@article{ShaFolKra,
author = {A.A Shah, G. Folino, N. Krasnogor},
title = {Towards High-Throughput, Multi-Criteria Protein Structure Comparison
and Analysis},
journal = {IEEE Transactions on NanoBioscience},
year = {2010},
volume = {9},
pages = {144-155},
number = {2},
doi = {10.1109/TNB.2010.2043851},
keywords = {Structural Bioinformatics, Protein Structure Comparison, Protein Structure
Alignments, High Performance Computing, Distributed Computing, Grid
Computing},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/TNB10.pdf},
timestamp = {2010.03.27},
url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5477191}
}
@article{ArnConMilHidKra2013,
author = {I. Arnaldo and I. Contreras and D. Millan-Ruiz and J.I. Hidalgo and
N. Krasnogor},
title = {Matching Island Topologies to Problem Structure in Parallel Evolutionary
Algorithms},
journal = {Soft Computing},
year = {2013},
volume = {17},
pages = {1209-1225},
number = {7},
doi = {10.1007/s00500-013-0995-9},
keywords = {Distributed Evolutionary Algorithms, Graphs Structure, Landscapes,
Self-Adaptation},
owner = {nxk},
pdf = {http://link.springer.com/content/pdf/10.1007%2Fs00500-013-0995-9.pdf},
timestamp = {2012.12.06},
url = {http://link.springer.com/article/10.1007%2Fs00500-013-0995-9}
}
@article{BacKraBur09,
author = {J. Bacardit and E.K. Burke and N. Krasnogor},
title = {Improving the scalability of rule-based evolutionary learning},
journal = {Memetic Computing},
year = {2009},
volume = {1},
pages = {55-67},
number = {1},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
doi = {10.1007/s12293-008-0005-4},
keywords = {Memetic Algorithms, Learning Classifier Systems, Scalability},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/jmc09.pdf},
timestamp = {2008.12.08},
url = {http://www.springer.com/engineering/journal/12293}
}
@article{BacKra08b,
author = {J. Bacardit and N. Krasnogor},
title = {Performance and Efficiency of Memetic Pittsburgh Learning Classifier
Systems},
journal = {Evolutionary Computation},
year = {2009},
volume = {17(3)},
pages = {307-342},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
keywords = {Learning Classifier Systems, Memetic Algorithms, Scalability, Data
Mining},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/paperMPLCS.pdf},
timestamp = {2008.07.10}
}
@article{BacStoHirValSmiKra09,
author = {J. Bacardit and M. Stout and J.D. Hirst and A. Valencia and R.E.
Smith and N. Krasnogor},
title = {Automated Alphabet Reduction for Protein Datasets},
journal = {BMC Bioinformatics},
year = {2009},
volume = {10(6)},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
doi = {DOI:10.1186/1471-2105-10-6},
keywords = {Protein Structure, Alphabet Reduction, Machine Learning, Learning
Classifier Systems, Mutual Information},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/paperAR.pdf},
timestamp = {2008.12.08},
url = {http://www.biomedcentral.com/1471-2105/10/6}
}
@article{BacWidMarDivAguKra2012,
author = {J. Bacardit and P. Widera and A. Marquez-Chamorro and F. Divina and
J.S. Aguilar-Ruiz and N. Krasnogor},
title = {Contact map prediction using a large-scale ensemble of rule sets
and the fusion of multiple predicted structural features},
journal = {Bioinformatics},
year = {2012},
volume = {18},
pages = {2441-2448},
number = {19},
doi = {10.1093/bioinformatics/bts472},
keywords = {Contact Map Prediction, Machine Learning, Structural Bioinformatics,
Protein Structure},
owner = {nxk},
timestamp = {2012.12.06},
url = {http://bioinformatics.oxfordjournals.org/content/28/19/2441.abstract?sid=e363d298-86c7-4c91-bbaf-edadb3d80de4}
}
@article{BarHirBlaBurKra,
author = {D. Barthel and J.D. Hirst and J. Blazewicz and E.K. Burke and N.
Krasnogor},
title = {ProCKSI: a decision support system for Protein (Structure) Comparison,
Knowledge, Similarity and Information},
journal = {BMC Bioinformatics},
year = {2007},
volume = {8:416},
doi = {10.1186/1471-2105-8-416},
keywords = {Protein Structure, Comparison, Alignment, CE, DaliLite, FAST, MaxCMO,
TMalign, URMS, USM, Vorolign},
owner = {nxk},
timestamp = {2007.10.27},
url = {http://www.biomedcentral.com/bmcbioinformatics/}
}
@article{BasLan11,
author = {G.W. Bassel and H. Lanc and E. Glaa and D.J. Gibbs and T. Gerjets
and N. Krasnogor and A.J. Bonner and M.J. Holdsworth and N.J. Provart},
title = {Genome-wide Network Model Capturing Seed Germination Reveals Coordinated
Rregulation of Plant Cellular Phase Transitions},
journal = {Proceedings of the National Academy of Sciences of the United States
of America (PNAS)},
year = {2011},
volume = {(on line first)},
pages = {(to appear)},
doi = {10.1073/pnas.1100958108},
keywords = {Genome Network Analysis, Systems Biology, Plant Computational Models},
owner = {nxk},
pdf = {www.cs.nott.ac.uk/~nxk/PAPERS/PNAS-2011.pdf},
timestamp = {2011.06.24},
url = {http://www.pnas.org/content/early/2011/05/17/1100958108.abstract}
}
@article{F.2006,
author = {F. Bernardini and M. Gheorghe and N. Krasnogor.},
title = {Quorum sensing P systems},
journal = {Theoretical Computer Science},
year = {2007},
volume = {371},
pages = {20-33},
number = {1-2},
month = {February},
note = {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)},
__markedentry = {[nxk]},
comment = {(for the latest version of this paper please refer to the journal
website)},
doi = {http://dx.doi.org/10.1016/j.tcs.2006.10.012},
keywords = {Quorum Sensing, Systems Biology, P Systems},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/popQS.pdf},
url = {http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&_urlVersion=4&_origin=SDTOPTWOFIVE&_version=1&_piikey=S0304397506007493&md5=bd072a6dd2b7999a36f9895cf70bc8e0}
}
@article{RomTwyCamBenGheKra09,
author = {F. J. Romero-Campero and J. Twycross and M. Camara and M. Bennett
and M. Gheorghe and N. Krasnogor},
title = {Modular Assembly of Cell Systems Biology Models Using P Systems},
journal = {International Journal of Foundations of Computer Science},
year = {2009},
volume = {20},
pages = {427-442},
number = {3},
note = {A set of slides related to this paper is available at http://www.slideshare.net/nxk/executable-biology-tutorial},
doi = {10.1142/S0129054109006668},
keywords = {Systems Biology, Synthetic Biology, Computational Modeling, Cell Biology,
P Systems, Executable Biology, Infobiotics},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/IJFCS_Nottingham.pdf},
timestamp = {2009.03.24},
url = {http://www.worldscinet.com/ijfcs/20/preserved-docs/2003/S0129054109006668.pdf}
}
@article{CaoRomHeeCamKra09,
author = {H. Cao and F.J. Romero-Campero and S. Heeb and M. Camara and N. Krasnogor},
title = {Evolving Cell Models for Systems and Synthetic Biology},
journal = {Systems and Synthetic Biology (Springer)},
year = {2010},
volume = {4},
pages = {55-84},
number = {1},
doi = {DOI 10.1007/s11693-009-9050-7},
keywords = {Systems Biology, Synthetic Biology, Automated Modelling, Parameter/Structure
Optimisation},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk:/~nxk/PAPERS/SSB09a.pdf},
timestamp = {2009.12.17},
url = {http://www.springerlink.com/content/66671m1186474455/fulltext.pdf}
}
@article{ChaRusKra,
author = {J.C. Chaplin and N.A. Russell and N. Krasnogor},
title = {Implementing conventional logic unconventionally: Photochromic molecular
populations as registers and logic gates},
journal = {Biosystems},
year = {2012},
volume = {109},
pages = {35-51},
number = {1},
keywords = {Novel Computation, Unconventional Computing, Vesicles Computing, P
Systems, Molecular Computation,},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/PhotochromicLogic.pdf},
timestamp = {2012.07.11},
url = {http://www.sciencedirect.com/science/article/pii/S0303264711002061}
}
@article{Leroy2006,
author = {L. Cronin and N. Krasnogor and B. G. Davis and C. Alexander and N.
Robertson and J.H.G. Steinke and S.L.M. Schroeder and A.N. Khlobystov
and G. Cooper and P. Gardner and P. Siepmann and B. Whitaker},
title = {The imitation game - a computational chemical approach to recognizing
life},
journal = {Nature Biotechnology},
year = {2006},
volume = {24},
pages = {1203-1206},
doi = {doi:10.1038/nbt1006-1203},
keywords = {Artificial Life, Protocells, Chells, Imitation Game, Turing Test,
Synthetic Biology},
owner = {nxk},
url = {http://www.nature.com/nbt/journal/v24/n10/full/nbt1006-1203.html}
}
@article{Deketal2013,
author = {B.J.W. Dekkers and S. Pearce and R.P. van Bolderen-Veldkamp and A.
Marshall and P. Widera and J. Gilbert and H.G. Drost and G.W. Bassel
and K. Muller and J.R. King and A.T. Wood and I. Grosse and M. Quint
and N. Krasnogor and G. Leubner-Metzger and M.J. Holdsworth and L.
Bentsink},
title = {Transcriptional Dynamics of Two Seed Compartments with Opposing Roles
in Arabidopsis Seed Germination},
journal = {Plant Physiology},
year = {2013},
volume = {(to appear, first published online)},
pages = {113.223511},
doi = {10.1104/pp.113.223511},
keywords = {Seed Germination, Gene Expression Profiling, Transcriptional Phases,
Development, Data Analysis},
owner = {nxk},
pdf = {http://www.plantphysiol.org/content/early/2013/07/16/pp.113.223511.full.pdf+html},
timestamp = {2013.08.04},
url = {http://www.plantphysiol.org/content/early/2013/07/16/pp.113.223511.abstract}
}
@article{Dupeaxetal2011,
author = {F. Dupeux and J. Santiago and K. Betz and J. Twycross and S.Y. Park
and L. Rodriguez and M. Gonzalez-Guzman and M.R. Jensen and N. Krasnogor
and M. Blackledge and M. Holdsworth and S.R. Cutler and P.L. Rodriguez
and J.A. Marquez},
title = {A thermodynamic switch modulates abscisic acid receptor sensitivity},
journal = {The EMBO Journal},
year = {2011},
volume = {30},
pages = {4171-4184},
doi = {doi:10.1038/emboj.2011.294},
keywords = {Hormone Regulation, Plant Growth, ABA, Systems Biology, In Silico
Simulations},
owner = {nxk},
timestamp = {2011.10.26},
url = {http://www.nature.com/emboj/journal/v30/n20/full/emboj2011294a.html}
}
@article{FraKraBac2013,
author = {M.A. Franco and N. Krasnogor and J. Bacardit},
title = {GAssist vs. BioHEL: Critical Assessment of Two Paradigms of Genetics-based
Machine Learning},
journal = {Soft Computing},
year = {2013},
volume = {17},
pages = {953-981},
number = {6},
doi = {10.1007/s00500-013-1016-8},
keywords = {Rule Base Learning, Machine Learning, Evolutionary Algorithms, Classifier
Systems},
owner = {nxk},
pdf = {http://link.springer.com/content/pdf/10.1007%2Fs00500-013-1016-8.pdf},
timestamp = {2013.08.04},
url = {http://link.springer.com/article/10.1007%2Fs00500-013-1016-8}
}
@article{FraKraBac2012,
author = {M.A. Franco and N. Krasnogor and J. Bacardit},
title = {Analysing BioHEL using challenging boolean functions},
journal = {Evolutionary Intelligence},
year = {2012},
volume = {5},
pages = {87-102},
number = {2},
doi = {DOI: 10.1007/s12065-012-0080-9},
keywords = {Genetic Based Machine Learning, Rule Based Machine Learning, Learning
Classifier Systems, Benchmarking Data Sets},
owner = {nxk},
pdf = {http://www.springerlink.com/content/5888745388k18432/fulltext.pdf},
timestamp = {2012.07.11},
url = {http://www.springerlink.com/content/5888745388k18432/}
}
@article{GheKraCam2007,
author = {M. Gheorghe and N. Krasnogor and M. Camara},
title = {P Systems Applications to Systems Biology},
journal = {Biosystems},
year = {2008},
volume = {91},
pages = {435-437},
keywords = {P Systems, Systems Biology, Bioological Modeling},
owner = {nxk},
timestamp = {2008.02.12},
url = {http://www.sciencedirect.com/science?_ob=PublicationURL&_ctockey=%23toc%234921%232008%23999089996%23680312%23FLA%23&_cdi=4921&_pubType=J&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=aecbf325366f51e1612198af54b75fce&jchunk=xxx}
}
@article{GilJarKraLor10,
author = {D. Gilbert and A. Jaramillo and N. Krasnogor and V. de Lorenzo},
title = {Synthetic biology gains momentum in Europe},
journal = {Systems and Synthetic Biology},
year = {2010},
volume = {4},
pages = {145-147},
number = {3},
doi = {10.1007/s11693-010-9065-0},
keywords = {Synthetic Biology},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/SysSyntBioEditorial.pdf},
timestamp = {2011.06.24},
url = {http://www.springerlink.com/content/n2w430717vg5306r/}
}
@article{GlaBacGarKra12a,
author = {E. Glaab and J. Bacardit and J.M. Garibaldi and N. Krasnogor},
title = {Using rule-based machine learning for candidate disease gene prioritization
and sample classification of cancer gene expression data},
journal = {PLoS One},
year = {2012},
volume = {7},
pages = {e39932},
number = {7},
doi = {10.1371/journal.pone.0039932},
keywords = {Rule Based Machine Learning, Learning Classifier Systems, Gene Prioritisation,
Cancer Gene Expression},
owner = {nxk},
timestamp = {2012.07.11},
url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039932}
}
@article{GlaBauKraSchVal12a,
author = {E. Glaab and A. Baudot and N. Krasnogor and R.Schneider and A. Valencia.},
title = {EnrichNet: network-based gene set enrichment analysis},
journal = {Bioinformatics},
year = {2012},
volume = {28},
pages = {451-457},
number = {18},
note = {This paper was also accepted as a full oral presentation at the 2012
European Conference on Computational Biology},
doi = {10.1093/bioinformatics/bts389},
keywords = {Gene Sets, Enrichment Analysis, Interaction Networks, Tissue Specific
Gene Expression},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/DRAFTECCB2012.pdf},
timestamp = {2012.07.11},
url = {http://bioinformatics.oxfordjournals.org/content/28/18/i451.abstract}
}
@article{GlaBauKraVal10,
author = {E. Glaab and A. Baudot and N. Krasnogor and A. Valencia},
title = {TopoGSA: network topological gene set analysis},
journal = {Bioinformatics},
year = {2010},
volume = {26(9)},
pages = {1271},
month = {March},
citeseerurl = {http://bioinformatics.oxfordjournals.org/cgi/content/full/btq131?ijkey=SqxkO44BdiOAqBF&keytype=ref},
doi = {DOI 10.1093/bioinformatics/btq131},
keywords = {Systems Biology, Network Topology, Gene Sets, Protein Sets, Cellular
Pathways, Betweeness, Clustering Coeficient, Average Path Length},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/btq131v1.pdf},
timestamp = {2010.03.27},
url = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btq131?ijkey=SqxkO44BdiOAqBF&keytype=ref}
}
@article{GlaBauKraVal2010,
author = {E. Glaab and A. Baudot and N. Krasnogor and A. Valencia},
title = {Extending pathways and processes using molecular interaction networks
to analyse cancer genome data},
journal = {BMC Bioinformatics},
year = {2010},
volume = {11},
number = {597},
doi = {doi:10.1186/1471-2105-11-597},
keywords = {Cellular Processes, Biological Pathways, Networks, Genomics, Cancer},
owner = {nxk},
timestamp = {2010.12.29},
url = {http://www.biomedcentral.com/1471-2105/11/597}
}
@article{GlaGarKra09,
author = {E. Glaab and J. Garibaldi and N. Krasnogor},
title = {ArrayMining: a modular web-application for microarray analysis combining
ensemble and consensus methods with cross-study normalization},
journal = {BMC Bioinformatics},
year = {2009},
volume = {10(1)},
pages = {358},
number = {1},
__markedentry = {[nxk]},
doi = {10.1186/1471-2105-10-358},
issn = {1471-2105},
keywords = {Gene Expression, Consensus, Ensemble, Intelligent Data Analysis},
pdf = {http://www.biomedcentral.com/1471-2105/10/358},
pubmedid = {19863798},
url = {http://www.arraymining.net/}
}
@article{GlaKarKra2010,
author = {E. Glaab and J. M. Garibaldi and N. Krasnogor},
title = {VRMLGen: An R package for 3D Data Visualization on the Web},
journal = {Journal of Statistical Software},
year = {2010},
volume = {36},
pages = {1-18},
number = {8},
__markedentry = {[nxk]},
keywords = {R, 3D Visualisation, Clustering, Statistics},
owner = {nxk},
timestamp = {2010.08.08},
url = {http://www.jstatsoft.org/v36/i08}
}
@article{QMC2010a,
author = {H.O. Habashy and D.G. Powe and E. Glaab and N. Krasnogor and J.M.
Garibaldi and E.A. Rakha and G. Ball and A.R. Green and I.O. Ellis},
title = {RERG (Ras-related and oestrogen-regulated growth-inhibitor) expression
in breast cancer: A marker of ER-positive luminal-like subtype},
journal = {Breast Cancer Research and Treatment},
year = {2010},
volume = {(on line first)},
pages = {1-12},
keywords = {Breast Cancer, Data Mining, Biomarker, Gene Expression},
owner = {nxk},
timestamp = {2010.08.08},
url = {http://dx.doi.org/10.1007/s10549-010-1073-y}
}
@article{HarKraSmi04,
author = {W.E. Hart and N. Krasnogor and J.E. Smith},
title = {Editorial Introduction, Special Issue on Memetic Algorithms},
journal = {Evolutionary Computation},
year = {2004},
volume = {12},
pages = {v-vi},
number = {3},
keywords = {Memetic Algorithms},
owner = {nxk},
timestamp = {2008.02.12},
url = {http://www.mitpressjournals.org/doi/abs/10.1162/1063656041775009}
}
@article{BlaTwyRomKra11,
author = {J.Blakes and J. Twycross and F.J. Romero-Campero and N. Krasnogor},
title = {The Infobiotics Workbench: an integrated in silico modelling platform
for Systems and Synthetic Biology},
journal = {Bioinformatics},
year = {2011},
volume = {(first published on line)},
doi = {doi:10.1093/bioinformatics/btr571},
keywords = {Systems Biology, Synthetic Biology, Infobiotics, Optimisation, Simulation,
Model Checking, Specification, Prototyping, P Systems},
owner = {nxk},
timestamp = {2011.10.26},
url = {http://bioinformatics.oxfordjournals.org/content/early/2011/10/12/bioinformatics.btr571.full.pdf+html}
}
@article{TwyBanBenKinKra10,
author = {J.Twycross and L.R. Band and M. J. Bennett and J.R. King and N. Krasnogor},
title = {Stochastic and deterministic multiscale models for systems biology:
an auxin-transport case study},
journal = {BMC Systems Biology},
year = {2010},
volume = {4},
number = {:34},
month = {March},
keywords = {Systems Biology, P systems, Executable Biology, Infobiotics, Algorithmic
Systems Biology, Stochastic Modeling, Deterministic Modeling, Auxin
Transport, A. thaliana},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/1752-0509-4-34.pdf},
timestamp = {2010.03.27},
url = {http://www.biomedcentral.com/1752-0509/4/34/abstract}
}
@article{JasBlaLukMilKra2007,
author = {Wojciech Ja{\'s}kowski and Jacek Blazewicz and Piotr Lukasiak and
Maciej Milostan and Natalio Krasnogor},
title = {3D-Judge - A Metaserver Approach to Protein Structure Prediction},
journal = {Foundations of Computing and Decision Sciences},
year = {2007},
volume = {31},
number = {1},
keywords = {Protein Structure Prediction, Metaserver},
owner = {nxk},
timestamp = {2007.06.08},
url = {http://www.cs.put.poznan.pl/wjaskowski/pub/papers/jaskowski073djudge.pdf}
}
@article{Krasnogor2004b,
author = {N. Krasnogor},
title = {Self-Generating metaheuristics in bioinformatics: the protein structure
comparison case},
journal = {Genetic Programming and Evolvable Machines},
year = {2004},
volume = {5},
pages = {181-201},
number = {2},
keywords = {Self-Generation, Self-Organisation, Optimisation, Metaheuristics,
Memetic Algorithms, Bioinformatics},
owner = {nxk},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/GPEM04.pdf}
}
@article{Krasnogor2005d,
author = {N. Krasnogor and M. Gheorghe and G. Terrazas and S. Diggle and P.
Williams and M. Camara},
title = {An Appealing Computational Mechanism Drawn from Bacterial Quorum
Sensing},
journal = {Bulletin of the European Association of Theoretical Computer Science},
year = {2005},
pages = {135-148},
number = {85},
month = {February},
editor = {European Association for Theoretical Computer Science},
keywords = {Nonstandard Computation, Bacterial Modeling, Quorum Sensing},
owner = {nxk},
publisher = {European Association for Theoretical Computer Science},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/eatcs-qs.pdf}
}
@article{Krasnogor2004a,
author = {N. Krasnogor and D.A. Pelta},
title = {Measuring the similarity of protein structures by means of the universal
similarity metric.},
journal = {Bioinformatics},
year = {2004},
volume = {20},
pages = {1015-1021},
number = {7},
doi = {http://dx.doi.org/10.1093/bioinformatics/bth031},
keywords = {Protein Structure, Comparison, Alignment, Universal Similarity Metric},
owner = {nxk},
url = {http://bioinformatics.oupjournals.org/cgi/content/abstract/20/7/1015?etoc}
}
@article{KraSmi2007,
author = {N. Krasnogor and J.E. Smith},
title = {Memetic Algorithms: The Polynomial Local Search Complexity Theory
Perspective},
journal = {Journal of Mathematical Modelling and Algorithms},
year = {2008},
volume = {7},
pages = {3-24},
keywords = {Memetic Algorithms, Local Search, Theory, Complexity},
owner = {nxk},
timestamp = {2007.04.02},
url = {http://www.springerlink.com/content/6441u64412043167/fulltext.pdf}
}
@article{Krasnogor2005,
author = {N. Krasnogor and J.E. Smith},
title = {A Tutorial for competent memetic algorithms: model, taxonomy and
design issues},
journal = {IEEE Transactions on Evolutionary Computation},
year = {2005},
volume = {9},
pages = {474- 488},
number = {5},
keywords = {Tutoria, Memetic Algorithm, Model, Taxonomy, Classification},
owner = {nxk},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/IEEE-TEC-lastVersion.pdf}
}
@article{LiGarKra2007,
author = {L. Li and J. Garibaldi and N. Krasnogor},
title = {Automated Self-Assembly Programming Paradigm: The Impact of Network
Topology},
journal = {International Journal of Intelligent Systems (IJIS)},
year = {2009},
volume = {24(7)},
pages = {793-817},
note = {Special issue on Nature Inspired Cooperative Strategies for Optimisation},
comment = {(please refer to the journal for the corrected final version of this
paper)},
keywords = {Self-Assembly, Automated Programming, Genetic Programming},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/LinLi.pdf},
timestamp = {2007.05.18},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/122407885/PDFSTART}
}
@article{Lozano2004,
author = {M. Lozano and F. Herrera and N. Krasnogor and D. Molina},
title = {Real-coded memetic algorithms with crossover hill-climbing},
journal = {Evolutionary Computation},
year = {2004},
volume = {12},
pages = {273-302},
number = {3},
doi = {http://dx.doi.org/10.1162/1063656041774983},
keywords = {Memetic Algorithms, Continous Optimisation, Self-Adaptation, Local
Search},
owner = {nxk},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/ecj-R.pdf}
}
@article{Luietal2013,
author = {L.T. Lui and X. Xue and C. Sui and A. Brown and D.I. Pritchard and
N. Halliday and K. Winzer and S.M. Howdle and F. Fernandez-Trillo
and N. Krasnogor and C. Alexander},
title = {Bacteria clustering by polymers induces the expression of quorum
sense controlled phenotypes},
journal = {Nature Chemistry},
year = {2013},
volume = {(to appear)},
keywords = {Synthetic Biology, Quorum Sensing, Computational Modelling, Polymers
Engineering, Biofilms},
owner = {nxk},
timestamp = {2013.08.07}
}
@article{MarkSorLeoLanKra2012,
author = {O. Markovitch and D. Sorek and L.T. Leong and D. Lancet and N. Krasnogor},
title = {Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?},
journal = {Origins of Life and Evolution of Biospheres},
year = {2012},
volume = {42},
pages = {469-474},
number = {5},
keywords = {Open Ended Evolution, Origins of Life, Measuring Complexity,},
owner = {nxk},
timestamp = {2013.08.04},
url = {http://link.springer.com/content/pdf/10.1007%2Fs11084-012-9309-y.pdf}
}
@article{MoyKraPerLat09,
author = {A. Moya and N. Krasnogor and J. Pereto and A. Latorre},
title = {Goethe's Dream. Challenges and Opportunities for Synthetic Biology.},
journal = {EMBO reports},
year = {2009},
volume = {10, S1,},
pages = {28-32},
doi = {doi:10.1038/embor.2009.120},
keywords = {Synthetic Biology, Systems Biology, Executable Biology, Algorithmic
Systems Biology},
owner = {nxk},
timestamp = {2009.08.10},
url = {http://www.nature.com/embor/journal/v10/n1s/pdf/embor2009120.pdf}
}
@article{Krasnogor2004,
author = {N.Krasnogor and S. Gustafson},
title = {A Study on the use of ``Self-Generation'' in memetic algorithms},
journal = {Natural Computing},
year = {2004},
volume = {3},
pages = {53 - 76},
number = {1},
keywords = {Self-Generation, Self-Organisation, Optimisation, Metaheuristics,
Memetic Algorithms, NK Landscapes},
owner = {nxk},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/KrasnogorGustafson.pdf}
}
@article{OakBarBykGarBurKraHir08,
author = {M.T. Oakley and D. Barthel and Y. Bykov and J.M. Garibaldi and E.K.
Burke and N. Krasnogor and J.D. Hirst},
title = {Search Strategies in Structural Bioinformatics},
journal = {Current Protein and Peptide Science (Bentham Science Publishers)},
year = {2008},
volume = {9},
pages = {260-274},
number = {3},
keywords = {Bioinformatics, Protein Structure Prediction, Search, Optimisation,
Protein Structure Comparison},
owner = {nxk},
timestamp = {2007.12.03},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/CPPS2008.pdf}
}
@article{OngKraIsh2007,
author = {Y.S. Ong and N. Krasnogor and H. Ishibuchi},
title = {Special Issue on Memetic Algorithms},
journal = {IEEE Transactions on Systems, Man and Cybernetics, Part B},
year = {2007},
volume = {37},
pages = {2-5},
number = {1},
keywords = {Memetic Algorithms},
owner = {nxk},
timestamp = {2008.02.12},
url = {http://ieeexplore.ieee.org/xpl/tocresult.jsp?isYear=2007&isnumber=4067063&Submit32=Go+To+Issue}
}
@article{SieMarVanMorKra2007,
author = {P.Siepmann and C.P. Martin and I. Vancea and P.J. Moriarty and N.
Krasnogor},
title = {A Genetic Algorithm Approach to Probing the Evolution of Self-Organised
Nanostructured Systems},
journal = {Nano Letters},
year = {2007},
volume = {7(7)},
pages = {1985-1990},
note = {(for the latest version please check the official journal site)},
doi = {10.1021/nl070773m},
keywords = {Nanoscience, Genetic Algorithms, Self-Organisation, Inverse Problems},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/galley.pdf},
timestamp = {2007.05.11},
url = {http://pubs.acs.org/cgi-bin/download.pl?nl070773m/o7do}
}
@article{PasKraCroDavAle09,
author = {G. Pasparakis and N. Krasnogor and L. Cronin and B.G. Davis and C.
Alexander},
title = {Controlled Polymer Synthesis: from Biomimicry towards Synthetic Biology},
journal = {Chemical Society Reviews},
year = {2009},
doi = {DOI: 10.1039/B809333B},
keywords = {Synthetic Biology, Non standard Computation, Computational Modeling},
owner = {nxk},
timestamp = {2009.10.06}
}
@article{PasVamKraCam09,
author = {G. Pasparakis and M. Vamvakaki and N. Krasnogor and C. Alexander},
title = {Diol-boronic acid complexes integrated by responsive polymers - a
route to chemical sensing and logic operations},
journal = {Soft Matter},
year = {2009},
doi = {doi:10.1039/b911341j},
keywords = {Molecular Computing, Chemical Logic Gates},
owner = {nxk},
timestamp = {2009.08.19},
url = {http://www.rsc.org/publishing/journals/SM/article.asp?doi=B911341J}
}
@article{Pelta2005a,
author = {D.A. Pelta and N. Krasnogor and C. Bousono-Calzon and J.L. Verdegay
and J. Hirst and E.K. Burke},
title = {A fuzzy sets based generalization of contact maps for the overlap
of protein structures},
journal = {Journal of Fuzzy Sets and Systems},
year = {2005},
volume = {152},
pages = {103-123},
number = {2},
keywords = {Contact Map, Fuzzy Sets, Optimisation, Bioinformatics},
owner = {nxk},
url = {http://dx.doi.org/10.1016/j.fss.2004.10.017}
}
@article{PorDanLorSanKraRasMoy11,
author = {M. Porcar and A. Danchin and V. de Lorenzo and V.A. dos Santos and
N. Krasnogor and S. Rasmussen and A. Moya},
title = {The Ten Grand Challenges of Synthetic Life},
journal = {Systems and Synthetic Biology},
year = {2011},
volume = {5},
pages = {1-9},
number = {1-2},
doi = {DOI: 10.1007/s11693-011-9084-5},
keywords = {Synthetic Biology, Chells, Proto Cells, Artificial Life, Executable
Biology, Algorithmic Biology, Minimal Organisms},
owner = {nxk},
timestamp = {2011.06.24},
url = {http://www.springerlink.com/content/p241t21t54g10601/}
}
@article{QuaOngLimKra09,
author = {Q.H. Quang and Y.S. Ong and M.H. Lim and N. Krasnogor},
title = {Adaptive Cellular Memetic Algorithm},
journal = {Evolutionary Computation},
year = {2009},
volume = {17(3)},
pages = {231-256},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
keywords = {Cellular Genetic Algorithms, Memetic Algorithms},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/CMA.PDF},
timestamp = {2008.07.25},
url = {http://www.mitpressjournals.org/doi/pdf/10.1162/evco.2009.17.2.231}
}
@article{ShaBarLukBlaKra07,
author = {A.A. Shah and D. Barthel and P. Lukasiak and J. Blazewicz and N.
Krasnogor},
title = {Web \& Grid technologies in Bioinformatics, Computational and Systems
Biology: A Review},
journal = {Current Bioinformatics},
year = {2008},
volume = {3},
pages = {10-31(22)},
number = {1},
doi = {http://dx.doi.org/10.2174/157489308783329850},
keywords = {Web based, Grid Based, Bioinformatics},
owner = {nxk},
timestamp = {2007.10.05},
url = {http://www.cs.nott.ac.uk/~nxk/PAPERS/cbio.pdf}
}
@article{SmaRomFerGheAleKra2010,
author = {J. Smaldon and F. J. Romero-Campero and F. Fernandez Trillo and M.
Gheorghe and C. Alexander and N. Krasnogor},
title = {A computational study of liposome logic: towards cellular computing
from the bottom up},
journal = {Systems and Synthetic Biology (Springer)},
year = {2010},
volume = {4},
pages = {157-179},
number = {3},
doi = {10.1007/s11693-010-9060-5},
keywords = {Synthetic Biology, Protocells, Bottom-Up, Dissipative Particle Dynamics,
P systems, DPD},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/DPDPSys.pdf},
timestamp = {2010.08.08},
url = {http://www.springerlink.com/content/f358p17724332627/}
}
@article{SmiJiaBacStoKraHir10,
author = {R.E. Smith and M.K. Jiang and J. Bacardit and M. Stout and N. Krasnogor
and J.D. Hirst},
title = {A Learning Classifier System with Mutual-Information-Based Fitness},
journal = {Evolutionary Intelligence},
year = {2010},
volume = {3},
pages = {31-50},
number = {1},
month = {March},
keywords = {Data Mining, Classification, Learning Classifier Systems, Mutual Information,
XCS, UCS, BioHel, Naive Bayes, C4.5},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxl/PAPERS/MILCS.pdf},
timestamp = {2010.03.27},
url = {http://springerlink.com/content/6ku352557t1tn667/?p=79d797d17f9647f3aaf10cb9dc1a9fde&pi=2}
}
@article{StoBacHirKra08,
author = {M. Stout and J. Bacardit and J.D. Hirst and N. Krasnogor},
title = {Prediction of Recursive Convex Hull Class Assignment for Protein
Residues},
journal = {Bioinformatics},
year = {2008},
volume = {24(7)},
pages = {916-923},
keywords = {Protein Structure Prediction, Convex Hull, Learning Classifier Systems},
owner = {nxk},
timestamp = {2008.01.25},
url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn050v1?ct=ct}
}
@article{StoBacHirSmiKra07,
author = {M. Stout and J. Bacardit and J.D. Hirst and R.E Smith and N. Krasnogor},
title = {Prediction of Topological Contacts in Proteins Using Learning Classifier
Systems},
journal = {Journal Soft Computing - A Fusion of Foundations, Methodologies and
Applications},
year = {2008},
volume = {13},
pages = {245-258},
number = {3},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
doi = {DOI 10.1007/s00500-008-0318-8},
keywords = {Protein Structure Prediction, Delaunay Triangulation, Voronoi, Gabriel
Graphs, Relative Neighborhood Graph, Learning Classifier Systems,
Data Mining},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/softComputing.pdf},
timestamp = {2008.01.16},
url = {http://www.springerlink.com/content/f437410653r73vj8/fulltext.pdf}
}
@article{SunGarKraZha12,
author = {J. Sun and J.M. Garibaldi and N. Krasnogor and Q. Zhang},
title = {An Intelligent Multi-Restart Memetic Algorithm for Box Constrained
Global Optimisation},
journal = {Evolutionary Computation},
year = {2013},
volume = {21},
pages = {107-147},
number = {1},
doi = {doi:10.1162/EVCO_a_00068},
keywords = {Memetic Algorithms, Global Optimisation, Continuous Optimisation},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/sun2012.pdf},
timestamp = {2012.07.11},
url = {http://www.mitpressjournals.org/doi/abs/10.1162/EVCO_a_00068}
}
@article{TerKra2013,
author = {G. Terrazas and N. Krasnogor},
title = {A genotype-phenotype-fitness assessment protocol for evolutionary
self-assembly Wang tiles design},
journal = {Memetic Computing},
year = {2013},
volume = {5},
pages = {19-33},
number = {1},
doi = {10.1007/s12293-012-0092-0},
keywords = {Genotype Phenotype Mapping, Self-assembly, Wang tiles, Evolutionary
Algorithms},
owner = {nxk},
timestamp = {2012.12.18},
url = {http://link.springer.com/article/10.1007%2Fs12293-012-0092-0#page-1}
}
@article{TerSieKenKra07,
author = {G. Terrazas and P. Siepman and G. Kendal and N. Krasnogor},
title = {An Evolutionary Methodology for the Automated Design of Cellular
Automaton-Based Complex Systems},
journal = {Journal of Cellular Automata},
year = {2007},
volume = {2(1)},
pages = {77-102},
note = {(for the latest version of this paper please refer to the journal
website)},
comment = {(for the latest version of this paper please refer to the journal
website)},
keywords = {Inverse Problems, Cellular Automata, Evolutionary Algorithms, Self-Organisation},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/terrazasetal.pdf},
timestamp = {2007.01.12},
url = {http://www.oldcitypublishing.com/JCA/JCA.html}
}
@article{WidGarKra09a,
author = {P. Widera and J. Garibaldi and N. Krasnogor},
title = {GP challenge: evolving the energy function for protein structure
prediction},
journal = {Journal of Genetic Programming and Evolvable Machines},
year = {2010},
volume = {11},
pages = {61-88},
month = {1},
note = {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 www.slideshare.com/nxk
.
For the latest version please consult the journal website.},
doi = {DOI: 10.1007/s10710-009-9087-0},
keywords = {Genetic Programming, Protein Structure Prediction, Protein Folding,
Challenge},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/article_genp.pdf},
timestamp = {2009.07.25},
url = {http://www.springerlink.com/content/44723718j03p8jwn/fulltext.pdf}
}
@article{WooStirRadKraMor11,
author = {R.A.J. Woolley and J. Stirling and A. Radocea and N. Krasnogor and
P. Moriarty},
title = {Automated probe microscopy via evolutionary optimization at the atomic
scale},
journal = {Applied Physics Letters},
year = {2011},
volume = {98},
pages = {253104},
number = {25},
note = {This paper won the Silver Medal in the THE 2012 HUMIES AWARDS FOR
HUMAN-COMPETITIVE RESULTS PRODUCED BY GENETIC AND EVOLUTIONARY COMPUTATION.},
keywords = {optimisation, automation, genetic algorithms, graphite, optimisation,
scanning probe microscopy},
owner = {nxk},
pdf = {http://www.cs.nott.ac.uk/~nxk/PAPERS/SPMEA.pdf},
timestamp = {2011.10.26},
url = {http://apl.aip.org/resource/1/applab/v98/i25/p253104_s1}
}
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