Journal Articles


[1] I. Arnaldo, I. Contreras, D. Millan-Ruiz, J.I. Hidalgo, and N. Krasnogor. Matching island topologies to problem structure in parallel evolutionary algorithms. Soft Computing, 17(7):1209-1225, 2013. [ bib | DOI | http | .pdf ]
Keywords: Distributed Evolutionary Algorithms, Graphs Structure, Landscapes, Self-Adaptation
[2] B.J.W. Dekkers, S. Pearce, R.P. van Bolderen-Veldkamp, A. Marshall, P. Widera, J. Gilbert, H.G. Drost, G.W. Bassel, K. Muller, J.R. King, A.T. Wood, I. Grosse, M. Quint, N. Krasnogor, G. Leubner-Metzger, M.J. Holdsworth, and L. Bentsink. Transcriptional dynamics of two seed compartments with opposing roles in arabidopsis seed germination. Plant Physiology, (to appear, first published online):113.223511, 2013. [ bib | DOI | http | http ]
Keywords: Seed Germination, Gene Expression Profiling, Transcriptional Phases, Development, Data Analysis
[3] M.A. Franco, N. Krasnogor, and J. Bacardit. Gassist vs. biohel: Critical assessment of two paradigms of genetics-based machine learning. Soft Computing, 17(6):953-981, 2013. [ bib | DOI | http | .pdf ]
Keywords: Rule Base Learning, Machine Learning, Evolutionary Algorithms, Classifier Systems
[4] L.T. Lui, X. Xue, C. Sui, A. Brown, D.I. Pritchard, N. Halliday, K. Winzer, S.M. Howdle, F. Fernandez-Trillo, N. Krasnogor, and C. Alexander. Bacteria clustering by polymers induces the expression of quorum sense controlled phenotypes. Nature Chemistry, (to appear), 2013. [ bib ]
Keywords: Synthetic Biology, Quorum Sensing, Computational Modelling, Polymers Engineering, Biofilms
[5] J. Sun, J.M. Garibaldi, N. Krasnogor, and Q. Zhang. An intelligent multi-restart memetic algorithm for box constrained global optimisation. Evolutionary Computation, 21(1):107-147, 2013. [ bib | DOI | http | .pdf ]
Keywords: Memetic Algorithms, Global Optimisation, Continuous Optimisation
[6] G. Terrazas and N. Krasnogor. A genotype-phenotype-fitness assessment protocol for evolutionary self-assembly wang tiles design. Memetic Computing, 5(1):19-33, 2013. [ bib | DOI | http ]
Keywords: Genotype Phenotype Mapping, Self-assembly, Wang tiles, Evolutionary Algorithms
[7] J. Bacardit, P. Widera, A. Marquez-Chamorro, F. Divina, J.S. Aguilar-Ruiz, and N. Krasnogor. Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features. Bioinformatics, 18(19):2441-2448, 2012. [ bib | DOI | http ]
Keywords: Contact Map Prediction, Machine Learning, Structural Bioinformatics, Protein Structure
[8] J.C. Chaplin, N.A. Russell, and N. Krasnogor. Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates. Biosystems, 109(1):35-51, 2012. [ bib | http | .pdf ]
Keywords: Novel Computation, Unconventional Computing, Vesicles Computing, P Systems, Molecular Computation,
[9] M.A. Franco, N. Krasnogor, and J. Bacardit. Analysing biohel using challenging boolean functions. Evolutionary Intelligence, 5(2):87-102, 2012. [ bib | DOI | http | .pdf ]
Keywords: Genetic Based Machine Learning, Rule Based Machine Learning, Learning Classifier Systems, Benchmarking Data Sets
[10] E. Glaab, J. Bacardit, J.M. Garibaldi, and N. Krasnogor. Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data. PLoS One, 7(7):e39932, 2012. [ bib | DOI | http ]
Keywords: Rule Based Machine Learning, Learning Classifier Systems, Gene Prioritisation, Cancer Gene Expression
[11] E. Glaab, A. Baudot, N. Krasnogor, R.Schneider, and A. Valencia. Enrichnet: network-based gene set enrichment analysis. Bioinformatics, 28(18):451-457, 2012. This paper was also accepted as a full oral presentation at the 2012 European Conference on Computational Biology. [ bib | DOI | http | .pdf ]
Keywords: Gene Sets, Enrichment Analysis, Interaction Networks, Tissue Specific Gene Expression
[12] O. Markovitch, D. Sorek, L.T. Leong, D. Lancet, and N. Krasnogor. Is there an optimal level of open-endedness in prebiotic evolution? Origins of Life and Evolution of Biospheres, 42(5):469-474, 2012. [ bib | .pdf ]
Keywords: Open Ended Evolution, Origins of Life, Measuring Complexity,
[13] G.W. Bassel, H. Lanc, E. Glaa, D.J. Gibbs, T. Gerjets, N. Krasnogor, A.J. Bonner, M.J. Holdsworth, and N.J. Provart. Genome-wide network model capturing seed germination reveals coordinated rregulation of plant cellular phase transitions. Proceedings of the National Academy of Sciences of the United States of America (PNAS), (on line first):(to appear), 2011. [ bib | DOI | http | .pdf ]
Keywords: Genome Network Analysis, Systems Biology, Plant Computational Models
[14] F. Dupeux, J. Santiago, K. Betz, J. Twycross, S.Y. Park, L. Rodriguez, M. Gonzalez-Guzman, M.R. Jensen, N. Krasnogor, M. Blackledge, M. Holdsworth, S.R. Cutler, P.L. Rodriguez, and J.A. Marquez. A thermodynamic switch modulates abscisic acid receptor sensitivity. The EMBO Journal, 30:4171-4184, 2011. [ bib | DOI | .html ]
Keywords: Hormone Regulation, Plant Growth, ABA, Systems Biology, In Silico Simulations
[15] J.Blakes, J. Twycross, F.J. Romero-Campero, and N. Krasnogor. The infobiotics workbench: an integrated in silico modelling platform for systems and synthetic biology. Bioinformatics, (first published on line), 2011. [ bib | DOI | http ]
Keywords: Systems Biology, Synthetic Biology, Infobiotics, Optimisation, Simulation, Model Checking, Specification, Prototyping, P Systems
[16] M. Porcar, A. Danchin, V. de Lorenzo, V.A. dos Santos, N. Krasnogor, S. Rasmussen, and A. Moya. The ten grand challenges of synthetic life. Systems and Synthetic Biology, 5(1-2):1-9, 2011.bib | DOI | http ]
Keywords: Synthetic Biology, Chells, Proto Cells, Artificial Life, Executable Biology, Algorithmic Biology, Minimal Organisms
[17] R.A.J. Woolley, J. Stirling, A. Radocea, N. Krasnogor, and P. Moriarty. Automated probe microscopy via evolutionary optimization at the atomic scale. Applied Physics Letters, 98(25):253104, 2011. This paper won the Silver Medal in the THE 2012 HUMIES AWARDS FOR HUMAN-COMPETITIVE RESULTS PRODUCED BY GENETIC AND EVOLUTIONARY COMPUTATION. [ bib | http | .pdf ]
Keywords: optimisation, automation, genetic algorithms, graphite, optimisation, scanning probe microscopy
[18] E. Glaab, A. Baudot, N. Krasnogor, and A. Valencia. Topogsa: network topological gene set analysis. Bioinformatics, 26(9):1271, March 2010. [ bib | DOI | http | .pdf ]
Keywords: Systems Biology, Network Topology, Gene Sets, Protein Sets, Cellular Pathways, Betweeness, Clustering Coeficient, Average Path Length
[19] J.Twycross, L.R. Band, M. J. Bennett, J.R. King, and N. Krasnogor. Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. BMC Systems Biology, 4(:34), March 2010. [ bib | http | .pdf ]
Keywords: Systems Biology, P systems, Executable Biology, Infobiotics, Algorithmic Systems Biology, Stochastic Modeling, Deterministic Modeling, Auxin Transport, A. thaliana
[20] R.E. Smith, M.K. Jiang, J. Bacardit, M. Stout, N. Krasnogor, and J.D. Hirst. A learning classifier system with mutual-information-based fitness. Evolutionary Intelligence, 3(1):31-50, March 2010. [ bib | http | .pdf ]
Keywords: Data Mining, Classification, Learning Classifier Systems, Mutual Information, XCS, UCS, BioHel, Naive Bayes, C4.5
[21] N. Krasnogor A.A Shah, G. Folino. Towards high-throughput, multi-criteria protein structure comparison and analysis. IEEE Transactions on NanoBioscience, 9(2):144-155, 2010. [ bib | DOI | http | .pdf ]
Keywords: Structural Bioinformatics, Protein Structure Comparison, Protein Structure Alignments, High Performance Computing, Distributed Computing, Grid Computing
[22] H. Cao, F.J. Romero-Campero, S. Heeb, M. Camara, and N. Krasnogor. Evolving cell models for systems and synthetic biology. Systems and Synthetic Biology (Springer), 4(1):55-84, 2010.bib | DOI | .pdf | .pdf ]
Keywords: Systems Biology, Synthetic Biology, Automated Modelling, Parameter/Structure Optimisation
[23] D. Gilbert, A. Jaramillo, N. Krasnogor, and V. de Lorenzo. Synthetic biology gains momentum in europe. Systems and Synthetic Biology, 4(3):145-147, 2010. [ bib | DOI | http | .pdf ]
Keywords: Synthetic Biology
[24] E. Glaab, A. Baudot, N. Krasnogor, and A. Valencia. Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics, 11(597), 2010.bib | DOI | http ]
Keywords: Cellular Processes, Biological Pathways, Networks, Genomics, Cancer
[25] E. Glaab, J. M. Garibaldi, and N. Krasnogor. Vrmlgen: An r package for 3d data visualization on the web. Journal of Statistical Software, 36(8):1-18, 2010. [ bib | http ]
Keywords: R, 3D Visualisation, Clustering, Statistics
[26] H.O. Habashy, D.G. Powe, E. Glaab, N. Krasnogor, J.M. Garibaldi, E.A. Rakha, G. Ball, A.R. Green, and I.O. Ellis. Rerg (ras-related and oestrogen-regulated growth-inhibitor) expression in breast cancer: A marker of er-positive luminal-like subtype. Breast Cancer Research and Treatment, (on line first):1-12, 2010. [ bib | http ]
Keywords: Breast Cancer, Data Mining, Biomarker, Gene Expression
[27] J. Smaldon, F. J. Romero-Campero, F. Fernandez Trillo, M. Gheorghe, C. Alexander, and N. Krasnogor. A computational study of liposome logic: towards cellular computing from the bottom up. Systems and Synthetic Biology (Springer), 4(3):157-179, 2010.bib | DOI | http | .pdf ]
Keywords: Synthetic Biology, Protocells, Bottom-Up, Dissipative Particle Dynamics, P systems, DPD
[28] P. Widera, J. Garibaldi, and N. Krasnogor. Gp challenge: evolving the energy function for protein structure prediction. Journal of Genetic Programming and Evolvable Machines, 11:61-88, 1 2010. This paper won the Gold Medal in the THE 2010 HUMIES AWARDS FOR HUMAN-COMPETITIVE RESULTS PRODUCED BY GENETIC AND EVOLUTIONARY COMPUTATION. A pdf slide show about this paper is available at . For the latest version please consult the journal website. [ bib | DOI | .pdf | .pdf ]
Keywords: Genetic Programming, Protein Structure Prediction, Protein Folding, Challenge
[29] J. Bacardit, E.K. Burke, and N. Krasnogor. Improving the scalability of rule-based evolutionary learning. Memetic Computing, 1(1):55-67, 2009. (for the latest version of this paper please refer to the journal website). [ bib | DOI | http | .pdf ]
Keywords: Memetic Algorithms, Learning Classifier Systems, Scalability
[30] J. Bacardit and N. Krasnogor. Performance and efficiency of memetic pittsburgh learning classifier systems. Evolutionary Computation, 17(3):307-342, 2009. (for the latest version of this paper please refer to the journal website). [ bib | .pdf ]
Keywords: Learning Classifier Systems, Memetic Algorithms, Scalability, Data Mining
[31] J. Bacardit, M. Stout, J.D. Hirst, A. Valencia, R.E. Smith, and N. Krasnogor. Automated alphabet reduction for protein datasets. BMC Bioinformatics, 10(6), 2009. (for the latest version of this paper please refer to the journal website). [ bib | DOI | http | .pdf ]
Keywords: Protein Structure, Alphabet Reduction, Machine Learning, Learning Classifier Systems, Mutual Information
[32] F. J. Romero-Campero, J. Twycross, M. Camara, M. Bennett, M. Gheorghe, and N. Krasnogor. Modular assembly of cell systems biology models using p systems. International Journal of Foundations of Computer Science, 20(3):427-442, 2009. A set of slides related to this paper is available at [ bib | DOI | .pdf | .pdf ]
Keywords: Systems Biology, Synthetic Biology, Computational Modeling, Cell Biology, P Systems, Executable Biology, Infobiotics
[33] E. Glaab, J. Garibaldi, and N. Krasnogor. Arraymining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics, 10(1)(1):358, 2009. [ bib | DOI | http | http ]
Keywords: Gene Expression, Consensus, Ensemble, Intelligent Data Analysis
[34] L. Li, J. Garibaldi, and N. Krasnogor. Automated self-assembly programming paradigm: The impact of network topology. International Journal of Intelligent Systems (IJIS), 24(7):793-817, 2009. Special issue on Nature Inspired Cooperative Strategies for Optimisation. [ bib | http | .pdf ]
Keywords: Self-Assembly, Automated Programming, Genetic Programming
[35] A. Moya, N. Krasnogor, J. Pereto, and A. Latorre. Goethe's dream. challenges and opportunities for synthetic biology. EMBO reports, 10, S1,:28-32, 2009. [ bib | DOI | .pdf ]
Keywords: Synthetic Biology, Systems Biology, Executable Biology, Algorithmic Systems Biology
[36] G. Pasparakis, N. Krasnogor, L. Cronin, B.G. Davis, and C. Alexander. Controlled polymer synthesis: from biomimicry towards synthetic biology. Chemical Society Reviews, 2009. [ bib | DOI ]
Keywords: Synthetic Biology, Non standard Computation, Computational Modeling
[37] G. Pasparakis, M. Vamvakaki, N. Krasnogor, and C. Alexander. Diol-boronic acid complexes integrated by responsive polymers - a route to chemical sensing and logic operations. Soft Matter, 2009. [ bib | DOI | http ]
Keywords: Molecular Computing, Chemical Logic Gates
[38] Q.H. Quang, Y.S. Ong, M.H. Lim, and N. Krasnogor. Adaptive cellular memetic algorithm. Evolutionary Computation, 17(3):231-256, 2009. (for the latest version of this paper please refer to the journal website). [ bib | http | .PDF ]
Keywords: Cellular Genetic Algorithms, Memetic Algorithms
[39] M. Gheorghe, N. Krasnogor, and M. Camara. P systems applications to systems biology. Biosystems, 91:435-437, 2008. [ bib | http ]
Keywords: P Systems, Systems Biology, Bioological Modeling
[40] N. Krasnogor and J.E. Smith. Memetic algorithms: The polynomial local search complexity theory perspective. Journal of Mathematical Modelling and Algorithms, 7:3-24, 2008. [ bib | .pdf ]
Keywords: Memetic Algorithms, Local Search, Theory, Complexity
[41] M.T. Oakley, D. Barthel, Y. Bykov, J.M. Garibaldi, E.K. Burke, N. Krasnogor, and J.D. Hirst. Search strategies in structural bioinformatics. Current Protein and Peptide Science (Bentham Science Publishers), 9(3):260-274, 2008. [ bib | .pdf ]
Keywords: Bioinformatics, Protein Structure Prediction, Search, Optimisation, Protein Structure Comparison
[42] A.A. Shah, D. Barthel, P. Lukasiak, J. Blazewicz, and N. Krasnogor. Web & grid technologies in bioinformatics, computational and systems biology: A review. Current Bioinformatics, 3(1):10-31(22), 2008. [ bib | DOI | .pdf ]
Keywords: Web based, Grid Based, Bioinformatics
[43] M. Stout, J. Bacardit, J.D. Hirst, and N. Krasnogor. Prediction of recursive convex hull class assignment for protein residues. Bioinformatics, 24(7):916-923, 2008. [ bib | http ]
Keywords: Protein Structure Prediction, Convex Hull, Learning Classifier Systems
[44] M. Stout, J. Bacardit, J.D. Hirst, R.E Smith, and N. Krasnogor. Prediction of topological contacts in proteins using learning classifier systems. Journal Soft Computing - A Fusion of Foundations, Methodologies and Applications, 13(3):245-258, 2008. (for the latest version of this paper please refer to the journal website). [ bib | DOI | .pdf | .pdf ]
Keywords: Protein Structure Prediction, Delaunay Triangulation, Voronoi, Gabriel Graphs, Relative Neighborhood Graph, Learning Classifier Systems, Data Mining
[45] F. Bernardini, M. Gheorghe, and N. Krasnogor. Quorum sensing p systems. Theoretical Computer Science, 371(1-2):20-33, February 2007. NOTE: This paper is the 3rd of the "Top 25 Hottest Articles" (most downloaded) since its appearance up until 24/September/2007. (for the latest version of this paper please refer to the journal website). [ bib | DOI | http | .pdf ]
Keywords: Quorum Sensing, Systems Biology, P Systems
[46] D. Barthel, J.D. Hirst, J. Blazewicz, E.K. Burke, and N. Krasnogor. Procksi: a decision support system for protein (structure) comparison, knowledge, similarity and information. BMC Bioinformatics, 8:416, 2007. [ bib | DOI | http ]
Keywords: Protein Structure, Comparison, Alignment, CE, DaliLite, FAST, MaxCMO, TMalign, URMS, USM, Vorolign
[47] Wojciech Jaśkowski, Jacek Blazewicz, Piotr Lukasiak, Maciej Milostan, and Natalio Krasnogor. 3d-judge - a metaserver approach to protein structure prediction. Foundations of Computing and Decision Sciences, 31(1), 2007. [ bib | .pdf ]
Keywords: Protein Structure Prediction, Metaserver
[48] Y.S. Ong, N. Krasnogor, and H. Ishibuchi. Special issue on memetic algorithms. IEEE Transactions on Systems, Man and Cybernetics, Part B, 37(1):2-5, 2007. [ bib | http ]
Keywords: Memetic Algorithms
[49] P.Siepmann, C.P. Martin, I. Vancea, P.J. Moriarty, and N. Krasnogor. A genetic algorithm approach to probing the evolution of self-organised nanostructured systems. Nano Letters, 7(7):1985-1990, 2007. (for the latest version please check the official journal site). [ bib | DOI | http | .pdf ]
Keywords: Nanoscience, Genetic Algorithms, Self-Organisation, Inverse Problems
[50] G. Terrazas, P. Siepman, G. Kendal, and N. Krasnogor. An evolutionary methodology for the automated design of cellular automaton-based complex systems. Journal of Cellular Automata, 2(1):77-102, 2007. (for the latest version of this paper please refer to the journal website). [ bib | .html | .pdf ]
Keywords: Inverse Problems, Cellular Automata, Evolutionary Algorithms, Self-Organisation
[51] L. Cronin, N. Krasnogor, B. G. Davis, C. Alexander, N. Robertson, J.H.G. Steinke, S.L.M. Schroeder, A.N. Khlobystov, G. Cooper, P. Gardner, P. Siepmann, and B. Whitaker. The imitation game - a computational chemical approach to recognizing life. Nature Biotechnology, 24:1203-1206, 2006. [ bib | DOI | .html ]
Keywords: Artificial Life, Protocells, Chells, Imitation Game, Turing Test, Synthetic Biology
[52] N. Krasnogor, M. Gheorghe, G. Terrazas, S. Diggle, P. Williams, and M. Camara. An appealing computational mechanism drawn from bacterial quorum sensing. Bulletin of the European Association of Theoretical Computer Science, (85):135-148, February 2005. [ bib | .pdf ]
Keywords: Nonstandard Computation, Bacterial Modeling, Quorum Sensing
[53] N. Krasnogor and J.E. Smith. A tutorial for competent memetic algorithms: model, taxonomy and design issues. IEEE Transactions on Evolutionary Computation, 9(5):474- 488, 2005. [ bib | .pdf ]
Keywords: Tutoria, Memetic Algorithm, Model, Taxonomy, Classification
[54] D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J. Hirst, and E.K. Burke. A fuzzy sets based generalization of contact maps for the overlap of protein structures. Journal of Fuzzy Sets and Systems, 152(2):103-123, 2005. [ bib | http ]
Keywords: Contact Map, Fuzzy Sets, Optimisation, Bioinformatics
[55] W.E. Hart, N. Krasnogor, and J.E. Smith. Editorial introduction, special issue on memetic algorithms. Evolutionary Computation, 12(3):v-vi, 2004. [ bib | http ]
Keywords: Memetic Algorithms
[56] N. Krasnogor. Self-generating metaheuristics in bioinformatics: the protein structure comparison case. Genetic Programming and Evolvable Machines, 5(2):181-201, 2004. [ bib | .pdf ]
Keywords: Self-Generation, Self-Organisation, Optimisation, Metaheuristics, Memetic Algorithms, Bioinformatics
[57] N. Krasnogor and D.A. Pelta. Measuring the similarity of protein structures by means of the universal similarity metric. Bioinformatics, 20(7):1015-1021, 2004. [ bib | DOI | http ]
Keywords: Protein Structure, Comparison, Alignment, Universal Similarity Metric
[58] M. Lozano, F. Herrera, N. Krasnogor, and D. Molina. Real-coded memetic algorithms with crossover hill-climbing. Evolutionary Computation, 12(3):273-302, 2004. [ bib | DOI | .pdf ]
Keywords: Memetic Algorithms, Continous Optimisation, Self-Adaptation, Local Search
[59] N.Krasnogor and S. Gustafson. A study on the use of “self-generation” in memetic algorithms. Natural Computing, 3(1):53 - 76, 2004. [ bib | .pdf ]
Keywords: Self-Generation, Self-Organisation, Optimisation, Metaheuristics, Memetic Algorithms, NK Landscapes

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