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My research interests include combinatorics, algorithms and coding theory, including some applications to bioinformatics.
Prospective Students: If you are a student considering completing a Master's degree or an Honours project and you are interested in any of the above topics, then please contact me. Students should be motivated and comfortable with mathematics (primarily discrete mathematics). Since it can be very difficult to evaluate applications, you should provide as much information as possible about your interests - for example, you might describe projects which you have already undertaken or in which you are interested.
I work closely with my students and ensure that all research students will have the opportunity to publish their work in journals or conference proceedings. You should also look at the list of projects completed by some of my past and present students. See my personal webpage for more information.
- BSc (Mathematics, Science College), Concordia University
- Master of Computer Science, Concordia University
- PhD (Computer Science), Concordia University
- 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, 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, 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).
- 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.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, p.65-92, 2010.
- 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.
Recent M.Sc. Graduate Student Thesis
- Mohammad Goodarzi, Algorithms for De Novo Assembly of Short DNA Reads, 2014
- Farhad Alizadeh Noori, Motif Discovery, 2012
- Martin Derka, Self-Dual Codes, 2012
- John Orth, The Salmon Algorithm - A New Population Based Search Metaheuristic, 2012
- Zhiyuan Li, Construction of 1-Deletion-Correcting Ternary Codes, 2011
- Pascal Comte, Bio-Inspired Optimization & Sampling Technique for Side-chain Packing in MCCE, 2010
- Jing Sun, Bounds on Edit Metric Codes with Combinatorial DNA Constraints, 2009
- Joseph Brown, Decoding Algorithms using Side Eﬀect Machines, 2009
Current M.Sc. Graduate Student Thesis
- Ashkan Entezari, In Progress
- Koosha Tahmasebipour, Gene Prioritization
- James Hughes, Ordered Gene Problems including DNA Fragment Assembly
- Collin Price, Modeling Protein Complexes using Genetic Algorithms