Papers submitted for publication:

J.Hughes, S.Houghten and D.Ashlock, Restarting and Recentering Genetic Algorithm Variations for DNA Fragment Assembly: The Necessity of a Multi-Strategy Approach, submitted.

J.Orth and S.Houghten, Evaluation of the Salmon Algorithm for Combinatorial Optimization, submitted.

Papers already published or accepted for publication:

J.A. Brown, S. Houghten, T. Kennedy Collins and Q. Qu, Evolving Graph Compression using Similarity Measures for Bioinformatics Applications, 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, accepted.

P.E. Becker, M. Derka, S. Houghten and J. Ulrich, Build a Sporadic Group in Your Basement, American Mathematical Monthly, accepted.

J.A. Hughes, S. Houghten and D. Ashlock, Permutation Problems, Genetic Algorithms, and Dynamic Representations, book chapter for “Nature Inspired Computing and Optimization: Theory and Applications”, Springer book series on Modelling and Optimization in Science and Technology, to appear (2016).

A. Entezari Heravi and S. Houghten, A Methodology for Disease Gene Association using Centrality Measures, 2016 IEEE World Congress on Computational Intelligence, accepted.

L. Plant and S. Houghten, Properties of Optimal and Near Optimal Edit Metric Error Correcting Codes, Congressus Numerantium 224, p.147-157, 2015.

D. Ashlock and S. Houghten, Lexicode Crossover for Embeddable Biomarkers, 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-7, 2015.

A. Entezari Heravi, K. Tahmasebipour and S. Houghten, Evolutionary Computation for Disease Gene Association, 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8, 2015.

M. Goodarzi, S. Houghten and P. Liang, Effect of Multi-K Contig Merging in de novo DNA Assembly, 2014 IEEE Conference on Bioinformatics and Bioengineering, 355-361, 2014.

K. Tahmasebipour and S. Houghten, Disease-Gene Association using a Genetic Algorithm, 2014 IEEE Conference on Bioinformatics and Bioengineering, 191-197, 2014

J. Hughes, S. Houghten and D. Ashlock, Recentering and Restarting a Genetic Algorithm using a Generative Representation for an Ordered Gene Problem, International Journal of Hybrid Intelligent Systems, Vol.11, No.4, 257-271, 2014.

C. Price, S. Houghten, S. Vassiliev and D. Bruce, Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Evolutionary Algorithms, 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8, 2014.

J. Hughes, S. Houghten, G. Mallen-Fullerton and D. Ashlock, Recentering and Restarting Genetic Algorithm Variations for DNA Fragment Assembly, 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8, 2014.

G. Mallen-Fullerton, J. Hughes, S. Houghten and G. Fernandez-Anaya, Benchmark Data Sets for the DNA Fragment Assembly Problem, International Journal of Bio-Inspired Computation, Vol.5, No.6, p.384-394, 2013.

J. Hughes, S. Houghten and D. Ashlock, Recentering, Reanchoring and Restarting an Evolutionary Algorithm, 5th World Congress on Nature and Biologically Inspired Computing, p.76-83, 2013.

J. Hughes, J. Brown, S. Houghten and D. Ashlock, Edit Metric Decoding: Representation Strikes Back, IEEE Congress on Evolutionary Computation, p.229-236, 2013.

M. Derka, S. Houghten and P. Becker, A methodology for constructing the basis of a putative (72,36,16) extremal code for a given automorphism group, Congressus Numerantium 212, p.173-193, 2012.

Z. Li and S. Houghten, Searching for optimal deletion correcting codes: new properties and extensions of Tenengolts Codes, 12th IEEE International Conference on Computer and Information Technology (CIT 2012), p. 647-654, 2012.

D. Ashlock, S. Houghten, J.A. Brown and and J. Orth, "On the Synthesis of DNA Error Correcting Codes", BioSystems 110, p.1-8, 2012.

D.E. McCarney, S. Houghten and B.J. Ross, Evolutionary Approaches to the Generation of Optimal Error Correcting Codes, Genetic and Evolutionary Computation Conference (GECCO 2012), ACM, p.1135-1142, 2012.

F. Alizadeh Noori and S. Houghten, A MultiObjective Algorithm with Side Effect Machines for Motif Discovery, 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, p.275-282, 2012.

P.Comte, S.Vassiliev, S.Houghten and D.Bruce, “Genetic Algorithm with Alternating Selection Pressure for Protein Sidechain Packing and pK(a) Prediction”, BioSystems 105, p.263-270, 2011.

J.A.Brown, D.Ashlock, S.Houghten and J.Orth,  “Autogeneration of Fractal Photographic Mosaic Images”, 2011 IEEE Congress on Evolutionary Computation, p.1116-1123, June 2011.

J.Orth and S.Houghten, “Optimizing the Salmon Algorithm for the Construction of DNA Error-Correcting Codes”, 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, April 2011.

J.Sun, S.Houghten and J.Ross, "Bounds on Edit Metric Codes with Combinatorial DNA Constraints", Congressus Numerantium 204 (2010), 65-92.

D.Ashlock and S.Houghten, "Ring Optimization of Edit Metric Codes in DNA", ACM International Conference on Bioinformatics and Computational Biology 2010.

J.A.Brown, S.Houghten and D.Ashlock, "Side Effect Machines for Quaternary Edit Metric Decoding", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Intelligence 2010, 103-110.

P.Comte, S.Vassil'ev, A.Mahmood, M.R.Gunner, D.Bruce and S.Houghten, “Conformational Sampling of Proteins for the Generation of Molecular Ensemble Distributions", 27th Annual Eastern Regional Photosynthesis Conference (2010), poster p.35.

J.A.Brown, S.Houghten and D.Ashlock, "Edit Metric Decoding: A New Hope", Canadian Conference on Computer Science and Engineering 2009 (C3S2E09), 233-242.

J.A.Brown, S.Houghten and B.Ombuki-Berman, “Genetic Algorithm Cryptanalysis of a Substitution Permutation Network”, IEEE Symposium on Computational Intelligence in Cyber Security 2009, 115-121.

D.Ashlock and S.K.Houghten, “DNA Error-Correcting Codes: No Crossover”, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2009, 38-45.

R.Flack and S.Houghten, "Generation of Good Edit Codes from Classical Hamming Distance Codes", Congressus Numerantium 190 (2008), 97-108.

S.Baker, R.Flack and S.Houghten, "Optimal Variable-Length Insertion-Deletion Correcting Codes and Edit Metric Codes", Congressus Numerantium 186 (2007), 65-80.

P.E.Becker, S.K.Houghten and W.Haas, "A Search for Solvable Weighing Matrices", The Journal of Combinatorial Mathematics and Combinatorial Computing 62 (2007), 65-84.

W.Haas and S.Houghten, "A Comparison of Evolutionary Algorithms for Finding Optimal Error-Correcting Codes", Proceedings of the 3rd IASTED Conference on Computational Intelligence (CI 2007), 64-70.

S.K.Houghten, D.Ashlock and J.Lenarz, "Construction of Optimal Edit Metric Codes", Proceedings of the 2006 IEEE Workshop on Information Theory (ITW 2006), 259-263.

D.Ashlock and S.K.Houghten, "A Novel Variation Operator for More Rapid Evolution of DNA Error Correcting Codes", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 2005, 1-8.

W.Haas and S.Houghten, "Evolutionary Algorithms for Optimal Error-Correcting Codes", Late Breaking Papers, Genetic and Evolutionary Computation Conference (GECCO 2005).

M.J.Letourneau and S.K.Houghten, "Optimal Ternary (11,7) and (14,10) Codes", The Journal of Combinatorial Mathematics and Combinatorial Computing 51 (2004), 159-164.

S.K.Houghten, C.W.H. Lam, L.H. Thiel and J.A. Parker, "The Extended Quadratic Residue Code is the only (48,24,12) Self-Dual Doubly-Even Code", IEEE Transactions on Information Theory 49 (2003), 53-59.

M.J.Letourneau and S.K.Houghten, "Optimal Ternary (10,7) Error-Correcting Codes", Congressus Numerantium 155 (2003), 71-80.

J.L.Wallis and S.K.Houghten, "A Comparative Study of Search Techniques Applied to the Minimum Distance Problem of BCH Codes", 6th IASTED International Conference on Artificial Intelligence and Soft Computing, July 2002, 164-169.

S.K.Houghten, L.H.Thiel, J.Janssen and C.W.H.Lam, "There is no (46,6,1) Block Design", Journal of Combinatorial Designs 9 (2001), 60-71.

Y.Ding, S.Houghten, C.Lam, S.Smith, L.Thiel and V.D.Tonchev, "Quasi-symmetric 2-(28,12,11) Designs with an Automorphism of Order 7", Journal of Combinatorial Designs 6 (1998), 213-223.

S.Houghten, C.Lam and L.Thiel, "Construction of (48,24,12) Doubly-Even Self-Dual Codes", Congressus Numerantium 103 (1994), 41-53.

Technical Reports:

S.K.Houghten, D.Ashlock and J.Lenarz, "Bounds on Optimal Edit-Metric Codes", Brock Computer Science Technical Report CS-05-07, July 2005.

P.Becker, S.Houghten and W.Haas, "Investigation of Perfect Ternary Arrays PTA(60,25)", Brock Computer Science Technical Report CS-03-10, October 2003.

Theses:

S.K.Houghten, "On Combinatorial Searches for Designs and Codes", Ph.D. Thesis, Concordia University, 1999.

S.K.Houghten, "Construction of Extremal (48,24,12) Doubly-Even Codes", Master's Thesis, Concordia University, 1993.

This page last modified 26th July 2016
© Copyright Sheridan Houghten, 2005-2016