-Silva (2014) Towards efficient optimization in package management systems ICSE, 745 - 755 Available Online  
Yuri Malitsky and Barry O'Sullivan and Alessandro Previti and Joao Marques-Silva (2014) A Portfolio Approach to Enumerating Minimal Correction Subsets for Satisfiability Problems CPAIOR, 368 - 376 Available Online  
Arie Gurfinkel and Anton Belov and Joao Marques-Silva (2014) Synthesizing Safe Bit-Precise Invariants TACAS, 93 - 108 Available Online  
Alexey Ignatiev and Antonio Morgado and Jordi Planes and Joao Marques-Silva (2013) Maximal Falsifiability - Definitions, Algorithms, and Applications LPAR, 439 - 456 Available Online  
Mikoláš Janota and Radu Grigore and Joao Marques-Silva (2013) On QBF Proofs and Preprocessing LPAR, 473 - 489 Available Online  
Anton Belov and Antonio Morgado and Joao Marques-Silva (2013) SAT-Based Preprocessing for MaxSAT LPAR, 96 - 111 Available Online  
Antonio Morgado and Federico Heras and Joao Marques-Silva (2013) Model-Guided Approaches for MaxSAT Solving ICTAI, Washington DC, USA,  
William Klieber and Mikolas Janota and Joao Marques-Silva and Edmund M. Clarke (2013) Solving QBF with Free Variables CP, 415 - 431 Available Online  
Dr James McDermott
James McDermott, Alexandros Agapitos, Anthony Brabazon and Michael ONeill (2014) Geometric Semantic Genetic Programming for Financial Data. In: Anna I Esparcia-Alc?r, Andrea Tettamanzi, Alexandros Agapitos eds. evoapplications: European Conference on the Applications of Evolutionary Computation: evoFIN Evolutionary computation in finance and economics, Granada, Spain,  
Professor Thomas Murphy
McDaid, A., Hurley, N. and Murphy, T.B. (2014) Overlapping Stochastic Community Finding. In: Xindong Wu, Martin Ester, Guandong Xu eds. 2014 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM'14), Beijing, China,  
Professor Michael O'Neill
Tuite, C., O'Neill, M., Brabazon, A. (2014) The Relationship between Semantic Distance and Performance in Dynamic Symbolic Regression Problems 20th International Conference on Soft Computing (Mendel 2014), Brno, Czech Republic,  
Agapitos, A., O'Neill, M. and Brabazon, A. (2014) Ensemble Bayesian Model Averaging in Genetic Programming IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Beijing, 2451 - 2458  
Brabazon, A., Cui, W. and O'Neill, M. (2014) A Framework for Bat Foraging Algorithm Design IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China,  
Byrne, J., Nicolau, M., Brabazon, A. and O'Neill, M. (2014) An Examination of Synchronisation in Artificial Gene Regulatory Networks IEEE World Congress on Computational Intelligence (IEEE WCCI 2014), Bejing, China, 2764 - 2769  
O'Neill M., Nicolau M., Agapitos A. (2014) Experiments in Program Synthesis with Grammatical Evolution: a focus on Integer Sorting IEEE Congress on Evolutionary Computation,  
Donne S., Nicolau M., Bean C., O'Neill M. (2014) Wave Height Quantification using Land Based Seismic Data with Grammatical Evolution IEEE Congress on Evolutionary Computation,  
Agapitos, A., McDermott, J., O'Neill, M. and Brabazon, A. (2014) Higher Order Functions for Kernel Regression 17th European Conference on Genetic Programming (EuroGP 2014), Granada, Spain, 1 - 12  
Nicolau, M., O'Neill, M. and Brabazon, A. (2014) Dynamic Index Trading using a Gene Regulatory Network Model 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
McDermott, J., Agapitos, A., Brabazon, A. and O'Neill, M. (2014) Geometric Semantic Genetic Programming for Financial Data 16th European Conference on the Applications of Evolutionary Computation (EvoApps 2014), Granada, Spain,  
Byrne,J., Cardiff, P., Brabazon, A. O'Neill, M. (2014) Evolving an Aircraft Using a Parametric Design System 16th European Conference on the Applications of Evolutionary Computation (EvoMusArt 2014), 119 - 130  


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Other Publications

Dr Claire Gormley
Nyamundanda, G., Gormley, I.C., Fan, Y., Gallagher, W and Brennan, L. (2013) MetSizeR: a statistical tool for estimating sample sizes for metabolomic experiments. Software.  
Dr Andrew Parnell
Andrew Parnell, Thinh Doan and James Sweeney (2014) Bclim: Bayesian Palaeoclimate Reconstruction from Pollen. Software. Available Online  


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