Areas of expertise

• Bioinformatics 060102
• Gene Expression (Incl. Microarray And Other Genome Wide Approaches) 060405
• Applied Statistics 010401
• Biological Mathematics 010202
• Probability Theory 010404
• Genetics 0604
• Population, Ecological And Evolutionary Genetics 060411

Publications

• Burden, C & Tang, Y 2016, 'An approximate stationary solution for multi-allele neutral diffusion with low mutation rates', Theoretical Population Biology, vol. 112, pp. 22-32.
• Burden, C & Simon, H 2016, 'Genetic drift in populations governed by a Galton-Watson branching process', Theoretical Population Biology, vol. 109, pp. 63-74.
• Subhani, N, Rueda, L, Ngom, A et al 2011, 'Alignment-Based Clustering of Gene Expression Time-Series Data', in Sumeet Dua & Rajendra Acharya U. (ed.), Data Mining in Biomedical Imaging, Signaling, and Systems, CRC Press, -, pp. 227-261pp.
• Lin, P, Foret, S, Wilson, S et al 2015, 'Estimation of the methylation pattern distribution from deep sequencing data', BMC Bioinformatics, vol. 16, no. 145, pp. 1-11.
• Burden, C 2015, 'Can evolutionary rate matrices be estimated from allele frequencies?', 6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015, ed. oa H.Fred A.Elias D., SciTePress, TBC, pp. 183-188.
• Burden, C, Qureshi, S & Wilson, S 2014, 'Error estimates for the analysis of differential expression fromRNA-seq count data', PeerJ, vol. 2014, no. 1, pp. e576/1-26.
• Burden, C, Leopardi, P & Foret, S 2014, 'Word match counts between markovian biological sequences', Communications in Computer and Information Science, pp. 147-161.
• Burden, C, Leopardi, P & Foret, S 2014, 'The distribution of word matches between markovian sequences with periodic boundary conditions', Journal of Computational Biology, vol. 21, no. 1, pp. 41-63.
• Burden, C, Leopardi, P & Foret, S 2013, 'The distribution of short word match counts between Markovian sequences', International Conference on Bioinformatics Models, Methods and Algorithms 2013, SciTePress, Barcelona Spain, pp. 25-33.
• Harrison, A, Binder, H, Buhot, A et al 2013, 'Physico-chemical foundations underpinning microarray and next-generation sequencing experiments', Nucleic Acids Research, vol. 41, no. 5, pp. 2779-2796.
• Burden, C, Qureshi, S & Wilson, S 2013, 'Controlling false discovery rates in RNA-sequencing data', ISI World Statistics Conference, International Statistical Institute, The Hague, The Netherlands, pp. 1339-1344.
• Burden, C, Jing, J & Wilson, S 2012, 'Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length', Statistical Applications in Genetics and Molecular Biology, vol. 11, no. 1, p. 29.
• Burden, C, Jing, J, Foret, S et al 2012, 'Application of k-word match statistics to the clustering of proteins with repeated domains', International Conference on Computational Statistics (COMPSTAT 2012), ed. Ana Colubi, Konstantinos Fokianos, Erricos John Kontoghiorghes, Gil Gonzalez-Ro, The International Association for Statistical Computing (IASC), Unknown, pp. 131-142.
• Robles, J, Qureshi, S, Stephen, S et al 2012, 'Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing', BMC Genomics, vol. 13, no. 1, pp. 1-14.
• Jing, J, Wilson, S & Burden, C 2011, 'Weighted k-word matches: a sequence comparison tool for proteins', ANZIAM Journal, vol. 52, pp. C172-C189.
• Subhani, N, Rueda, L, Ngom, A et al 2010, 'New approaches to clustering microarray time-series data using multiple expression profile alignment', 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010, IEEE, Montreal, QC, pp. 170-176.
• Subhani, N, Rueda, L, Ngom, A et al 2010, 'Multiple gene expression profile alignment for microarray time-series data clustering', Bioinformatics, vol. 26, no. 18, pp. 2281-2288.
• Jing, J, Burden, C, Foret, S et al 2010, 'Statistical considerations underpinning an alignment-free sequence comparison method', Journal of the Korean statistical society, vol. 39, no. 3, pp. 325-335.
• Binder, H, Krohn, K & Burden, C 2010, 'Washing scaling of GeneChip microarray expression', BMC Bioinformatics, vol. 11, p. 30.
• Burden, C & Binder, H 2010, 'Reply to 'linking probe thermodynamics to microarray quantification'', Physical Biology, vol. 7, no. 4.
• Burden, C & Binder, H 2010, 'Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays', Physical Biology, vol. 7, pp. 016004 (16).
• Subhani, N, Rueda, L, Ngom, A et al 2009, 'Clustering microarray time-series data using expectation maximization and multiple profile alignment', 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009, IEEE, Washington, DC, pp. 2-7.
• Numanul, S, Ngom, A, Rueda, L et al 2009, 'Microarray Time-Series Data Clustering via Multiple Alignment of Gene Expression Profiles', in V. Kadirkamanathan (ed.), Pattern Recognition in Bioinformatics: proceedings of the 4th international workshop on Pattern Recognition in Bioinformatics, Springer, Germany, pp. 377-390.
• Foret, S, Wilson, S & Burden, C 2009, 'Characterizing the D2 Statistic: Word Matches in Biological Sequences', Statistical Applications in Genetics and Molecular Biology, vol. 8, no. 1, pp. Article 43.
• Burden, C 2009, 'Intensity isotherms and distributions on oligonucleotide microarrays', Congress on Evolutionary Computation (CEC 2009), ed. Hussein Abbass, Mohammad Abido, Ajith Abraham, et all, Institute of Electrical and Electronics Engineers (IEEE Inc), USA, pp. 3095-3102.
• Binder, H, Brucker, J & Burden, C 2009, 'Nonspecific Hybridization Scaling of Microarray Expression Estimates: A Physicochemical Approach for Chip-to-Chip Normalization', Journal of Physical Chemistry B, vol. 113, no. 9, pp. 2874-2895.
• Burden, C 2008, 'Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed', Physical Biology, vol. 5, no. 1, p. 16004.
• Foret, S, Wilson, S & Burden, C 2008, 'Empirical distribution of k-word matches in biological sequences', Pattern Recognition, vol. 42, pp. 539-548.
• Burden, C 2008, 'Comment on "Stationary rotating strings as relativistic particle mechanics"', Physical Review D-Particles, Fields, Gravitation and Cosmology, vol. 78, p. 2.
• Burden, C, Kantorovitz, M & Wilson, S 2008, 'Approximate word matches between two random sequences', Annals of Applied Probability, vol. 18, no. 1, pp. 1-21.
• Burden, C, Foret, S & Wilson, S 2008, 'k-Word Matches: an Alignment-free Sequence Comparison Method', International Conference on Pattern Recognition (ICPR 2008), ed. Conference Program Committee, IEEE Computer Society, Melbourne, Australia, pp. 235-238.
• Hegland, T, Burden, C & Santoso, L 2008, 'Modelling Gene Regulatory Networks Using Galerkin Techniques Based on State Space Aggregation and Sparse Grids', International Conference on High Performance Scientific Computing (HPSC 2006), ed. Hans Georg Bock, Ekaterina Kostina, Hoang Xuan Phy, Rolf Rannacher, Springer, Berlin, Germany, pp. 259-272.
• Burden, C & Oakley, A 2007, 'Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations', Physical Biology, vol. 4, no. 2, pp. 79-90.
• Kantorovitz, M, Booth, H, Burden, C et al 2007, 'Asymptotic Behaviour of k-Word Matches Between Two Uniformly Distributed Sequences', Journal of Applied Probability, vol. 44, pp. 788-805.
• Hegland, T, Burden, C, Santoso, L et al 2007, 'A Solver for the Stochastic Master Equation Applied to Gene Regulatory Networks', Journal of Computational and Applied Mathematics, vol. 205, pp. 708-724.
• Foret, S, Burden, C & Wilson, S 2007, 'Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences', International Congress on Industrial and Applied Mathematics 2007, ed. Conference Program Committee, Wiley Interscience, Weinheim, Germany, pp. 1121801-1121802.
• Booth, H, Burden, C, Hegland, T et al 2007, 'A Stochastic Model of Gene Regulation Using the Chemical Master Equation', in Andreas Deutsch, Lutz Brusch, Helen Byrne, Gerda de Vries and (ed.), Mathematical modeling of biological systems, Birkhauser Verlag, Boston, US, pp. 73-84.
• Burden, C, Pittelkow, Y & Wilson, S 2007, 'Statistical Analysis and Physical Modelling of Oligonucleotide Microarrays', in Andreas Deutsch, Lutz Brusch, Helen Byrne, Gerda de Vries and (ed.), Mathematical modeling of biological systems, Birkhauser Verlag, Boston, US, pp. 323-336.
• Foret, S, Kantorovitz, M & Burden, C 2006, 'Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences', BMC Bioinformatics, vol. 7, no. Suppl 5, pp. S21.
• Burden, C, Pittelkow, Y & Wilson, S 2006, 'Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays', Journal of Physics: Condensed Matter, vol. 18, pp. 5545-5565.
• Burden, C, Pittelkow, Y & Wilson, S 2005, 'Oligonucleotide Microarrays and Langmuir Adsorption Theory', National Congress Australian Institute of Physics 2005, ed. Max Colla, Australian Institute of Physics, Canberra, p. 4.
• Maindonald, J & Burden, C 2005, 'Selection bias in plots of microarray or other data that have been sampled from a high-dimensional space', ANZIAM Journal, vol. 46, pp. C59-C74.
• Santoso, L, Booth, H, Burden, C et al 2005, 'A stochastic model of gene switches', ANZIAM Journal, vol. 46, pp. C530-543.
• Booth, H, Burden, C, Maindonald, J et al 2005, 'Discussion of "A Bayesian approach to DNA sequence segmentation"', Biometrics, vol. 61, no. 2, pp. 635-639.
• Booth, H, Burden, C, Hegland, T et al 2005, 'Markov process modelling of gene regulation', Australian Mathematical Society Gazette, vol. 32, no. 1, pp. 31-41.
• Burden, C, Pittelkow, Y & Wilson, S 2004, 'Statistical analysis of adsorption models for oligonucleotide microarrays', Statistical Applications in Genetics and Molecular Biology, vol. 3, no. 1-27, p. 29.
• Burden, C & Pichowsky, M 2002, 'J^PC-Exotic Mesons from the Bethe-Salpeter Equation', Few-Body Systems, vol. 32, no. 3, pp. 119-126.
• Burden, C 1999, 'The Effect of the Ultraviolet Part of the Gluon Propagator on the Heavy Quark Propagator', Physical Review D, vol. 59, no. 3, pp. 1-4.
• Walker, M & Burden, C 1999, 'Chiral Symmetry in Supersymmetric Three Dimensional Quantum Electrodynamics', Physical Review D, vol. 59, no. 12, pp. 1-7.
• Walker, M & Burden, C 1999, 'Nonperturbative Vertices in Supersymmetric Quantum Electrodynamics', Physical Review D, vol. 60, no. 10, pp. 1-10.

Projects and Grants

Grants are drawn from ARIES. To add Projects or Grants please contact your College Research Office.

• Novel techniques for statistical and mathematical analyses of sequence data (Primary Investigator)
• Mathematical Methods for Next Generation Sequencing (Primary Investigator)
• Development and Application of Statistical Methods and Software for Analysis of Complex Genetic Disease Data (Secondary Investigator)
• Statistical and Mathematical Analyses of Sequence and Array Data (Primary Investigator)
• Sequence to Sequence: Rigorous Statistical and Mathematical Analysis of Biological Sequence Data (Primary Investigator)