Dr Joshua Knowles - publications

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• Richard Allmendinger and Joshua Knowles. Evolutionary Search in Lethal Environments. Evolutionary Computing Theory and Applications. -. eScholarID:135649

2011

• Small, B.G., McColl, B.W., Allmendinger, R., Pahle, J., López-Castejón, G., Rothwell, N.J., Knowles, J., Mendes, P., Brough, D., Kell, D.B. Efficient discovery of anti-inflammatory small molecule combinations using evolutionary computing. Nature Chemical Biology. 2011; 7: 902-908. eScholarID:135647 | DOI:doi:10.1038/nchembio.689
• M Lopez-Ibanez; Joshua Knowles; Marco Laumanns. On sequential online archiving of objective vectors. Evolutionary Multi-Criterion Optimization. Berlin-Heidelberg: Springer LNCS 6576/2011: 2011: 46-60. eScholarID:123007
• R. Allmendinger and J. Knowles. Policy Learning in Resource-Constrained Optimization. Proceedings of the Genetic and evolutionary computation conference (GECCO 2011). ACM Press: 2011: -. eScholarID:123029
• Dunn W.B., Broadhurst D., Begley P., Zelena E., Francis-McIntyre S., Anderson N., Brown M., Knowles J.D., Halsall A., Haselden J.N., Nicholls A.W., Wilson I.D., Kell D.B., Goodacre R.; The Human Serum Metabolome (HUSERMET) Consortium. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols. 2011; 6(7): 1060-1083. eScholarID:135648 | DOI:10.1038/nprot.2011.335
• J. Handl, J. Knowles, R. Vernon, D. Baker, S. Lovell. The dual role of fragments in fragment-assembly methods for de novo protein structure prediction. Proteins: Structure, Function and Bioinformatics. 2011 November; 80(2): 490-504. eScholarID:135646 | DOI:DOI: 10.1002/prot.23215

2010

• Rowe W, Platt M, Wedge DC, Day PJ, Kell DB, Knowles J. Analysis of a complete DNA-protein affinity landscape. Journal of the Royal Society Interface. 2010 March; 7(44): 397-408. eScholarID:100202 | DOI:10.1098/rsif.2009.0193
• Jarvis, R.M., Rowe, W., Yaffe, N.R., O'Connor, R., Knowles, J.D., Blanch, E.W. and Goodacre, R. Multiobjective evolutionary optimisation for surface-enhanced Raman scattering. Analytical and Bioanalytical Chemistry. 2010 May; 397(5): 1893-1901. eScholarID:99977 | DOI:10.1007/s00216-010-3739-z
• Rowe, W., Wedge, D., Platt, M., Kell, D.B., and Knowles, J. Predictive Models for Population Performance on Real Biological Fitness Landscapes. Bioinformatics. 2010 September; 26(17): 2145-2152. eScholarID:99973 | DOI:doi: 10.1093/bioinformatics/btq353
• Mikhailov L., Knowles J. Priority Elicitation in the AHP by a Pareto Envelope-based Selection Algorithm. In: M Ehrgott, B Naujoks, T Stewart, J Wallenius, ed. Multiple Criteria Decision Making for Sustainable Energy and Transportation Systems. Berlin, Springer.2010: eScholarID:123032
• E.M. Humston, J.D. Knowles, A. McShea, R.E. Synovec. Quantitative Assessment of Moisture Damage for Cacao Bean Quality using Two-Dimensional Gas Chromatography Combined with Time-of-Flight Mass Spectrometry and Chemometrics. Journal of Chromatography A. 2010; 1217(12): 1963-1970. eScholarID:99980 | DOI:10.1016/j.chroma.2010.01.069

2009

• Platt, M., Rowe, W., Knowles, J., Day, P.J., Kell, D.B. Analysis of aptamer sequence-activity relationships. Integrative Biology. 2009 January; 1(1): 116-122. eScholarID:100203 | DOI:10.1039/b814892a
• Knight, C. G., Platt, M., Rowe, W., Wedge, D., Khan, F., McShea, A., Day, P.J., Knowles, J. and Kell, D.B. Array-based evolution of DNA aptamers allows modeling of an explicit sequence-fitness landscape. Nucleic Acids Research. 2009 January; 37(1 - e6): 1-10. eScholarID:8839 | DOI:10.1093/nar/gkn899
• Handl, J., Lovell, S. and Knowles, J. Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics. 2009 March; 25(10): 1271-1279. eScholarID:9710 | DOI:doi: 10.1093/bioinformatics/btp150
• Wedge, D.C., Rowe, W., Kell, D.B. and Knowles, J. In silico Modelling of Directed Evolution: Implications for Experimental Design and Stepwise Evolution. Journal of Theoretical Biology. 2009 March; 257(1): 131-141. eScholarID:8810 | DOI:doi:10.1016/j.jtbi.2008.11.005
• Platt M, Rowe W, Wedge D, Kell D, Knowles J, Day P. Aptamer evolution for array-based diagnostics. Analytical Biochemistry. 2009; 390(2): 203-205. eScholarID:149402 | DOI:10.1016/j.ab.2009.04.013

2008

• Joshua Knowles. EMO in the Lab: Optimization in Synthetic- and Systems Biology. Operations Research Society: 2008: -. eScholarID:8948
• Niklas Lüdtke; Stefano Panzeri; Martin Brown; David S. Broomhead; Joshua Knowles; Marcelo A. Montemurro; Douglas B. Kell. Information-theoretic sensitivity analysis: a general method for credit assignment in complex networks. Journal of the Royal Society Interface. 2008 June; 5 (19): 223-235. eScholarID:1a5818 | DOI:10.1098/rsif.2007.1079
• Farrelly, C.M., Kell, D.B., Knowles, J. Molecular Structure Elucidation Using Ant Colony Optimization. Ant Colony Optimization and Swarm Intelligence, Lecture Notes in Computer Science, Vol 5217. Springer-Verlag: 2008: 120-131. eScholarID:100206
• Jin, Y., Knowles, J., Hongmei, L., Yizeng, L. and Kell, D.B. The landscape adaptive particle swarm optimizer. Applied Soft Computing. 2008; 8(1): 295-304. eScholarID:8861 | DOI:10.1016/j.asoc.2007.01.009

2007

• J. Handl and J. Knowles. An evolutionary approach to multiobjective clustering. IEEE Transactions on Evolutionary Computation. 2007 February; 11(1): 56-76. eScholarID:1a9853 | DOI:10.1109/TEVC.2006.877146
• J. Handl, D. Kell and J. Knowles. Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2007 June; 4(2): 279-292. eScholarID:123005
• David Corne and Joshua Knowles. Techniques for highly multiobjective optimisation: some nondominated points are better than others. Proceedings of the 9th annual conference on Genetic and evolutionary computation (GECCO). New York: ACM: 2007: 773-780. eScholarID:123006
• Knowles, J, and D Corne. Quantifying the effects of objective space dimension in evolutionary multiobjective optimization. 4th International Conference on Evolutionary Multi-Criterion Optimization (EMO 2007). Springer-Verlag Berlin: 2007: 757-771. eScholarID:2f146
• O'Hagan S, Dunn W, Knowles J, Broadhurst D, Williams R, Ashworth J, Cameron M, Kell D. Closed-Loop, Multiobjective Optimization of Two-Dimensional Gas Chromatography/Mass Spectrometry for Serum Metabolomics. Analytical Chemistry. 2007; 79(2): 464-476. eScholarID:148819

2006

• Handl, J;Knowles, J;Dorigo, M. Ant-based clustering and topographic mapping. ARTIFICIAL LIFE. 2006; 12 (1): eScholarID:1a493
• Applications of Soft Computing. Berlin-Heidelberg: Springer:2006. eScholarID:148820
• KNOWLES JD. ParEGO: a hybrid algorithm with on-line landscape approximation for expensive multiobjective optimization problems. IEEE Transactions on Evolutionary Computation. 2006 February; 10: 50-66. eScholarID:1a9852 | DOI:10.1109/TEVC.2005.851274
• Handl J, Knowles J. Feature subset selection in unsupervised learning via multiobjective optimization. International Journal of Computational Intelligence Research. 2006; 2(3): 217-238. eScholarID:149400
• Handl J, Knowles J. Multiobjective clustering and cluster validation. Multiobjective Machine Learning. Springer.2006: eScholarID:148809
• Yue H, Brown M, Knowles J, Wang H, Broomhead D, Kell D. Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-$\kappa$B signalling pathway. Molecular BioSystems. 2006; 2(12): 640-649. eScholarID:149399

2005

• HANDL J; KNOWLES, J; KELL D. Computational cluster validation in post-genomic data analysis. Bioinformatics. 2005 May; 21(15): 3201-3212. eScholarID:1a9851 | DOI:10.1093/bioinformatics/bti517
• Bianchi, L;Knowles, J;Bowler, N. Local search for the probabilistic traveling salesman problem: Correction to the 2-p-opt and 1-shift algorithms. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH. 2005; 162 (1): eScholarID:1a198
• Brown M, Dunn W, Ellis D, Goodacre R, Handl J, Knowles J, O'Hagan S, Spasic I, Kell D. A metabolome pipeline: from concept to data to knowledge. Metabolomics. 2005; 1(1): 39-51. eScholarID:149403
• Handl, J, and J Knowles. Exploiting the trade-off - the benefits of multiple objectives in data clustering. Evolutionary Multi-Criterion Optimization (EMO 2005). Springer-Verlag: 2005: 547-560. eScholarID:148804
• Handl, J, and J Knowles. Improvements to the scalability of multiobjective clustering. Proceedings of IEEE Congress on Evolutionary Computation. 2005: 438-445. eScholarID:148807
• Handl, J, and J Knowles. Multiobjective clustering around medoids. Proceedings of IEEE Congress on Evolutionary Computation. 2005: 550-557. eScholarID:148810
• Knowles, J. A summary-attainment-surface plotting method for visualizing the performance of stochastic multiobjective optimizers. ISDA 2005. 2005: eScholarID:148802
• Knowles, J, and E J Hughes. Multiobjective optimization on a budget of 250 evaluations. Evolutionary Multi-Criterion Optimization (EMO 2005). Springer-Verlag: 2005: 176-190. eScholarID:148812

2004

• Handl, J, and J Knowles. Evolutionary Multiobjective Clustering. Parallel Problem Solving from Nature (PPSN VIII). Springer-Verlag: 2004: 1081-1091. eScholarID:148805
• Handl J, Knowles J, Dorigo M. Strategies for the increased robustness of ant-based clustering. Engineering Self-Organising Systems. 2977. Springer-Verlag Heidelberg.2004: eScholarID:148816
• Knowles J, Corne D. Bounded Pareto Archiving: Theory and Practice. Metaheuristics for Multiobjective Optimisation. 535. Springer.2004: eScholarID:148806
• Knowles J, Corne D. Memetic Algorithms for Multiobjective Optimization: Issues, Methods and Prospects. Recent Advances in Memetic Algorithms. Springer.2004: eScholarID:148811

2003

• KNOWLES JD; CORNE D. Properties of an adaptive archiving algorithm for storing nondominated vectors. IEEE Transactions on Evolutionary Computation. 2003 April; 7(2): 100-116. eScholarID:1a9854 | DOI:10.1109/TEVC.2003.810755
• Corne, D.W., Deb, K., Fleming, P.J., Knowles, J.D. The good of the many outweighs the good of the one: evolutionary multi-objective optimization. IEEE Connections. 2003; 1(1): 9-13. eScholarID:149346
• Corne, D, and J Knowles. No free lunch and free leftovers theorems for multiobjective optimisation problems. Evolutionary Multi-Criterion Optimization (EMO 2003). Springer: 2003: 327-341. eScholarID:148791
• Corne, D, and J Knowles. Some multiobjective optimizers are better than others. Proceedings of the IEEE Congress on Evolutionary Computation (CEC'03). 2003: 2506-2512. eScholarID:148815
• Handl J, Knowles J, Dorigo M. On the performance of ant-based clustering. Design and Application of Hybrid Intelligent Systems. 104. IOS Press.2003: eScholarID:148814
• Knowles, J, and D Corne. Instance Generators and Test Suites for the Multiobjective Quadratic Assignment Problem. Evolutionary Multi-Criterion Optimization (EMO 2003). Springer-Verlag Heidelberg: 2003: 295-310. eScholarID:148808
• Knowles, J D, D W Corne, and Mark Fleischer. Bounded Archiving using the Lebesgue Measure. Proceedings of the IEEE Congress on Evolutionary Computation (CEC'03). IEEE Press: 2003: 2490-2497. eScholarID:148803
• Rossi-Doria, O, M Sampels, M Birattari, M Chiarandini, M Dorigo, L M Gambardella, J Knowles, M Manfrin, M Mastrolilli, B Paechter, L Paquete, and T St?tzle. A comparison of the performance of different metaheuristics on the timetabling problem. Practice and Theory of Automated Timetabling (PATAT IV). Springer-Verlag: 2003: 329-351. eScholarID:148775

2002

• Blum, C, J Knowles, B Paechter, O Rossi-Doria, M Sampels, and K Socha. A local search for the timetabling problem. Proceedings of the 4th International Conference on the Practice and Theory of Automated Timetabling (PATAT IV), Gent, Belgium. 2002: 124-127. eScholarID:148776
• Knowles, J, and D Corne. On Metrics for Comparing Non-Dominated Sets. Proceedings of the 2002 Congress on Evolutionary Computation Conference (CEC02). IEEE Press: 2002: 711-716. eScholarID:148813
• Knowles J, Corne D. Towards landscape analyses to inform the design of a hybrid local search for the multiobjective quadratic assignment problem. Soft Computing Systems: Design, Management and Applications. IOS Press.2002: eScholarID:148797
• Local-Search and Hybrid Evolutionary Algorithms for Pareto Optimization. University of Reading, UK:2002. eScholarID:148788
• Knowles, J D, and R A Watson. On the Utility of Redundant Encodings in Mutation-based Evolutionary Search. Parallel Problem Solving from Nature (PPSN-VII). Springer-Verlag: 2002: 88-98. eScholarID:148792
• Socha, K, J Knowles, and M Sampels. A {$\cal MAX$}-{$\cal MIN$} Ant System for the University Course Timetabling Problem. Ant Algorithms (ANTS 2002). Springer-Verlag: 2002: 1-13. eScholarID:148781

2001

• Corne, D, N Jerram, J Knowles, and M Oates. {P}{E}{S}{A}-{I}{I}: Region-based selection in evolutionary multiobjective optimization. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001). Morgan Kaufmann: 2001: 283-290. eScholarID:148798
• Knowles, J D, and D W Corne. A Comparative Assessment of Memetic, Evolutionary, and Constructive Algorithms on Multiobjective $d$-MST Problems. Proceedings of the Genetic and Evolutionary Computation Conference Workshop Program. 2001: 162-167. eScholarID:148774
• Knowles, J D, and D W Corne. A Comparison of Encodings and Algorithms for Multiobjective Minimum Spanning Tree Problems. Proceedings of the Congress on Evolutionary Computation. IEEE Press: 2001: 544-551. eScholarID:148778
• Knowles, J D, and D W Corne. Benchmark Problem Generators and Results for the Multiobjective Degree-Constrained Minimum Spanning Tree Problem. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001). 2001: 424-431. eScholarID:148783
• Knowles, J D, R A Watson, and D W Corne. Reducing Local Optima in Single-Objective Problems by Multi-objectivization. Evolutionary Multi-Criterion Optimization (EMO'01). Springer-Verlag: 2001: 269-283. eScholarID:148794

2000

• Corne, D W, and J D Knowles. The Pareto-Envelope based Selection Algorithm for Multiobjective Optimization. Proceedings of the Sixth International Conference on Parallel Problem Solving from Nature (PPSN VI). Springer-Verlag: 2000: 839-848. eScholarID:148796
• Knowles J, Corne D. A New Evolutionary Approach to the Degree-Constrained Minimum Spanning Tree Problem. IEEE Transactions on Evolutionary Computation. 2000; 4(2): 125-134. eScholarID:149404
• Knowles, J D, and D W Corne. A comparison of diverse approaches to memetic multiobjective combinatorial optimization. Data Mining with Evolutionary Algorithms. 2000: 103-108. eScholarID:148779
• Knowles J, Oates M, Corne D. Advanced Multiobjective Evolutionary Algorithms Applied to two Problems in Telecommunications. BT Technology Journal. 2000; 18(4): 51-65. eScholarID:149401
• Knowles J, Corne D. Evolving Neural Networks for Cancer Radiotherapy. Practical Handbook of Genetic Algorithms: Applications, Second Edition. Boca Raton, Florida, Chapman Hall/CRC Press.2000: eScholarID:148785
• Knowles, J D, and D W Corne. Heuristics for Evolutionary Off-line Routing in Telecommunications Networks. Proceedings of the Genetic and Evolutionary Computation Conference. Morgan Kaufmann: 2000: 574-581. eScholarID:148786
• Knowles, J D, and D W Corne. M-PAES: A Memetic Algorithm for Multiobjective Optimization. Proceedings of the Congress on Evolutionary Computation (CEC'00). IEEE Press: 2000: 325-332. eScholarID:148789
• Knowles, J D, and D W Corne. Multiobjective Approaches to the Adaptive Distributed Database Management Problem. Proceedings of the SAB/PPSN Workshops (Evolutionary Computation in Telecommunications Workshop). 2000: eScholarID:148790
• Knowles, J D, D W Corne, and M J Oates. On the Assessment of Multiobjective Approaches to the Adaptive Distributed Management Problem. Proceedings of the Sixth International Conference of Parallel Problem Solving From Nature (PPSN VI). Springer-Verlag: 2000: 869-878. eScholarID:148793

1999

• Knowles, J, D Corne, and M Oates. A New Evolutionary Approach to the Degree Constrained Minimum Spanning Tree Problem. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-99). Morgan Kaufmann: 1999: 794. eScholarID:148780
• Knowles, J D, and D W Corne. Assessing the Performance of the Pareto Archived Evolution Strategy. Proceedings of the 1999 Genetic and Evolutionary Computation Conference Workshop Program. 1999: 123-124. eScholarID:148782
• Knowles, J D, and D W Corne. Local Search, Multiobjective Optimization and the Pareto Archived Evolution Strategy. Proceedings of Third Australia-Japan Joint Workshop on Intelligent and Evolutionary Systems. University of New South Wales and Ashikaga Institute of Technology: 1999: 209-216. eScholarID:148787
• Knowles, J D, and D W Corne. The Pareto Archived Evolution Strategy: A New Baseline Algorithm for Multiobjective Optimisation. Proceedings of the 1999 Congress on Evolutionary Computation (CEC'99). IEEE Service Center: 1999: 98-105. eScholarID:148795

1998

• Knowles, J D, D W Corne, and M Bishop. Evolutionary Training of Artificial Neural Networks for Radiotherapy Treatment of Cancers. Proceedings of 1998 International Conference on Evolutionary Computation (ICEC'98). IEEE Press: 1998: 398-403. eScholarID:148784